RatTransc: a rat long noncoding RNA database

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Data source we used/cited

	Study ID	Study title	Reads number	Reads length	# Intergenic transcripts	# Filtered transcripts	Sample number	Tissue
1	ERP001301	RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing	1367617352	100	4075	2918	9	heart
2	ERP001694	A comparison of brain gene expression levels in domesticated and wild animals	946281400	83	2798	1430	24	brain frontal cortex
3	ERP002602	Rat olfactory transcriptome	583971156	100	5610	3873	5	olfactory epithelium, vomeronasal organ
4	ERP003265	Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease	540592852	100	3018	2232	8	left ventricle
5	ERP004227	TCF7L2 is the master regulator of insulin production and processing	190474354	101	1593	1102	8	TCF7L2 KD and control in INS1 832/13 cells
6	ERP004249	Gata3 and Foxa2 mediate early brain development through the Sonic Hedgehog pathway	464636623	50	1250	781	3	PC12 cells
7	ERP006608	Genomic landscape of rat strain and substrain variation	480536506	101	9432	5484	12	inbred strains
8	SRP002416	mRNA-seq with Agnostic Splice Site Discovery for CNS Transcriptomics Tested in Chronic Pain	327513844	50	1436	673	24	dorsal root ganglion
9	SRP006893	Whole transcriptome profiling of the rat pineal gland	243269720	51	1975	1216	6	pineal gland
10	SRP007359	Digital gene expression and global mapping of polyadenylation sites with PolyA-Seq	37347330	76	79	62	2	brain, testis
11	SRP007413	Development of daily rhythmicity in the rat pineal transcriptome interrogated using RNA-Seq	309546420	101	3188	2203	8	pineal gland
12	SRP009272	The effects on transcriptome from absence of Spt4/Supt4h by RNA-seq	332220152	101	1686	1132	2	striatal neural cells
13	SRP013114	Whole transcriptome profiling of the rat pineal gland using mid-day and mid-night samples	109244096	101	1654	1269	2	pineal gland
14	SRP013116	Whole transcriptome profiling of the rat pineal gland using mid-day and mid-night samples	234405228	101	2816	2108	4	pineal gland, mixed (cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland)
15	SRP013262	Novel long noncoding RNAs are regulated by angiotensin II in vascular smooth muscle cells	346703900	80	1175	866	2	cultured primary vascular smooth muscle cells (VSMCs)
16	SRP013378	Whole transcriptome profiling of the rat pineal gland using mid-day and mid-night samples	1053632276	101	479	425	3	mixed (cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland), pool of 6 pineal glands
17	SRP016501	Evolutionary dynamics of gene and isoform regulation in mammalian tissues	3589177550	40	23659	17676	25	brain, heart, muscle, testis, colon, kidney, liver, lung, spleen
18	SRP017255	Whole-transcriptome analysis identifies re-expression of fetal splice variants in cardiac hypertrophy	535454054	63	1541	986	9	heart (left ventricle)
19	SRP017586	Paliperidone and aripiprazole differentially affect the strength of calcium-secretion coupling in female pituitary lactotrophs	234828178	101	1721	1235	1	pituitary gland
20	SRP017598	Rattus norvegicus strain:F344/N Transcriptome or Gene expression	396095298	76	1877	1243	8	liver
21	SRP017611	Gene expression defines natural changes in mammalian lifespan	293611018	51	2869	1860	9	liver, kidney, brain
22	SRP018322	Characterization of the rat developmental liver transcriptome	106422470	100	5002	3069	12	liver
23	SRP018407	Genome-wide analysis and comparison of E15 and adult rat lateral ventricular choroid plexus epithelial cells	228499467	50	2245	1345	6	lateral ventricular choroid plexus epithelial cells
24	SRP019984	rat IPSC mRNA-seq	332895573	45	3736	2070	7	embrionic stem cells, fibroblasts and induced plurepotency stem cells
25	SRP021090	Whole transcriptome profiling of rat pineal glands and retinas collected throughout a 24-hour cycle	879881684	101	6325	4453	14	pineal glands, retinas
26	SRP021119	Whole transcriptome profiling of the rat pineal gland during development from embryonic day 21 to adult	407977064	101	4103	2934	8	pineal gland
27	SRP022136	A Snapshot of the Hepatic Transcriptome: Ad Libitum Alcohol Intake Suppresses Expression of Cholesterol Synthesis Genes in Alcohol-Preferring (P) Rats	156970200	101	1027	667	12	liver
28	SRP022310	Whole transcriptome analysis using RNA extracted from FFPE liver samples	931134992	100	3642	2480	8	FFPE liver
29	SRP023266	Transcriptome Sequencing of Gene Expression in the brain of HIV transgenic transgenic rat	7909908416	50	9560	4507	144	brain
30	SRP023485	rodents' brain transcriptome analysis	46310098	115	671	469	2	brain
31	SRP026340	High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis	279154572	60	3831	2586	8	testis
32	SRP028515	Hypoxia transcriptome sequencing of blind mole rat (BMR, Spalax galili) and rat (Rattus norvegicus)	181521402	90	1730	1224	6	brain
33	SRP028544	Subcellular RNA Sequencing Reveals Broad Presence of Cytoplasmic Intron-sequence Retaining Transcripts in Mouse and Rat Neurons	271616688	50	422	337	5	hippocampus soma
34	SRP028932	Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat	3096777532	51	4272	2357	48	liver
35	SRP029332	Characterization of genome-wide transcriptional changes in liver and adipose tissues of ZDF (fa/fa) rats fed R-a-lipoic acid by next-generation sequencing	260798448	100	2121	1278	16	liver, adipose
36	SRP029760	Origins and functional evolution of Y chromosome gene repertoires across the class mammalia	329856012	101	10796	7067	12	heart, liver, kidney, frontal cortex, cerebellum, ovary, testis, fibroblast
37	SRP030211	Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators	213428604	100	10428	8388	1	testis
38	SRP035209	The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells	1482371160	50	4240	2022	37	hepatocytes
39	SRP036442	Bile acid flux is necessary for normal liver regeneration	1233335669	99	3922	2217	12	liver
40	SRP037986	A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages	13232746915	50	35668	16177	320	adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, testis, uterus
41	SRP039021	The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance	5074717186	101	6906	5026	116	liver
42	SRP040578	Peri-adolescent high-fructose diet effects on hypothalamic transcriptome	400879016	101	3358	2143	13	hypothalamus
43	SRP041119	Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation	1864023092	101	5283	2699	16	cortical pyramidal neurons, hippocampal pyramidal neurons
44	SRP041131	RNA-seq profiling of microdissected rat renal tubule segments	38482512201	50	11222	8136	125	glomerulus, cortical collecting duct, whole kidney, Inner medullary collecting duct, outer medullary collecting duct, connecting tubule, distal convoluted tubule, cortical thick ascending limb, medullary thick ascending limb, thin ascending limb, descending thin limb of long-loop nephron of inner medulla
45	SRP041741	mRNA-seq analysis of superficial zone (SFZ) and deeper layers (deep AC) of articular cartilage of adult rats	134195732	100	1537	1004	4	deeper layers of articular cartilage (AC) , superficial zone (SFZ)
46	SRP041920	Next-generation sequencing facilitates quantitative analysis of hepatic sex-differences in ZSF1 rats	310223395	51	1958	979	12	liver
47	SRP044684	Nova1 is a master regulator of alternative splicing in pancreatic beta cells	1062718264	12 to 101	3875	2848	6	pancreas
48	SRP045117	Epigenomics of neural cells: REST-induced down- and up-regulation of gene expression in a two clone PC12 cell model	306341914	101	2475	1911	4	high REST PC12 cells, wild type PC12 cells
49	SRP045237	Characteristics of Long Non-coding RNAs in the Brown Norway Rat and Alterations in the Dahl Salt-Sensitive Rat	96000000	101	1020	694	6	renal cortex, renal outer medulla, liver, cardiac left ventricle, adrenal gland, hypothalamus
50	SRP045303	Feedback Inhibition of CREB Signaling Promotes Beta Cell Dysfunction in Insulin Resistance	350097190	75	799	509	8	insulinoma cells, pancreatic beta cells
51	SRP045544	Fish oil alleviated high-fat diet–induced non-alcoholic fatty liver disease via regulating hepatic lipids metabolism and metaflammation: a transcriptomic study	114371778	80	527	318	3	liver
52	SRP046247	Islet-specific microRNA changes driven by nutrient shift trigger postnatal beta-cell maturation - dispersed islet cell mRNAs after miR-17-5p transfection	138381469	50	850	408	8	islets
53	SRP048593	Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity	199233133	151	2375	1483	6	primary hippocampal neuron, hippocampal CA1
54	SRP048960	In vivo activation of a conserved microRNA program induces mammalian heart regeneration	57728035	51	251	138	2	cardiomyocyte
55	SRP049463	Rattus norvegicus Transcriptome or Gene expression	829654806	100	3447	2143	12	white adipose
56	SRP049818	RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions	3485218346	101	12950	9280	36	cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland
57	SRP051483	Unique gene program of rat mesenteric arteries as revealed by Deep RNA Sequencing	379855318	101	1848	1386	4	mesenteric artery, aorta
58	SRP053358	Macrophage epoxygenase determines a pro-fibrotic transcriptomesignature	414638190	100	1266	953	6	macrophages
59	SRP053407	Evidence from mRNA-Sequencing that Acute Olanzapine Infusion is Initiating a Skeletal Muscle Fiber Type Transition In Rat Gastrocnemius	45525680	51	418	243	6	gastrocnemius muscle
60	SRP055430	DNMT inhibition in the Neonatal Preoptic Area	1054675190	101	5400	3698	12	brain preoptic area
61	SRP056012	Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats	676034584	50	4634	2412	12	liver, brain
62	SRP059752	The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis	264602520	50	2107	1213	6	chondrosarcoma (RCS) cells, rib
63	SRP060791	Changes of axonal transcriptomes in response to local Abeta	91011822	35 to 151	675	566	8	embryonic hippocampal neurons
64	SRP063362	Cross-species transcriptomic comparison of in vitro and in vivo mammalian neural cells	315390164	25 to 100	2925	1988	6	astrocytes, neurons, oligodendrocyte precursor cells
	Total		100346795298		79 to 35668	62 to 17676	1289

Contact us

 Aimin Li
Email: liaiminmail@gmail.com or emanlee815@163.com
School of Computer Science and Engineering, Xi’an University of Technology, Xi’an, China

 Lei Wang
Email: leiwang@xaut.edu.cn
School of Computer Science and Engineering, Xi’an University of Technology, Xi’an, China

 Zhong-Yin Zhou
Email: zhouzy1212@gmail.com or zhongyinzhou@163.com
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China

Disclaimer

These data are provided as-is and without any warranty for research use only, and are not intended for use in diagnostic procedures. Use of this data is offered to individuals who understand and accept the associated terms and conditions. The data being provided is subject to change without notice. We assumes no responsibility for any errors or omissions in the data provided. Certain notices, terms, conditions and/or use restrictions may pertain to your use of RatTransc products and/or third party products.