ENCODE_dataportal_hg38 smRNA-seq peaks Track Settings
 
DASHR v2.0 ENCODE_dataportal_hg38 small RNA-seq called peaks

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 All Strand Positive  Negative 
Tissue
A375-rep1 ENCSR376XXO 
A375-rep2 ENCSR376XXO 
A549-rep1 ENCSR000CRW 
A549-rep2 ENCSR000CRW 
A549-rep3 ENCSR000CSL 
A549-rep3 ENCSR000CSO 
A549-rep4 ENCSR000CSL 
A549-rep4 ENCSR000CSO 
adrenal-gland-rep1 ENCSR264COY 
adrenal-gland-rep1 ENCSR612WDT 
articular-chondrocyte-of-knee-joint-rep1 ENCSR000CVB 
articular-chondrocyte-of-knee-joint-rep2 ENCSR000CVB 
bipolar-spindle-neuron-rep1 ENCSR603RPC 
bipolar-spindle-neuron-rep2 ENCSR603RPC 
body-of-pancreas-rep1 ENCSR033TKS 
body-of-pancreas-rep1 ENCSR099ACU 
cerebellum-rep1 ENCSR000AFQ 
cerebellum-rep2 ENCSR000AFQ 
diencephalon-rep1 ENCSR000AFR 
diencephalon-rep2 ENCSR000AFR 
esophagus-muscularis-mucosa-rep1 ENCSR233DGJ 
esophagus-muscularis-mucosa-rep1 ENCSR295NAK 
esophagus-muscularis-mucosa-rep1 ENCSR383PLJ 
esophagus-squamous-epithelium-rep1 ENCSR262TBN 
esophagus-squamous-epithelium-rep1 ENCSR289GGY 
esophagus-squamous-epithelium-rep1 ENCSR379GPS 
esophagus-squamous-epithelium-rep1 ENCSR779BVZ 
fibroblast-of-dermis-rep1 ENCSR000CUY 
fibroblast-of-dermis-rep2 ENCSR000CUY 
fibroblast-of-the-aortic-adventitia-rep1 ENCSR000CUV 
fibroblast-of-the-aortic-adventitia-rep2 ENCSR000CUV 
fibroblast-of-villous-mesenchyme-rep1 ENCSR000CUX 
fibroblast-of-villous-mesenchyme-rep2 ENCSR000CUX 
frontal-cortex-rep1 ENCSR000AFS 
frontal-cortex-rep2 ENCSR000AFS 
gastroesophageal-sphincter-rep1 ENCSR269YSX 
gastroesophageal-sphincter-rep1 ENCSR646HQQ 
gastroesophageal-sphincter-rep1 ENCSR866ZSG 
gastroesophageal-sphincter-rep1 ENCSR998CRC 
GM12878-rep1 ENCSR000AEJ 
GM12878-rep2 ENCSR000AEJ 
hair-follicle-dermal-papilla-cell-rep1 ENCSR000CVC 
hair-follicle-dermal-papilla-cell-rep2 ENCSR000CVC 
heart-rep1 ENCSR000AFT 
heart-rep2 ENCSR000AFT 
hematopoietic-multipotent-progenitor-cell-rep1 ENCSR000CSR 
hepatocyte-rep1 ENCSR673PND 
hepatocyte-rep2 ENCSR673PND 
HT-29-rep1 ENCSR807KQN 
HT-29-rep2 ENCSR807KQN 
IMR-90-rep1 ENCSR000CSE 
IMR-90-rep1 ENCSR000CTH 
IMR-90-rep1 ENCSR000CTI 
IMR-90-rep2 ENCSR000CSE 
IMR-90-rep2 ENCSR000CTH 
IMR-90-rep2 ENCSR000CTI 
induced-pluripotent-stem-cell-rep1 ENCSR722POQ 
induced-pluripotent-stem-cell-rep2 ENCSR722POQ 
K562-rep1 ENCSR000AES 
K562-rep2 ENCSR000AES 
Karpas-422-rep1 ENCSR905KHW 
Karpas-422-rep2 ENCSR905KHW 
lung-rep1 ENCSR000AFW 
lung-rep2 ENCSR000AFW 
mammary-epithelial-cell-rep1 ENCSR000CVF 
MCF-7-rep1 ENCSR000CRR 
MCF-7-rep2 ENCSR000CRR 
MCF-7-rep3 ENCSR000CSW 
MCF-7-rep3 ENCSR000CSX 
MCF-7-rep4 ENCSR000CSW 
MCF-7-rep4 ENCSR000CSX 
melanocyte-of-skin-rep1 ENCSR000CVK 
melanocyte-of-skin-rep1 ENCSR000CVM 
melanocyte-of-skin-rep2 ENCSR000CVK 
melanocyte-of-skin-rep2 ENCSR000CVM 
mesenchymal-stem-cell-of-adipose-rep1 ENCSR000CVD 
mesenchymal-stem-cell-of-adipose-rep2 ENCSR000CVD 
mesenchymal-stem-cell-of-the-bone-marrow-rep1 ENCSR000CVS 
mesenchymal-stem-cell-of-the-bone-marrow-rep2 ENCSR000CVS 
mesenchymal-stem-cell-of-Whartons-jelly-rep1 ENCSR000CVL 
mesenchymal-stem-cell-of-Whartons-jelly-rep2 ENCSR000CVL 
metanephros-rep1 ENCSR000AFU 
metanephros-rep2 ENCSR000AFU 
neural-cell-rep1 ENCSR000CVP 
neural-cell-rep1 ENCSR000CVQ 
neural-cell-rep1 ENCSR000CVR 
neural-cell-rep2 ENCSR000CVP 
neural-cell-rep2 ENCSR000CVQ 
neural-cell-rep2 ENCSR000CVR 
neural-progenitor-cell-rep1 ENCSR828LSC 
neural-progenitor-cell-rep2 ENCSR828LSC 
occipital-lobe-rep1 ENCSR000AFX 
occipital-lobe-rep2 ENCSR000AFX 
OCI-LY7-rep1 ENCSR740DKM 
OCI-LY7-rep2 ENCSR740DKM 
omental-fat-pad-rep1 ENCSR610GDH 
osteoblast-rep1 ENCSR000CUW 
osteoblast-rep2 ENCSR000CUW 
ovary-rep1 ENCSR024CRN 
parietal-lobe-rep1 ENCSR000AFY 
parietal-lobe-rep2 ENCSR000AFY 
pericyte-cell-rep1 ENCSR000CVG 
pericyte-cell-rep2 ENCSR000CVG 
Peyers-patch-rep1 ENCSR091JNF 
Peyers-patch-rep1 ENCSR718AXQ 
placental-epithelial-cell-rep1 ENCSR000CVH 
placental-epithelial-cell-rep2 ENCSR000CVH 
prostate-gland-rep1 ENCSR227FNZ 
prostate-gland-rep1 ENCSR332RHR 
right-lobe-of-liver-rep1 ENCSR603XUX 
right-lobe-of-liver-rep1 ENCSR634VLA 
sigmoid-colon-rep1 ENCSR635SLB 
sigmoid-colon-rep1 ENCSR880LXP 
sigmoid-colon-rep1 ENCSR882DFF 
sigmoid-colon-rep1 ENCSR968DMR 
skeletal-muscle-satellite-cell-rep1 ENCSR000CUZ 
skeletal-muscle-satellite-cell-rep2 ENCSR000CUZ 
skeletal-muscle-tissue-rep1 ENCSR000AFZ 
skeletal-muscle-tissue-rep2 ENCSR000AFZ 
skin-of-body-rep1 ENCSR000AGA 
skin-of-body-rep2 ENCSR000AGA 
SK-N-SH-rep3 ENCSR000CSJ 
SK-N-SH-rep3 ENCSR000CTD 
SK-N-SH-rep3 ENCSR000CTJ 
SK-N-SH-rep4 ENCSR000CSJ 
SK-N-SH-rep4 ENCSR000CTD 
SK-N-SH-rep4 ENCSR000CTJ 
smooth-muscle-cell-rep1 ENCSR250STJ 
smooth-muscle-cell-rep2 ENCSR250STJ 
spinal-cord-rep1 ENCSR000AGB 
spinal-cord-rep2 ENCSR000AGB 
spleen-rep1 ENCSR307FBN 
spleen-rep1 ENCSR587CPE 
spleen-rep1 ENCSR593MVW 
spleen-rep1 ENCSR917CQJ 
stomach-rep1 ENCSR003SZJ 
stomach-rep1 ENCSR133GQJ 
stomach-rep1 ENCSR418FVT 
stomach-rep1 ENCSR573RGL 
subcutaneous-adipose-tissue-rep1 ENCSR020VES 
subcutaneous-preadipocyte-rep1 ENCSR000CVJ 
subcutaneous-preadipocyte-rep2 ENCSR000CVJ 
temporal-lobe-rep1 ENCSR000AGD 
temporal-lobe-rep2 ENCSR000AGD 
testis-rep1 ENCSR229WIW 
testis-rep1 ENCSR626GVP 
thoracic-aorta-endothelial-cell-rep1 ENCSR000CVA 
thoracic-aorta-endothelial-cell-rep2 ENCSR000CVA 
thyroid-gland-rep1 ENCSR000AGE 
thyroid-gland-rep1 ENCSR359CVC 
thyroid-gland-rep2 ENCSR000AGE 
tibial-nerve-rep1 ENCSR203DPX 
tongue-rep1 ENCSR000AGF 
tongue-rep2 ENCSR000AGF 
transverse-colon-rep1 ENCSR168XPO 
transverse-colon-rep1 ENCSR183YQY 
transverse-colon-rep1 ENCSR316SXP 
transverse-colon-rep1 ENCSR525WFB 
upper-lobe-of-left-lung-rep1 ENCSR539RDF 
upper-lobe-of-left-lung-rep1 ENCSR737NPO 
upper-lobe-of-left-lung-rep1 ENCSR961FIG 
upper-lobe-of-left-lung-rep1 ENCSR996VHB 
uterus-rep1 ENCSR000AGH 
uterus-rep1 ENCSR887HNW 
uterus-rep2 ENCSR000AGH 
vagina-rep1 ENCSR812JEU 
vein-endothelial-cell-rep1 ENCSR000CVI 
vein-endothelial-cell-rep2 ENCSR000CVI 
Tissue
 All Strand Positive  Negative 
List subtracks: only selected/visible    all    ()
  Tissue↓1   Track Name↓2  
dense
 K562-rep1 ENCSR000AES  K562-rep1_ENCSR000AES [+] peaks   Schema 
dense
 K562-rep1 ENCSR000AES  K562-rep1_ENCSR000AES [-] peaks   Schema 
    

DASHR v2.0 ENCODE dataportal hg38 small RNA signal tracks

This collection of tracks contains called small RNA peaks using SPAR small RNA-seq pipeline [3] across human tissues and cell types included in ENCODE dataportal data collection in DASHR v2.0 (see DASHR 2.0 data summary for information on data collections and included small RNA-seq experiments). Additional details are provided in (Kuksa PP et al, 2018) [1] and (Leung YY et al, 2016) [2].

Peak calling

Small RNA peaks were called using SPAR small RNA-seq pipeline (https://www.lisanwanglab.org/SPAR) described in reference [3].

DASHR 2.0. database

DASHR 2.0 database of small non-coding RNAs can be accessed at https://lisanwanglab.org/DASHRv2

References

  1. Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. DASHR v2.0: database of small human noncoding RNAs in human tissues and cell types. Bioinformatics, 2018 doi.org/10.1093/bioinformatics/bty709
  2. Yuk Yee Leung*, Pavel P. Kuksa*, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, and Li-San Wang. DASHR: database of small human noncoding RNAs. Nucl. Acids Res., 2016 (Database Issue) doi:10.1093/nar/gkv1188
  3. Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. SPAR: small RNA-seq portal for analysis of sequencing experiments. NAR 2018 (Web Server issue). https://doi.org/10.1093/nar/gky330

Funding

National Institute of General Medical Sciences [R01-GM099962]; National Institute on Aging [U54-AG052427, U01-AG032984, U24-AG041689, UF1-AG047133], National Institute on Aging [T32-AG00255].