|
| Status |
Public on Oct 16, 2022 |
| Title |
DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB266YMD) |
| Sample type |
SRA |
| |
|
| Source name |
Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell, preserved by cryopreservation
|
| Organism |
Homo sapiens |
| Characteristics |
cell_type: naive thymus-derived CD8-positive, alpha-beta T cell
biomaterial_type: primary cell
description: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-
biosample encode accession: ENCBS938EKE (SAMN30348086)
Sex: not collected
health state: healthy
dev stage: not collected
age: not collected
donor_id: ENCDO922TOC
lab: Bradley Bernstein, Broad
source: David Hafler
link: ENCBS938EKE at ENCODE; https://www.encodeproject.org/ENCBS938EKE/
link: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
extraction protocol: https://www.encodeproject.org/documents/980de32c-f7ec-4cd7-b736-61faf723c186/@@download/attachment/newnuclei_isolation_from_human_tissue-combined.pdf
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
https://www.encodeproject.org/experiments/ENCSR400YJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR400YJR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB266YMD
|
| Data processing |
See GSM*_README.txt supplementary file linked below
|
| |
|
| Submission date |
Oct 13, 2022 |
| Last update date |
Oct 17, 2022 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
|
| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE215463 |
DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR400YJR) |
|
| Relations |
| BioSample |
SAMN30348086 |
| SRA |
SRX17911674 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6637596_ENCFF210AYU_footprints_GRCh38.bigBed |
2.4 Mb |
(ftp)(http) |
BIGBED |
| GSM6637596_ENCFF244OKB_footprints_GRCh38.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSM6637596_ENCFF267KCX_FDR_cut_rate_GRCh38.bigBed |
278.5 Mb |
(ftp)(http) |
BIGBED |
| GSM6637596_ENCFF488STM_peaks_GRCh38.bigBed |
1.8 Mb |
(ftp)(http) |
BIGBED |
| GSM6637596_ENCFF524ZRE_peaks_GRCh38.bed.gz |
865.3 Kb |
(ftp)(http) |
BED |
| GSM6637596_ENCFF550EQD_peaks_GRCh38.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSM6637596_ENCFF556BRB_FDR_cut_rate_GRCh38.bed.gz |
278.1 Mb |
(ftp)(http) |
BED |
| GSM6637596_ENCFF563KPE_read-depth_normalized_signal_GRCh38.bigWig |
671.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM6637596_ENCFF907YBT_peaks_GRCh38.bigBed |
1.4 Mb |
(ftp)(http) |
BIGBED |
| GSM6637596_ENCFF994SZV_peaks_GRCh38.starch |
951.9 Kb |
(ftp)(http) |
STARCH |
| GSM6637596_ENCLB266YMD_README.txt.gz |
1.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
