GSM4255762: 870 G1E; Mus musculus; ATAC-seq - SRA

SRX7518368: GSM4255762: 870 G1E; Mus musculus; ATAC-seq
1 ILLUMINA (NextSeq 500) run: 61.3M spots, 3.1G bases, 1Gb downloads

Submitted by: NCBI (GEO)

Study: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [ATAC-seq]

PRJNA599439 • SRP239918 • All experiments • All runs

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Thousands of epigenomic datasets have been generated in the past decade, but it is difficult for researchers to effectively utilize all the data relevant to their projects. Systematic integrative analysis can help meet this need, and the VISION project was established for ValIdated Systematic IntegratiON of epigenomic data in hematopoiesis. Here, we systematically integrated extensive data recording epigenetic features and transcriptomes from many sources, including individual laboratories and consortia, to produce a comprehensive view of the regulatory landscape of differentiating hematopoietic cell types in mouse. By employing IDEAS as our Integrative and Discriminative Epigenome Annotation System, we identified and assigned epigenetic states simultaneously along chromosomes and across cell types, precisely and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of over 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and promoters. The transitions in epigenetic states of these cCREs across cell types provided insights into mechanisms of regulation, including decreases in numbers of active cCREs during differentiation of most lineages, transitions from poised to active or inactive states, and shifts in nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at cCREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website (usevision.org) to aid research in genomics and hematopoiesis. Overall design: Twelve samples, each in replicate

Sample: 870 G1E

SAMN13751651 • SRS5957987 • All experiments • All runs

Organism: Mus musculus

Library:

Instrument: NextSeq 500

Strategy: ATAC-seq

Source: GENOMIC

Selection: other

Layout: SINGLE

Construction protocol: Approximately 50,000 cells were collected by centrifugation at 600 xg for 10 min at 4 °C. Cells were washed once with cold 1x PBS and centrifuged as above. Cells were lysed by gently pipetting to resuspend cell pellet in cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged as above. Cells were suspended in the following mix: 25 μl 2X Tagment DNA buffer (Illumina cat# FC-121-1030), 3 μl Tn5 Transposase (Illumina cat#FC-121-1030), 22 μl nuclease-free H2O and incubated for 30 min at 37 °C. Reactions were terminated by adding 5 μl of 1% SDS solution and purified using SPRIselect beads. Following purification, library fragments were amplified using NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min. Libraries were amplified for a total of 17–19 cycles and then purified using AMPure XP beads (Beckman Coulter cat #A63881).

Experiment attributes:

GEO Accession: GSM4255762

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 61.3M spots, 3.1G bases, 1Gb

Run	# of Spots	# of Bases	Size	Published
SRR10847772	61,288,454	3.1G	1Gb	2020-01-11

ID:: 9814822

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