GSM2147569: L4-B [ATAC-seq]; Mus musculus; OTHER - SRA

SRX1753510: GSM2147569: L4-B [ATAC-seq]; Mus musculus; OTHER
9 ILLUMINA (Illumina HiSeq 2500) runs: 32.3M spots, 3.2G bases, 2Gb downloads

Submitted by: NCBI (GEO)

Study: Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility [ATAC-seq]

PRJNA321073 • SRP074733 • All experiments • All runs

show Abstracthide Abstract

We describe Nfib as an important regulator of chromatin accessibility in Small cell lung cancer (SCLC). Overall design: ATAC seq was performed on [1] ex vivo samples from primary tumors and metastases of a mouse model for SCLC (4 samples of each plus technical replicates of 7 samples for a total of 15 samples) [2] cell lines derived from mouse models for SCLC. [3] Nfib loss of function in murine SCLC cell lines (shLuc are controls, sh2 is shRNA that knocks down Nfib) [4] Nfib gain of function in murine SCLC cell lines and human SCLC lines (empty indicates control cells, Nfib indicates cells overexpressing Nfib)

Sample: L4-B [ATAC-seq]

SAMN04965834 • SRS1430383 • All experiments • All runs

Organism: Mus musculus

Library:

Instrument: Illumina HiSeq 2500

Strategy: OTHER

Source: GENOMIC

Selection: other

Layout: PAIRED

Construction protocol: Cells were lysed, incubated with Tn5 transposase, and purified with Qiagen MinElute kit. Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as per Buenrostro et al. (2013).

Experiment attributes:

GEO Accession: GSM2147569

Links:

NCBI link: NCBI Entrez (gds)

Runs: 9 runs, 32.3M spots, 3.2G bases, 2Gb

Run	# of Spots	# of Bases	Size	Published
SRR3493524	4,000,000	400M	260.2Mb	2016-05-12
SRR3493525	4,000,000	400M	259.1Mb	2016-05-12
SRR3493526	4,000,000	400M	258.6Mb	2016-05-12
SRR3493527	2,440,605	244.1M	158.9Mb	2016-05-12
SRR3493528	3,445,831	344.6M	180.1Mb	2016-05-12
SRR3493529	4,000,000	400M	259.1Mb	2016-05-12
SRR3493530	4,000,000	400M	258.8Mb	2016-05-12
SRR3493531	4,000,000	400M	258.4Mb	2016-05-12
SRR3493532	2,388,164	238.8M	155.4Mb	2016-05-12

ID:: 2512520

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