H3K36 methyltransferase SETD2 regulates lymphoid and neural development [seq]

Default Boolean Operator: Terms in a search string will be connected by the AND operator, EXAMPLE: searching genomic melanoma will produce the same results as genomic AND melanoma .
AND, OR, NOT: Combine terms in a search with the boolean operators AND (to add specificity), OR (to broaden), or NOT (to eliminate a term). Operators must be capitalized (all other search terms are not case-sensitive).
Wild Card: Add wild card symbols * (open-ended) and ? (single character) to truncate terms. EXAMPLE: searching gen* shows results for 'gene', 'genetic', 'genomic, etc. Searching gene? returns results for 'gene' or 'genes' but not for 'genome'.
Phrase Searching: Enclose search in quotation marks "keyword or search term" to search for an exact phrase. EXAMPLE: "transcription factors" returns results for records where transcription is immediately followed by the word factors .
Diacritics: Words containing diacritics translate those characters to non-diacritic form. EXAMPLE: massague returns results for Massague&#769 .
Filter by: Located on the homepage (left panel), use filters to search for records or narrow the search. From search results page, filters can be removed by clicking on the term at the top of the page.

UID: 10510

Author(s): Chu, Scott Haihua*, Koche, Richard Patrick*, Armstrong, Scott Allen* * MSK affiliated

Description: Summary from the GEO: "We study the role of loss of Setd2 and H3K36me3 in early B cell development through NGS methods including RNA, ChIP and ATAC Seq of sorted B cell populations of control and Setd2KO primary B cells from mice. From age-matched littermate controls and Setd2KO mouse, we sorted early proB cells (B220+CD43+CD19-Cd25-IgM-) and performed ATAC-seq, RNA-Seq, and ChIP-seq using an antibody against H3K36me3."

Subject of Study

Subject(s)

OncoTree Cancer Type(s)

Lymphoid

Access via GEO
Raw and HTSeq sequencing data
Accession #: GSE130904

Access via SRA
ChIP-Seq, RNA-Seq, ATAC-Seq reads for 28 samples
Accession #: SRP197106

Access via BioProject
Additional information about overall initiative.
Accession #: PRJNA541930
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Chu S, Chabon J, Matovina C, et al. Loss of H3K36 methyltransferase Setd2 impairs V(D)J recombination during lymphoid development. iScience. 2020; 23(3):100941.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2000
High throughput gene sequencing system

Illumina HiSeq 2500
High throughput sequencing system
Dataset Format(s): Plain Text, SRA, TAR, BIGWIG
Dataset Size: 569.8 Kb (TXT), 3.0 Gb (TAR of BW), SRA broken up into files of 1-13 Gb.

Do you have or know of a dataset that should be added to the catalog? Let us know!