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Sample GSM2254217 Query DataSets for GSM2254217
Status Public on Jan 28, 2017
Title Combinatorial scHi-C Library ML3
Sample type SRA
Source name Cultured Cell Lines
Organisms Homo sapiens; Mus musculus
Characteristics cell lines: Contains K562, GM12878, Patski, and primary MEF cells
Treatment protocol Cells are fixed using 2% (HeLa, HAP1, GM12878, K562, MEF) or 2.5% (Patski) formaldehyde.
Growth protocol Cells are grown under standard tissue culture conditions (10 - 15% FBS, 5% CO2, DMEM or RPMI media, and 1X Pen-Strep) as the Coriell culture practices demand)
Extracted molecule genomic DNA
Extraction protocol Cells are lysed using 0.2% NP-40; 10 mM NaCl; 10 mM Tris pH 8.0 in ddH2O
Combinatorial single-cell Hi-C is carried out using a similar protocol to the insitu Hi-C and in situ DNase protocols
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Data processing Library strategy: Hi-C-seq
Reads were mapped to a combined Burrows-Wheeler reference of hg19 and mm10 using bowtie2. They were then filtered using custom Python scripts to generate validPairs files (see README file on series record).
Submission date Jul 27, 2016
Last update date May 15, 2019
Contact name Vijay Ramani
Organization name UCSF
Department Biochemistry & Biophysics
Lab Ramani Lab
Street address 600 16th St, GH-S312B
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
Platform ID GPL22245
Series (1)
GSE84920 Massively multiplex single-cell Hi-C
BioSample SAMN05449631
SRA SRX1981064

Supplementary file Size Download File type/resource
GSM2254217_ML3.percentages.txt.gz 251.6 Kb (ftp)(http) TXT
GSM2254217_ML3.validPairs.txt.gz 221.2 Mb (ftp)(http) TXT
GSM2254217_ML3_R1.bed.gz 160.8 Mb (ftp)(http) BED
GSM2254217_ML3_R2.bed.gz 151.3 Mb (ftp)(http) BED
GSM2254217_ML3_assignments.txt.gz 97.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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