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Sample GSM2254218 Query DataSets for GSM2254218
Status Public on Jan 28, 2017
Title Combinatorial scHi-C Library PL1
Sample type SRA
Source name Cultured Cell Lines
Organisms Homo sapiens; Mus musculus
Characteristics cell lines: Contains HeLa S3, HAP1, 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 Jan 29, 2017
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 SAMN05449630

Supplementary file Size Download File type/resource
GSM2254218_PL1.percentages.txt.gz 455.7 Kb (ftp)(http) TXT
GSM2254218_PL1.validPairs.txt.gz 1.2 Gb (ftp)(http) TXT
GSM2254218_PL1_R1.bed.gz 885.3 Mb (ftp)(http) BED
GSM2254218_PL1_R2.bed.gz 865.5 Mb (ftp)(http) BED
GSM2254218_PL1_assignments.txt.gz 541.5 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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