title: T86_P1_E9_ILC3


title: T86_P1_E1_ILC3

status: Public on Jan 27 2016

type: SRA

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

library_source: transcriptomic

data_processing:
All reads were aligned to the human (hg19) genomes using STAR (Dobin et al. 2013)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq and Ensembl  (Feb 2013) and ERCC-spike in annotations.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

molecule: polyA RNA

organism: Homo sapiens

source_name: cDNA

extract_protocol:
cDNA was generated from FACS sorted cells using to Smart-seq2 (Picelli et al. Nature Methods 2013)
Nextera XT DNA Sample Preparation Index Kit (24 index primers, Illumina)

tag: tonsil donor

value: Donor T86

tag: facs gating

tag: cell type

value: tonsil Innate lymphoid cells


title: T86_P1_F6_ILC3


title: T86_P1_E10_ILC3


title: T86_P1_D3_ILC3


title: T86_P1_D2_NK

value: NK


title: T86_P1_D5_ILC3


title: T86_P1_E5_ILC3


title: T86_P1_D12_ILC3


title: T86_P1_D1_ILC3


title: T86_P1_D11_NK


title: T86_P1_D10_ILC3


title: T86_P1_C8_ILC3


title: T86_P1_C9_ILC3


title: T86_P1_C3_ILC3


title: T86_P1_C7_ILC3


title: T86_P1_C6_ILC3


title: T86_P1_C12_ILC3


title: T86_P1_C1_ILC3


title: T86_P1_C5_ILC3


title: T86_P1_C2_ILC3


title: T86_P1_C4_ILC3


title: T86_P1_C10_ILC3


title: T86_P1_E11_ILC3


title: T86_P1_C11_ILC3


title: T86_P1_B8_ILC3


title: T86_P1_D8_ILC3


title: T86_P1_D6_ILC3


title: T86_P1_D7_ILC3


title: T86_P1_B7_ILC3


title: T86_P1_B6_ILC3


title: T86_P1_B5_ILC3


title: T86_P1_B3_ILC3


title: T86_P1_B1_ILC3


title: T86_P1_B12_ILC3


title: T86_P1_A5_ILC3


title: T86_P1_A3_ILC3


title: T86_P1_A1_ILC3


title: T86_P1_A10_ILC3


title: T86_P1_B9_NK


title: T75_P4_H9_ILC1

value: Donor T75


title: T75_P4_H8_ILC1


title: T75_P4_H5_ILC1


title: T75_P4_H3_ILC1


title: T75_P4_H12_ILC1


title: T75_P4_G7_ILC1


title: T75_P4_G3_ILC1


title: T75_P4_G8_ILC1


title: T75_P4_G12_ILC1


title: T75_P4_G9_NK


title: T75_P4_G10_ILC1


title: T75_P4_F9_ILC1


title: T75_P4_F8_ILC1


title: T75_P4_F7_ILC1


title: T75_P4_G1_ILC1


title: T75_P4_F3_ILC1


title: T75_P4_F5_ILC1


title: T75_P4_F12_ILC1


title: T86_P1_A12_ILC3


title: T75_P4_F11_ILC1


title: T86_P1_A8_ILC3


title: T75_P4_F10_ILC1


title: T75_P4_E9_ILC1


title: T75_P4_E7_NK


title: T75_P4_E6_NK


title: T75_P4_G6_ILC1


title: T75_P4_G5_ILC1


title: T75_P4_E4_ILC1


title: T75_P4_E5_ILC1


title: T75_P4_E3_ILC1


title: T75_P4_E1_ILC1


title: T75_P4_D8_ILC1


title: T75_P4_E12_ILC1


title: T75_P4_D6_ILC1


title: T75_P4_D5_ILC1


title: T75_P4_F6_ILC1


title: T75_P4_D2_NK


title: T75_P4_E10_ILC1


title: T75_P4_D12_ILC1


title: T75_P4_D7_ILC1


title: T75_P4_C9_ILC1


title: T75_P4_D3_ILC1


title: T75_P4_D11_NK


title: T75_P4_D10_ILC1


title: T75_P4_C5_ILC1


title: T75_P4_E8_ILC1


title: T75_P4_C6_ILC1


title: T75_P4_C8_ILC1


title: T75_P4_C4_ILC1


title: T75_P4_C1_ILC1


title: T75_P4_C7_ILC1


title: T75_P4_C12_ILC1


title: T75_P4_C3_ILC1


title: T75_P4_C10_ILC1


title: T75_P4_C11_ILC1


title: T75_P4_B8_ILC1


title: T75_P4_E2_ILC1


title: T75_P4_B5_ILC1


title: T75_P4_B9_NK


title: T75_P4_B4_NK


title: T75_P4_B12_ILC1


title: T75_P4_B10_ILC1


title: T75_P4_A9_ILC1


title: T75_P4_A1_ILC1


title: T75_P4_A5_ILC1


title: T75_P4_A8_ILC1


title: T75_P4_A11_ILC1


title: T75_P4_A10_ILC1


title: T75_P3_H5_ILC2


title: T75_P3_H8_ILC2


title: T75_P3_H4_ILC2


title: T75_P3_H3_ILC2


title: T75_P3_H11_ILC2


title: T75_P3_H10_ILC2


title: T75_P3_G8_ILC2


title: T75_P3_G9_NK


title: T75_P3_G7_ILC2


title: T75_P3_G5_ILC2


title: T75_P3_G6_ILC2


title: T75_P3_G3_ILC2


title: T75_P4_B1_ILC1


title: T75_P3_G1_ILC2


title: T75_P3_G10_ILC2


title: T75_P3_G12_ILC2


title: T75_P3_F9_ILC2


title: T75_P3_F8_ILC2


title: T75_P3_F7_ILC2


title: T75_P3_F4_ILC2


title: T75_P3_F5_ILC2


title: T75_P3_F2_ILC2


title: T75_P3_H9_ILC2


title: T75_P3_F12_ILC2


title: T75_P3_F10_ILC2


title: T75_P3_F11_ILC2


title: T75_P3_E8_ILC2


title: T75_P3_H2_ILC2


title: T75_P3_E9_ILC2


title: T75_P3_E7_NK


title: T75_P3_E6_NK


title: T75_P3_E5_ILC2


title: T75_P3_E2_ILC2


title: T75_P3_E10_ILC2


title: T75_P3_E4_ILC2


title: T75_P3_D8_ILC2


title: T75_P3_E12_ILC2


title: T75_P3_E3_ILC2


title: T75_P3_D5_ILC2


title: T75_P3_D7_ILC2


title: T75_P3_D12_ILC2


title: T75_P3_D3_ILC2


title: T75_P3_D10_ILC2


title: T75_P3_F3_ILC2


title: T75_P3_D11_NK


title: T75_P3_C6_ILC2


title: T75_P3_C5_ILC2


title: T75_P3_C8_ILC2


title: T75_P3_C9_ILC2


title: T75_P3_C7_ILC2


title: T75_P3_C3_ILC2


title: T75_P3_C2_ILC2


title: T75_P3_C12_ILC2


title: T75_P3_C11_ILC2


title: T75_P3_C10_ILC2


title: T75_P3_B8_ILC2


title: T75_P3_B7_ILC2


title: T75_P3_B4_NK


title: T75_P3_B5_ILC2


title: T75_P3_B3_ILC2


title: T75_P3_A8_ILC2


title: T75_P3_B1_ILC2


title: T75_P3_A7_ILC2


title: T75_P3_A5_ILC2


title: T75_P3_A3_ILC2


title: T75_P3_A12_ILC2


title: T75_P2_H9_ILC3


title: T75_P2_H5_ILC3


title: T75_P2_H3_ILC3


title: T75_P2_H4_ILC3


title: T75_P2_H12_ILC3


title: T75_P2_H2_ILC3


title: T75_P2_H11_ILC3


title: T75_P3_C4_ILC2


title: T75_P2_G8_ILC3


title: T75_P2_G6_ILC3


title: T75_P2_G5_ILC3


title: T75_P2_G3_ILC3


title: T75_P2_G12_ILC3


title: T75_P2_G9_NK


title: T75_P2_F6_ILC3


title: T75_P2_F8_ILC3


title: T75_P2_G7_ILC3


title: T75_P3_B6_ILC2


title: T75_P2_F3_ILC3


title: T75_P2_F2_ILC3


title: T75_P2_F1_ILC3


title: T75_P2_F5_ILC3


title: T75_P2_F4_ILC3


title: T75_P2_F11_ILC3


title: T75_P2_E8_ILC3


title: T75_P2_F10_ILC3


title: T75_P2_E9_ILC3


title: T75_P2_E7_NK


title: T75_P2_E6_NK


title: T75_P2_E5_ILC3


title: T75_P2_E4_ILC3


title: T75_P2_F7_ILC3


title: T75_P2_E10_ILC3


title: T75_P2_E11_ILC3


title: T75_P2_E3_ILC3


title: T75_P2_D8_ILC3


title: T75_P2_E2_ILC3


title: T75_P2_E1_ILC3


title: T75_P2_D1_ILC3


title: T75_P2_D5_ILC3


title: T75_P2_D2_NK


title: T75_P2_D7_ILC3


title: T75_P2_D3_ILC3


title: T75_P2_D12_ILC3


title: T75_P2_D11_NK


title: T75_P2_D6_ILC3


title: T75_P2_D10_ILC3


title: T75_P2_C9_ILC3


title: T75_P2_C8_ILC3


title: T75_P2_C3_ILC3


title: T75_P2_C6_ILC3


title: T75_P2_C4_ILC3


title: T75_P2_C5_ILC3


title: T75_P2_C1_ILC3


title: T75_P2_C11_ILC3


title: T75_P2_B9_NK


title: T75_P2_C10_ILC3


title: T75_P2_B8_ILC3


title: T75_P2_B5_ILC3


title: T75_P2_A9_ILC3


title: T75_P2_B12_ILC3


title: T75_P2_B3_ILC3


title: T75_P2_A8_ILC3


title: T75_P2_B4_NK


title: T75_P2_A7_ILC3


title: T75_P2_A5_ILC3


title: T75_P1_H5_ILC3


title: T75_P2_A3_ILC3


title: T75_P1_H3_ILC3


title: T75_P1_H8_ILC3


title: T75_P1_H4_ILC3


title: T75_P1_H11_ILC3


title: T75_P1_H2_ILC3


title: T75_P2_B7_ILC3


title: T75_P1_G7_ILC3


title: T75_P1_G3_ILC3


title: T75_P1_G1_ILC3


title: T75_P1_G8_ILC3


title: T75_P2_C2_ILC3


title: T75_P1_F6_ILC3


title: T75_P1_G10_ILC3


title: T75_P2_B6_ILC3


title: T75_P1_F7_ILC3


title: T75_P1_G5_ILC3


title: T75_P2_B1_ILC3


title: T75_P1_F8_ILC3


title: T75_P1_F5_ILC3


title: T75_P1_F4_ILC3


title: T75_P1_F2_ILC3


title: T75_P2_A1_ILC3


title: T75_P1_F3_ILC3


title: T75_P1_F10_ILC3


title: T75_P1_F11_ILC3


title: T75_P1_F12_ILC3


title: T75_P1_E6_NK


title: T75_P1_E5_ILC3


title: T75_P1_G6_ILC3


title: T75_P1_E2_ILC3


title: T75_P1_E1_ILC3


title: T75_P1_E12_ILC3


title: T75_P1_E11_ILC3


title: T75_P1_D8_ILC3


title: T75_P1_E10_ILC3


title: T75_P1_D6_ILC3


title: T75_P1_D7_ILC3


title: T75_P1_D5_ILC3


title: T75_P1_D3_ILC3


title: T75_P1_D2_NK


title: T75_P1_D1_ILC3


title: T75_P1_D12_ILC3


title: T75_P1_D10_ILC3


title: T75_P1_D11_NK


title: T75_P1_F1_ILC3


title: T75_P1_C7_ILC3


title: T75_P1_C8_ILC3


title: T75_P1_C6_ILC3


title: T75_P1_E4_ILC3


title: T75_P1_C4_ILC3


title: T75_P1_C3_ILC3


title: T75_P1_C1_ILC3


title: T75_P1_C10_ILC3


title: T75_P1_C2_ILC3


title: T75_P1_C11_ILC3


title: T75_P1_B8_ILC3


title: T75_P1_B7_ILC3


title: T75_P1_B6_ILC3


title: T75_P1_B4_NK


title: T75_P1_B5_ILC3


title: T75_P1_B3_ILC3


title: T75_P1_A5_ILC3


title: T75_P1_B1_ILC3


title: T75_P1_B12_ILC3


title: T75_P1_A3_ILC3


title: T75_P1_A1_ILC3


title: T75_P1_A12_ILC3


title: T75_P1_A10_ILC3


title: T75_P1_A11_ILC3


title: T74_P4_H9_ILC3

value: Donor T74


title: T75_P1_C5_ILC3


title: T74_P4_H4_ILC3


title: T74_P4_H8_ILC3


title: T74_P4_H6_ILC3


title: T74_P4_H5_ILC3


title: T74_P4_H3_ILC3


title: T74_P4_H1_ILC3


title: T74_P4_E7_NK


title: T74_P4_F5_ILC2


title: T74_P4_G9_NK


title: T74_P4_D2_NK


title: T74_P4_G4_NK


title: T74_P4_E6_NK


title: T75_P1_E3_ILC3


title: T75_P1_A7_ILC3


title: T74_P4_C3_ILC2


title: T74_P4_A9_ILC3


title: T74_P4_A8_ILC3


title: T75_P1_A8_ILC3


title: T74_P3_F4_ILC3


title: T74_P3_F3_ILC3


title: T74_P3_G9_NK


title: T74_P3_H1_ILC2


title: T74_P3_F1_ILC3


title: T74_P3_E9_ILC2


title: T74_P3_F2_ILC3


title: T74_P3_C6_ILC2


title: T74_P3_D11_NK


title: T74_P3_B9_NK


title: T74_P3_C2_ILC2


title: T74_P3_D7_ILC3


title: T74_P3_D6_ILC3


title: T74_P3_B4_NK


title: T74_P4_B4_NK


title: T74_P2_F1_ILC3


title: T74_P2_E7_NK


title: T74_P2_G9_NK


title: T74_P2_E12_ILC3


title: T74_P2_G4_NK


title: T74_P3_G4_NK


title: T74_P2_D11_NK


title: T74_P2_C9_ILC3


title: T74_P2_C6_ILC3


title: T74_P2_C5_ILC3


title: T74_P2_C4_ILC3


title: T74_P2_C3_ILC3


title: T74_P3_E4_ILC2


title: T74_P2_C8_ILC3


title: T74_P3_E7_NK


title: T74_P2_C2_ILC3


title: T74_P2_C11_ILC3


title: T74_P2_C10_ILC3


title: T74_P2_C12_ILC3


title: T74_P2_B4_NK


title: T74_P3_A11_ILC2


title: T74_P1_H10_ILC2


title: T74_P1_F5_ILC3


title: T74_P1_G9_NK


title: T74_P2_D2_NK


title: T74_P1_F4_ILC3


title: T74_P1_G1_ILC3


title: T74_P1_F3_ILC3


title: T74_P1_F2_ILC3


title: T74_P1_E5_ILC3


title: T74_P1_E2_ILC3


title: T74_P1_E4_ILC3


title: T74_P1_E3_ILC3


title: T74_P1_E1_ILC3


title: T74_P1_D10_ILC2


title: T74_P1_B9_NK


title: T74_P1_A9_ILC1


title: delXF6-Input

status: Public on May 30 2013

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

country: USA

institute: Stanford University

description: Input DNA (after preclear) for delXF6 male embryonic stem cells induced with doxycycline

library_source: genomic

data_processing:
Library strategy: RAP-Seq
Align: BWA version 0.5.9 with default parameters
Filter: Remove reads with mapping qualities less than 30 or if flagged as PCR duplicates for both read pairs by Picard
Count: Count read-pairs that overlap a given window in the genome
Normalize:  Divide read-pair count in a RAP experiment by the read-pair count in the input + 0.1
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files represent normalized enrichment ratios in windows across the genome.  Windows deemed "unmappable" are omitted (see Engreitz et al. 2013).  For the pSM33 timecourse, replicate Xist RAP experiments were combined to generate the final processed data.  For pSM33 timecourse and female ES timecourse, counts in the input files were also combined across time points.

molecule: genomic DNA

organism: Mus musculus

source_name: delXF6 3hr dox

growth_protocol: Male ES cells were grown on plates coated with 0.2% gelatin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).  Xist expression was induced by adding 2 micrograms per milliliter (ug/mL) doxycycline at a defined time before harvesting cells.

extract_protocol:
RNA Antisense Purification (RAP) was performed as described in Engreitz et al. 2013
NEBNext ChIP-Seq Library Prep Kit

tag: cell line

value: embryonic stem cell

tag: induction time

value: 3 hours

tag: experiment type

value: Input

tag: gender

value: male


title: T74_P1_B4_NK


title: T74_P2_B9_NK


title: T74_P1_G4_NK


title: T74_P1_F1_ILC3


title: T74_P1_E7_NK


title: T74_P1_E6_NK


title: T74_P1_B7_ILC2