title: R71D08_11C_08B

description:
R71D08_11C_08
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATCACG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 63_RNA_BM_ILC2p_rpt1

status: Public on May 05 2016

type: SRA

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
alignment, ATAC-seq: ATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
peak-calling, ATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used for peak calling with MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Peaks called from replicates of the same cell type were merged using the mergePeaks module in HOMER. Only peaks called in both replicates were used to generate a bed file for a cell type.
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0.
bw file, RNA-seq: Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
alignment, ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
peaks, ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958 for histone mark K27Ac. Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0E-05 fortransscription factors p300 and Tbet.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq (p300, Tbet); bedgraph for histone modification ChIP-seq (K27Ac). bed file for common ATAC-seq peaks of replicates (linked as supplementary files on Series record).

molecule: total RNA

organism: Mus musculus

source_name: ILC2 precursor cells

growth_protocol:
cell isolation protocol: Cells from bone marrow, liver, and spleen were obtained by mechanical disruption. Cells from lung were isolated after incubating lungfragments with 0.5 mg/ml Liberase TL for 1h followed by purification with 40% Percoll (GE Healthcare) (Meylan et al., 2013). Cells from siLP were isolated after incubating fine-cut intestine in HBSS solution with 0.5 mg/ml DNase I (Roche) and 0.25 mg/ml  Liberase TL (Roche) followed by filtering with 100 μm cell strainer and purification with 40% Percoll (Sciumé et al., 2012). NK cells were isolated from spleen and liver; ILC1s were isolated from liver; Treg, IL17GFP+Th17, ILC2s, CD4+ILC3 and NCR+ILC3 were isolated from siLP; HSC, CLP, NKp, immature NK, and ILC2p were isolated from bone marrow; Nippo-infected ILC2 and Th2 cells were isolated from lung. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Nippostrongylus brasiliensis infection protocol: Mice of at least 8 weeks of age were infected with 500 infective third-stage N. brasiliensis by subcutaneous injection. Cells from lungs were isolated after 10 days of infection.

extract_protocol:
RNA-seq was performed as described previously with slight modification (Hirahara et al., Immunity 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol following manufacture’s protocol (Life Technologies).
RNA-seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ATAC-seq was performed according to published protocol (Buenrostro et al., 2013) with minor modification. 50,000 cells were pelleted and washed with 50ul 1xPBS, followed by treatment with 50ul lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% of IGEPAL CA-630). After pelleting the nuclei by centrifuging at 500x g for 10min, the pellets were re-suspended in 40ul transposition reaction with 2ul Tn5  transposase (Illumina Cat# FC-121-1030) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37ºC with shaking at 300rpm for 30min. The fragmentalized DNAs were then purified using Qiagen MinElute Kit and amplified with 10-11 cycles of PCR based on the amplification curve. Once the libraries are purified using Qiagen PCR Cleanup Kit, they were further sequenced for 50 cycles (paired-end reads) on HiSeq2500.
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on GAII, HiSeq 2000 or 2500 following the manufacturer's protocols.

tag: strain

tag: tissue

value: Bone marrow

tag: surface marker

tag: culture condition

value: ex vivo

tag: cell type

value: ILC2 precursor cells


title: sample 62_RNA_GT_NCRILC3_IL23_rpt2

description: 150730_0381 and 150806_0382 (merged)_S6

source_name: Group 3 innate lymphoid cells

value: Small intestine lamina propria

value: in vitro culture for 4 hours w/ IL23

value: Group 3 innate lymphoid cells


title: sample 60_RNA_GT_ILC2_IL33_IL25_rpt2

description: 150730_0381 and 150806_0382 (merged)_S35

source_name: Group 2 innate lymphoid cells

value: in vitro culture for 4 hours w/ IL33 + IL25

value: Group 2 innate lymphoid cells


title: R71D08_5T_08B

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description:
R71D08_5T_08
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GAGTGG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Neuron

growth_protocol: Flies were raised at 25C.  Parents consisted of 5 females of the UAS-eGFP;UAS-eGFP;+ and 4 males of corresponding GAL4 line.  Parents were placed in a new vial every 4 days for 2 weeks to minimize overcrowding and keep the larval density relatively constant.  All flies were kept in a 12:12 Light Dark cycle.

extract_protocol:
Neurons were identified through anatomical location and GFP expression and then harvested into a patch pipet on an electrophysiology rig from alive flies.  Cells were harvested into .5ul Nuclease Free water to cause the cells to lyse.
cDNA was made and amplified using the Clontech SMARTer Ultra low RNA kit (version 2 HV). 15 rounds of amplification was perfromed on the samples.   This was then sheared to 200bp and put into an IXI Chip-seq protocol  (automated system) and barcoded following another 12 rounds of amplification. 12 samples were run in a lane and each sample was run across two lanes.

treatment_protocol: Animals undergoing memory formation were subjected to 8 spaced trainings of an odor (either 3-Octanol or 4-Methylcyclohexanol) with a 12 cycle 5 second 60V shock for 1 minute.

tag: cell class

tag: number cells

tag: training

value: Trained

tag: quality

value: more than >4 million mapped reads-across 2 lanes


title: R71D08_2C_09B

description:
R71D08_2C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ACTGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Control


title: 32 hr Hi-C

city: Ann Arbor

first: Indika

last: Rajapakse

state: MI

address: 1600 Huron Parkway, NCRC Building 520, Rm. 3392

department: Department of Computational Medicine & Bioinformatics

institute: University of Michigan

library_source: genomic

data_processing:
Reads aligned to HG19 with Tophat 2.0.9 and Bowtie 2.1.0.0 with optional parameters “–b2-very-sensitive”,  “–no- coverage-search” and “–no-novel-juncs”.
Cufflinks and Cuffdiff were used for expression quantification with UCSC hg19.fa/.gtf as the reference genome and transcriptome with additional parameter settings “–multi-read-correct”, “–compatible-hits-norm” and “–upper-quartile- norm”.
Homer was used for Hi-C tabulation with “makeTagDirectory” with the “–tbp 1” setting, and with “analyzeHiC” with the “-raw” and “-res 1000000” settings to produce the raw contact matrix at 1MB resolution.
Genome_build: hg19
Supplementary_files_format_and_content: Each text file includes one of the time points 100 kb matrices. The csv contains the raw count  RNA-seq data while the xls file contains the  normalized (FPKM) RNA-seq values.

molecule: genomic DNA

organism: Homo sapiens

source_name: fibroblast

growth_protocol: Fibroblasts (CRL-2522) were grown in MEM, 10% FBS, X non-essential amino acids, and 1X antibiotic/antimycotic. Cells were dissociated with 0.25% trypsin then plated in 150mm plates for Hi-C, and 6-well plates for RNA-seq.

extract_protocol:
For Hi-C, 25 X 106 cells were cross linked with 1% formaldehyde in situ. Cross linked cells were harvested and flash frozen in liquid nitrogen. For RNA-seq, We used TRIzolr Reagent to extract RNA from cells grown in 6-well plates. Full details in PMC4491792.
All extracted RNA was treated with RNAse-free DNaseI, then submitted to the University of Michigan Bioinformaics Core lab for library construction andRNA-seq on the Illumina Hiseq-2000 platform. Single-end 50-base sequence reads were generated at a multiplex of 4 per sequencing lane. We adopted the methods for Hi- C library construction from Belton et al. (Methods 58:268, 2012). Full details in PMC4491792.

treatment_protocol: Cell cycle synchronization was performed by serum-starvation for 48 hours. After 48th hours, we added dexamethasone to 100nM or ethanol to the control group. 1 hr later baseline samples were taken and time 0 was set. Thereafter, time series sampling of cells treated with dexamethasone was performed at 8-hour intervals for a total of 56 hours. Full details in PMC4491792

tag: cell line

value: ATCC CRL-2522

tag: passages


title: R71D08_9C_08B

description:
R71D08_9C_08
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 59_RNA_GT_ILC2_IL33_IL25_rpt1


title: 24 hr Hi-C


title: sample 55_RNA_GT_CD4ILC3_rpt1

value: CD3ε-CD19-NKp46-CD127+ KLRG1-CD4+


title: sample 53_RNA_GT_NCRILC3_rpt1


title: R71D08_3T_08B

description:
R71D08_3T_08
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GATCAG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 56_RNA_GT_CD4ILC3i_rpt2

description: 150730_0381 and 150806_0382 (merged)_S28


title: R71D08_4T_08B

description:
R71D08_4T_08
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TTAGGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: 16 hr Hi-C


title: sample 66_RNA_BM_NKp_rpt2

source_name: NK precursor cells

value: NK precursor cells


title: sample 52_RNA_GT_ILC2_rpt2

description: 150730_0381 and 150806_0382 (merged)_S10


title: sample 49_RNA_LV_ILC1_rpt1

source_name: Group 1 innate lymphoid cells

value: Liver

value: Group 1 innate lymphoid cells


title: 0D Hi-C


title: sample 44_ATAC_Sp_NK_rpt2

description:
150331_150424_combined_s13
Sp_NK_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

source_name: Natural killer cells

value: Spleen

value: Natural killer cells


title: 8 hr Hi-C


title: sample 50_RNA_LV_ILC1_rpt2

value: ex vivo


title: 0E Hi-C


title: sample 43_ATAC_Sp_NK_rpt1

description:
combined_140626_140923_140930_s1
Please note that raw data files for this sample were combined reads from multiple runs which were done on HiSeq 2000 and HiSeq 2500.
Sp_NK_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: R71D08_9C_08


title: sample 45_ATAC_Sp_NK_IL2_IL12_rpt1

description:
combined_140626_140923_140930_s17
Please note that raw data files for this sample were combined reads from multiple runs which were done on HiSeq 2000 and HiSeq 2500.

value: in vitro culture for 6 hours w/ IL2 +IL12


title: R71D08_2T_0829B

description:
R71D08_2T_0829
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ACTTGA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 38_ATAC_LV_ILC1_rpt2


title: sample 39_ATAC_LV_NK_rpt1

description:
combined_140626_140923_140930_s3
Please note that raw data files for this sample were combined reads from multiple runs which were done on HiSeq 2000 and HiSeq 2500.


title: R71D08_6C_09

description:
R71D08_6C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GGTAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: JEG3_KO_rep2

city: Cambridge

first: William

last: Mallard

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: JEG3 cells with Enhancer L targeting Cas9

data_processing:
Reads were mapped to the hg19 reference genome using Bowtie v2.2.5 and TopHat v2.0.14 with the following options: --no-coverage-search; --transcriptome-index with an index built from Gencode v19.
Gene expression levels were estimated using Cuffdiff v2.2.1 with default options, against a reference transcriptome based on Gencode v19.
Genome_build: hg19
Supplementary_files_format_and_content: gene_expression.txt contains per-replicate gene expression levels (FPKM). gene_exp.diff contains raw Cuffdiff output, including: gene-level expression estimates (average FPKM across replicates), log2 fold change between relevant conditions, and associated FDR values.

source_name: JEG3 cells

growth_protocol: JEG3 cells (ATCC HTB-36) were cultured in RPMI-1640 medium (Gibco) supplemented with 10% FBS, Glutamax, and Penicillin-Streptomycin.

extract_protocol:
JEG3 cells grown to 70% confluence in 10 cm dishes were rinsed once with phosphate-buffered saline (PBS) and harvested with Trizol reagent (Life Technologies). Total RNA was extracted using Trizol, according to manufacturer's instructions and then purified by spin column purification (RNeasy mini kit, Qiagen) using a QIAcube system. RNA was quantified using a Nanodrop (Thermo Fisher) and its integrity assessed on a Bioanalyzer (Agilent) using the RNA 6000 RNA chip.
500 ng high-quality total RNA (RNA Integrity Number >=8) was used as input for TruSeq library construction using the TruSeq RNA Sample Preparation Kit (Illumina). Library purity, correct fragment size, and concentration were assessed using the Bioanalyzer DNA7500 chip. Libraries free of adapter dimers and with a peak region area (220-500 bp) >=80% of the total area were individually barcoded, pooled, and sequenced on an Illumina HiSeq 2000 platform.

treatment_protocol: JEG3 cells were transfected with Cas9-2A-GFP and guide RNAs targeting Enhancer L using FuGENE 6 (Promega) according to the manufacturer's instructions. GFP+ cells were sorted 48 hours post-transfection and plated at clonal density in 10 cm dishes. Approximately 10 days after plating, single cell-derived colonies were picked into 96-well plates and cultured for an additional 10 days. For PCR analysis, cells were harvested and genomic DNA extracted using prepGEM Tissue (ZyGEM). Selected WT and KO clones were then expanded and further characterized.

value: choriocarcinoma (trophoblast)

tag: transfected with

value: Cas9 with guide RNA targeting Enhancer L


title: sample 37_ATAC_LV_ILC1_rpt1

description:
combined_140626_140923_140930_s2
Please note that raw data files for this sample were combined reads from multiple runs which were done on HiSeq 2000 and HiSeq 2500.


title: R71D08_1C_09

description:
R71D08_1C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TAGCTT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 40_ATAC_LV_NK_rpt2


title: JEG3_KO_rep1


title: R71D08_2T_0821

description:
R71D08_2T_0821
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 35_ATAC_LU_Th2_rpt1

source_name: Effector CD4 T cells

value: Lung

value: ex vivo, infected w/ Nippo for 10 days

value: Effector CD4 T cells


title: JEG3_WT_rep3

description: JEG3 cells with non-targeting Cas9

value: Cas9 without guide RNA


title: JEG3_KO_rep3


title: JEG3_WT_rep2

description: JEG3 cells with non-targeting Cas9


title: R71D08_2C_09

value: more than >4 million mapped reads-across 2 lanes


title: sample 33_ATAC_LU_ILC2_rpt1

value: Group 2 innate lymphoid cells


title: sample 36_ATAC_LU_Th2_rpt2


title: sample 34_ATAC_LU_ILC2_rpt2


title: R71D08_11C_08

description:
R71D08_11C_08
Samples run across two lanes and pooled

value: Control


title: R71D08_5T_08

description:
R71D08_5T_08
Samples run across two lanes and pooled

value: Trained


title: sample 31_ATAC_GT_NCRILC3_IL23_rpt1

value: Small intestine lamina propria

value: in vitro culture for 4 hours w/ IL23

value: Group 3 innate lymphoid cells


title: sample 29_ATAC_GT_NCRILC3_rpt1

description:
combined_140626_140923_140930_s6
Please note that raw data files for this sample were combined reads from multiple runs which were done on HiSeq 2000 and HiSeq 2500.
GT_NCRILC3_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: sample 32_ATAC_GT_NCRILC3_IL23_rpt2


title: JEG3_WT_rep1

description: JEG3 cells with non-targeting Cas9


title: R71D08_4T_08


title: JEG3_rep2

description: JEG3 cells


title: sample 26_ATAC_GT_ILC2_rpt2

description:
150902_0386_s19
GT_ILC2_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: sample 27_ATAC_GT_ILC2_IL33_IL25_rpt1

value: in vitro culture for 4 hours w/ IL33 + IL25


title: JEG3_rep1

description: JEG3 cells


title: R71D08_3T_08

description:
R71D08_3T_08
Samples run across two lanes and pooled


title: sample 28_ATAC_GT_ILC2_IL33_IL25_rpt2


title: c739_12C_09_1

value: alpha/beta Kenyon Cells (c739-GAL4)

value: more than >4 million mapped reads-across


title: R71D08_2T_0829


title: sample 25_ATAC_GT_ILC2_rpt1

description:
combined_140626_140923_140930_s5
Please note that raw data files for this sample were combined reads from multiple runs which were done on HiSeq 2000 and HiSeq 2500.
GT_ILC2_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

value: ex vivo


title: sample 22_ATAC_GT_CD4ILC3_rpt1

description:
combined_140626_140923_140930_s4
Please note that raw data files for this sample were combined reads from multiple runs which were done on HiSeq 2000 and HiSeq 2500.
GT_CD4ILC3_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

value: CD3ε-CD19-NKp46-CD127+ KLRG1-CD4+


title: sample 21_ATAC_GT_CD25+SP

source_name: Memory CD4 T cells

value: Memory CD4 T cells


title: ATAC_77iSMA_C_rep3

first: Pamela

last: Milani

address: 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Library strategy: ATAC-Seq
We aligned sequencing reads to the hg19 genome build using BWA (version 0.7.10). We assessed the quality of the sequences using FastQC (version 0.11.2). We removed mitochondrial reads from the analysis using custom UNIX scripts. We determined open-chromatin regions (peaks) using MACS2 v.2.1.0.20150420 (q-value threshold = 0.05). We used the sequencing data from transposed naked DNA as a control. The differential analysis between fresh and cryopreserved samples was performed using the default settings in the package DiffBind version 1.16.0. Briefly, read counts for each site were computed and differentially enriched sites between fresh and cryopreserved conditions were identified using the edgeR package, with FDR < 0.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: We generated bigWig files from alignment BAM files with BEDTools; *.narrowPeak files contain MACS-called peak regions; the .bed file contains the differentially enriched sites between fresh and cryopreserved conditions computed with the diffBind package. There are 6 columns: seqnames, starts, ends, Fold, p.value and FDR.

source_name: Cryopreserved motor neurons

growth_protocol: Human induced pluripotent stem cells were differentiated as described by Fuller HR et al. (Front Cell Neurosci. 2016 Jan 11;9:506). On day 21, the motor neurons cultures were collected: the neurons were washed once with 1X PBS, isolated via cell scraper in 1X PBS, and centrifuged at 200 rcf for 5 minutes at 4°C. The pellet was immediately frozen by cryopreservation. Briefly, pellets were re-suspended in Cryostor media and frozen slowly in a Mr. Frosty isopropyl alcohol chamber (FisherSci) at -80°C overnight. This procedure allowed us to achieve a rate of cooling of -1°C/minute. Cryopreserved neurons were stored at -80°C until experimentation. To thaw the cryopreserved cells, cryovials were removed from -80°C and quickly warmed for 2 min in a 37°C water bath. Samples were transferred to 12 ml of warm 1X PBS supplemented with 1X protease inhibitor cocktail and centrifuged at 200 rcf for 5 min at 4°C.

extract_protocol:
The cell pellets were re-suspended in ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) supplemented with 1X protease inhibitor cocktail (Roche), incubated on ice for 5 min and centrifuged at 230 rcf for 5 min at 4°C. The supernatant was carefully removed and the nuclei were re-suspended in 25 µl of ice-cold 1X Tagment DNA Buffer (Illumina).
50,000 nuclei were used for the transposase reaction, which was carried out as described by Buenrostro et al. (Nat Methods. 2013 Dec;10(12):1213-8). The samples were purified with the DNA Clean & Concentrator-5 Kit (Zymo Research) and eluted with 20 µl of Elution Buffer (Qiagen). The samples were PCR-amplified using 25 µl of Nextera PCR Master Mix (Illumina), 5 µl of PCR Primer Cocktail (Illumina), 5 µl of Index primer 1 (i7, Illumina), and 5 µl of Index primer 2 (i5, Illumina). The following PCR reaction protocol was used: 3 min 72°C; 30 sec 98°C; 8 cycles (10 sec 98°C, 30 sec 63°C, 3 min 72°C). Samples were purified with the DNA Clean & Concentrator-5 Kit (Zymo Research), eluted with 20 µl of Elution Buffer (Qiagen), and loaded on 2% agarose gel (Invitrogen) for size-selection (175-250 bp). DNA was purified using the QIAquick Gel Extraction Kit (Qiagen) following the manufacturer's recommendation, and eluted with 20 µl of Elution Buffer (Qiagen). The DNA was further amplified with 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs), 200 nM of Primer 1 (5'-AATGATACGGCGACCACCGA-3'), and 200 nM of Primer 2 (5'-CAAGCAGAAGACGGCATACGA-3’). The following PCR reaction protocol was used: 30 sec 98°C; 4 cycles (10 sec 98°C, 30 sec 65°C, 30 sec 72°C); 5 min 72°C. The final libraries were purified using Agencourt AMPure XP beads (Beckman Coulter).

tag: primary tissue

value: Fibroblast

value: iPSC-derived motor neurons

tag: iPSc method

value: Episomal

tag: genotype/variation

value: Homozygous mutation of the SMN1 gene

tag: sample state

value: Cryopreserved


title: sample 24_ATAC_GT_IL17GFP+


title: ATAC_77iSMA_C_rep2


title: sample 30_ATAC_GT_NCRILC3_rpt2

description:
150331_150424_combined_s14
GT_NCRILC3_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: sample 23_ATAC_GT_CD4ILC3_rpt2

description:
150331_150424_combined_s16
GT_CD4ILC3_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: sample 19_ATAC_GT_CCR-CD25-DN


title: ATAC_77iSMA_C_rep1


title: c739_2T_0830B

description:
c739_2T_0830
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATGAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: more than >4 million mapped reads-across 2 lanes


title: sample 17_ATAC_BM_NKp_rpt1

description:
150331_150424_combined_s04
BM_NKp_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

value: Bone marrow

value: NK precursor cells


title: sample 20_ATAC_GT_CCR6+SP

value: Small intestine lamina propria


title: sample 18_ATAC_BM_NKp_rpt2

description:
150331_150424_combined_s05
BM_NKp_du_shared.bed (bed file for common ATAC-seq peaks of replicates)


title: sample 16_ATAC_BM_naive_CD8_rpt2

source_name: Naive CD8 T cells

value: Naive CD8 T cells


title: ATAC_77iSMA_F_rep3

source_name: Fresh motor neurons

growth_protocol: Human induced pluripotent stem cells were differentiated as described by Fuller HR et al. (Front Cell Neurosci. 2016 Jan 11;9:506). On day 21, the motor neurons cultures were collected: the neurons were washed once with 1X PBS, isolated via cell scraper in 1X PBS, and centrifuged at 200 rcf for 5 minutes at 4°C. The pellet was immediately re-suspended in cell lysis buffer for nuclei extraction.

value: Fresh


title: ATAC_77iSMA_F_rep2


title: c739_14C_08B

description:
c739_14C_08
Samples run across two lanes and pooled

value: Control


title: sample 11_ATAC_BM_memory_CD8_rpt1

source_name: Memory CD8 T cells

value: Memory CD8 T cells


title: sample 12_ATAC_BM_memory_CD8_rpt2


title: c739_12C_09_2

value: alpha/beta Kenyon Cells (c739-GAL4)

value: more than >4 million mapped reads-across


title: c739_10T_09B

description:
c739_10T_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GTAGAG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Trained


title: c739_11C_08B

description:
c739_11C_08
Samples run across two lanes and pooled


title: sample 15_ATAC_BM_naive_CD8_rpt1

value: ex vivo


title: 3wtALID7 sRNA-Seq

city: Göttingen

first: Orr

last: Shomroni

address: Grisebachstraße 5

country: Germany

institute: DZNE

description: WT rep3 day 7

data_processing:
Mapping, prediction of novel miRNAs, quality control, and differential expression (DE) analysis were carried out using Oasis1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Excel sheets containing sheets with (1) RPM normalised read counts for small RNA in each sample, and (2) base mean, log 2 fold change and adjusted p-value generated by DESeq2 for each small RNA in each day

source_name: Trachea

growth_protocol: Primary cultures of mouse tracheal epithelial cells (MTECs) were established on Transwell membranes  and  differentiated into multiciliated cells using air-liquid interface (ALI) conditions as previously described (You et al, Am J Physiol Lung Cell Mol Physiol, 2002, PMID 12388377)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina)

value: primary mouse tracheal epithelial cultures (MTECs)

tag: treatment

value: air-liquid interface (ALI)

tag: day

value: post ALI day 7

tag: genotype

value: wild type


title: c739_1T_08B

description:
c739_1T_08
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: AGTTCC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: c739_2C_09B

description:
c739_2C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CGTACG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 7_ATAC_BM_ILC2p_rpt1

description:
150331_150424_combined_s02
BM_ILC2p_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

data_processing:
alignment, ATAC-seq: ATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
peak-calling, ATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used for peak calling with MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Peaks called from replicates of the same cell type were merged using the mergePeaks module in HOMER. Only peaks called in both replicates were used to generate a bed file for a cell type.
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0.
bw file, RNA-seq: Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
alignment, ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
peaks, ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958 for histone mark K27Ac. Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0E-05 fortransscription factors p300 and Tbet.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq (p300, Tbet); bedgraph for histone modification ChIP-seq (K27Ac). bed file for common ATAC-seq peaks of replicates (linked as supplementary files on Series record).

tag: strain

tag: tissue

tag: surface marker

value: ILC2 precursor cells


title: Erythroid USF2

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Basecalls were performed using CASAVA version 1.7.0
ChIP-seq reads were aligned to the hg18 genome assembly using elandv2.
The eland extended format alignments were converted to bed format using the elandextended2bed.py script.
Peaks were called against the total input sample GSM1067273 using macs version 1.4.0rc2 with default parameters.
Quality scores in the fastq files were converted from Illumina1.3 to sanger using the fq_all2std.pl script.
Genome_build: hg18
Supplementary_files_format_and_content: The macs peaks.bed output files have a fifth field that is -10*log10(pvalue)

source_name: R3/R4 Erythroid cells

growth_protocol: Human CD34+-selected stem and progenitor cells were obtained from the Yale Center for Excellence in Molecular Hematology. To obtain primary human erythroid cells, CD34+ cells were cultured and selected as described.(Panzenbock, B., Bartunek, P., Mapara, M. Y., and Zenke, M. (1998) Blood 92, 3658-3668.  Migliaccio, A. R., Migliaccio, G., Di Baldassarre, A., and Eddleman, K. (2002) Bone Marrow Transplant 30, 75-80) Briefly, Human CD34-selected stem and progenitor cells were cultured in StemSpan SF expansion medium (StemSpan 09650) with estradiol (100 ng/ml), dexamethasone (10 ng/ml), human transferrin (200 ng/ml), insulin (10 ng/ml), Flt3 ligand (100 ng/ml), stem cell factor (100 ng/ml), interleukin-3 (50 ng/ml), interleukin-6 (20 ng/ml), insulin-like growth factor 1 (50 ng/ml), and erythropoietin (3 U/ml) for 9 to 14 days. FACS analysis was used to analyze cellular expression of CD71 (transferrin receptor) and CD235a (glycophorin A). These cells represent the R3/R4 cell population of nucleated erythroid cells defined by Zhang et al.(Zhang, J., Socolovsky, M., Gross, A. W., and Lodish, H. F. (2003) Blood 102, 3938-3946)

extract_protocol: ChIP libraries were prepared using the KAPA Library Preparation Kit (KAPA Biosystems) per the manufacturer's protocol. Briefly, ChIP DNA was end repaired, followed by addition of an adenine base at the 3' and NEXTflex ChIP-Seq Barcodes (BiooScientific) adaptor ligation. The modified DNA was then size selected on a 2% agarose and purified by using a gel extraction kit (Qiagen).  One microliter of size-selected adaptor ligated DNA was initially analyzed by SYBR Green Q-PCR to determine the number of cycles required to reach 50% of complete amplification.  Adaptor ligated DNA was PCR amplified with one initial heating step of 98°C for 45 second, followed by the pre-determined number of cycles with a melting temperature of 98°C for 15 s, an annealing temperature of 65°C for 30 s, and a product extension at 72°C for 30 s. At the end of the amplification, a final extension at 72°C for 1 min was performed. Amplified ChIP DNA was subjected to deep sequencing using standard Yale Center for Genome analysis protocols.

treatment_protocol: ChIP assays were performed as previously described with minor variations (Steiner, L. A., Maksimova, Y., Schulz, V., Wong, C., Raha, D., Mahajan, M. C., Weissman, S. M., and Gallagher, P. G. (2009) Mol Cell Biol). 1 × 107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by Dounce homogenization. Cross-linked nuclei were isolated, followed by sonication with a Covaris S2 shearing device (duty cycle 10%, intensity 5, 15 minutes), to obtain chromatin-containing DNA fragments with an average size of ~200-400bp. For each ChIP, 20 μg of antibody or the appropriate control IgG species was used. Samples were immunoprecipitated with antibodies against BPTF, H4R3me2a, SET1, USF1(H-86x, Santa Cruz) and USF2 (H-86x, Santa Cruz). The antigen-antibody complex was captured on protein G beads, washed four times with radioimmunoprecipitation assay buffer, and then washed with phosphate-buffered saline. The DNA-protein complex was eluted from the protein G beads with 1% sodium dodecyl sulfate at 65°C, and cross-linking of DNA-protein adducts was reversed by overnight incubation at 65°C.   After proteinase K and RNase digestion of the reverse-cross-linked sample, DNA was extracted with phenol-chloroform, precipitated with ethanol, then cleaned with the QIAquick PCR Purification Kit (Qiagen) according to manufacturer instructions.

tag: cell type

value: R3/R4 Erythroid cells

tag: chip antibody

tag: antibody info

value: Santa Cruz Cat#:C-20x


title: Erythroid SET1

value: Bethyl Laboratory  Cat#: A300-289A


title: sample 2_ATAC_BM_Bcell_rpt2

source_name: B cells

value: Bone marrow

tag: culture condition

value: B cells


title: c739_9C_08B

description:
c739_9C_08
Samples run across two lanes and pooled

tag: cell class

tag: number cells

tag: training

tag: quality

value: more than >4 million mapped reads-across 2 lanes


title: c739_3T_08B

description:
c739_3T_08
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TCGAAG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 1_ATAC_BM_Bcell_rpt1


title: 3wtALID14 sRNA-Seq

description: WT rep3 day 14

value: post ALI day 14


title: sample 82_p300_Sp_NK_IL2_IL12

value: Spleen

value: in vitro culture for 6 hours w/ IL2 +IL12

value: Santa Cruz sc585

value: Natural killer cells


title: 2wtALID4 sRNA-Seq

description: WT rep2 day 4

value: post ALI day 4


title: 2wtALID7 sRNA-Seq

description: WT rep2 day 7

value: primary mouse tracheal epithelial cultures (MTECs)


title: ATAC_77iSMA_F_rep1

tag: primary tissue

value: Fibroblast

value: iPSC-derived motor neurons

tag: iPSc method

value: Episomal

value: Homozygous mutation of the SMN1 gene

value: Fresh


title: 2wtALID14 sRNA-Seq

description: WT rep2 day 14

value: air-liquid interface (ALI)

value: wild type


title: c739_2T_0826B

description:
c739_2T_0826
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: TCGGCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: alpha/beta Kenyon Cells (c739-GAL4)

value: Trained


title: sample 81_p300_Sp_NK

value: ex vivo


title: sample 10_ATAC_BM_iNK_rpt2

description:
150331_150424_combined_s17
BM_iNK_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

source_name: Immature NK cells

value: Bone marrow

value: Immature NK cells


title: Erythroid USF1

value: R3/R4 Erythroid cells

value: Santa Cruz Cat#:H-86x


title: 2wtALID0 sRNA-Seq

description: WT rep2 day 0

value: post ALI day 0


title: 3p73koALID7 sRNA-Seq

description: P73-KO rep3 day 7

value: post ALI day 7

value: p73 knock-out


title: c739_2T_0823B

description:
c739_2T_0823
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: AGTCAA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: more than >4 million mapped reads-across 2 lanes


title: 2p73koALID7 sRNA-Seq

description: P73-KO rep2 day 7

value: primary mouse tracheal epithelial cultures (MTECs)


title: c739_1C_09B

description:
c739_1C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: GTGGCC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: Control


title: 2p73koALID4 sRNA-Seq

description: P73-KO rep2 day 4

value: post ALI day 4


title: Erythroid BPTF

value: BPTF

value: Polyclonal rabbit antibody against chicken BPT fragment (aa2775-2789)


title: ES58: Zfp36l3 KO Placenta RNA-seq

city: Durham

first: Perry

middle: J

last: Blackshear

address: 101 Alexander Dr.

institute: NIEHS

data_processing:
raw reads were mapped to mm10 RefSeq cDNA sequences using BWA default paired-end read mapping protocol
the reads that were not mapped in-pair were filtered out
total read count of each transcript were reported and normalized by EpiCenter
FPKM data were derived from the normalized read counts
Genome_build: mm10

source_name: placenta

growth_protocol: Living mice; normal growth conditions

extract_protocol:
RNA was isolated from embryonic day 15.5 placentas using the GE Healthcare RNA isolation kit. RNA was quantified using the Thermo Scientific Nanodrop 2000c.
Libraries were prepared according to Illumina's Instructions

value: Zfp36l3 KO

tag: development stage

value: Embryonic day 15.5

tag: tissue type

value: Placenta


title: ES59: Zfp36l3 KO Placenta RNA-seq


title: 3p73koALID14 sRNA-Seq

description: P73-KO rep3 day 14

tag: treatment

value: air-liquid interface (ALI)

tag: day

value: post ALI day 14


title: ES60: Zfp36l3 KO Placenta RNA-seq

tag: genotype


title: c739_2T_0830

source_name: Neuron

value: alpha/beta Kenyon Cells (c739-GAL4)

value: Trained


title: 2p73koALID14 sRNA-Seq

description: P73-KO rep2 day 14

tag: tissue


title: c739_14C_08

data_processing:
Multiplexing barcode: GAGTGG
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: ES57: Zfp36l3 KO Placenta RNA-seq


title: c739_1T_08


title: 3wtALID7 RNA-Seq

description: WT rep3 day 7

data_processing:
Murine RNA-seq data was aligned to the Mus musculus mm10 genome using STAR aligner (version 2.3.0e_r291) with default options and automatically generating alignment files in BAM format
Read counts for all genes and all exons (Ensembl annotation v72) were obtained using FeaturesCount (version 1.4.6)
Read counts were used to find differentially expressed genes (DEGs) between wild-type and p73 knock-out samples in the different time-points using DESeq2 (version 1.4.5)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Excel sheets containing sheets with (1) RPM normalised read counts for gene in each sample, and (2) base mean, log 2 fold change and adjusted p-value generated by DESeq2 for each gene in each day

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina)

value: wild type


title: 2wtALID7 RNA-Seq

description: WT rep2 day 7


title: ES55: WT Placenta RNA-seq

value: WT


title: c739_10T_09


title: c739_11C_08

data_processing:
Multiplexing barcode: ACTGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: 3p73koALID0 sRNA-Seq

description: P73-KO rep3 day 0

value: post ALI day 0


title: ES56: Zfp36l3 KO Placenta RNA-seq


title: 3wtALID4 RNA-Seq

description: WT rep3 day 4


title: 3p73koALID4 sRNA-Seq

description: P73-KO rep3 day 4

value: p73 knock-out


title: 2wtALID4 RNA-Seq

description: WT rep2 day 4


title: 3wtALID14 RNA-Seq

description: WT rep3 day 14


title: 1wtALID7 RNA-Seq

description: WT rep1 day 7

value: post ALI day 7


title: 2wtALID14 RNA-Seq

description: WT rep2 day 14

value: primary mouse tracheal epithelial cultures (MTECs)


title: 1wtALID3 RNA-Seq

description: WT rep1 day 4


title: c739_2C_09

value: Control

value: more than >4 million mapped reads-across 2 lanes


title: ES53: WT Placenta RNA-seq


title: 3wtALID0 RNA-Seq

description: WT rep3 day 0


title: 2p73koALID0 sRNA-Seq

description: P73-KO rep2 day 0


title: ES51: WT Placenta RNA-seq


title: c739_9C_08

data_processing:
Multiplexing barcode: GGTAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: 1wtALID14 RNA-Seq

description: WT rep1 day 14


title: c739_2T_0826


title: ES54: WT Placenta RNA-seq


title: 2wtALID0 RNA-Seq

description: WT rep2 day 0


title: 2p73koALID7 RNA-Seq

description: P73-KO rep2 day 7


title: ES52: WT Placenta RNA-seq


title: 1p73koALID7 RNA-Seq

description: P73-KO rep1 day 7


title: sample 87_T-bet_Sp_NK

tag: strain

value: Spleen

tag: surface marker

value: ex vivo

value: Santa Cruz sc21003

value: Natural killer cells


title: c739_2T_0823


title: 2p73koALID4 RNA-Seq

description: P73-KO rep2 day 4

value: post ALI day 4


title: sample 8_ATAC_BM_ILC2p_rpt2

description:
150331_150424_combined_s03
BM_ILC2p_du_shared.bed (bed file for common ATAC-seq peaks of replicates)

source_name: ILC2 precursor  cells

value: Bone marrow

tag: cell type

value: ILC2 precursor  cells


title: c739_1C_09

value: alpha/beta Kenyon Cells (c739-GAL4)


title: sample 85_Input_Sp_NK


title: 2p73koALID14 RNA-Seq

description: P73-KO rep2 day 14

value: air-liquid interface (ALI)

value: post ALI day 14


title: NP1131_3C_0916B

description:
NP1131_3C_0916
Samples run across two lanes and pooled

value: Gamma Kenyon Cells (NP1131-GAL4)


title: c739_3T_08

value: Trained


title: sample 86_Input_Sp_NK_IL2_IL12

value: in vitro culture for 6 hours w/ IL2 +IL12


title: 1p73koALID14 RNA-Seq

description: P73-KO rep1 day 14

value: p73 knock-out


title: 1p73koALID3 RNA-Seq

description: P73-KO rep1 day 4

value: primary mouse tracheal epithelial cultures (MTECs)


title: 1wtALID0 RNA-Seq

description: WT rep1 day 0

value: post ALI day 0

value: wild type


title: 1p73koALID0 RNA-Seq

description: P73-KO rep1 day 0


title: 2p73koALID0 RNA-Seq

description: P73-KO rep2 day 0


title: NP1131_13T_0924B

description:
NP1131_13T_0924
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACGAT
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

value: more than >4 million mapped reads-across 2 lanes


title: ES617: Zfp36l3 KO Yolk Sac RNA-seq

source_name: yolk sac

extract_protocol:
RNA was isolated from embryonic day 15.5 yolk sacs using the GE Healthcare RNA isolation kit. RNA was quantified using the Thermo Scientific Nanodrop 2000c.
Libraries were prepared according to Illumina's Instructions

value: Zfp36l3 KO

value: Embryonic day 15.5

value: yolk sac tissue


title: sample 83_H3K27ac_Sp_NK

value: Spleen

value: ex vivo

tag: chip antibody

value: AbCam ab4729

value: Natural killer cells


title: sample 84_H3K27ac_Sp_NK_IL2_IL12

tag: culture condition


title: NP1131_14T_09B

description:
NP1131_14T_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATGAGC
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

tag: cell class


title: ES616: Zfp36l3 KO Yolk Sac RNA-seq


title: sample 80_RNA_Sp_Naive_CD4_rpt2

source_name: Naïve CD4 T cells

value: Naive CD4 T cells


title: ES615: Zfp36l3 KO Yolk Sac RNA-seq


title: ES614: Zfp36l3 KO Yolk Sac RNA-seq


title: sample 79_RNA_Sp_Naive_CD4_rpt1


title: ES613: WT Yolk Sac RNA-seq

value: WT


title: ES612: WT Yolk Sac RNA-seq


title: NP1131_4C_09B

description:
NP1131_4C_09
Samples run across two lanes and pooled

value: Gamma Kenyon Cells (NP1131-GAL4)

tag: number cells

value: Control


title: NP1131_9T_09B

description:
NP1131_9T_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: CACTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.

tag: training

value: Trained


title: ES611: WT Yolk Sac RNA-seq


title: ES610: WT Yolk Sac RNA-seq


title: NP1131_7C_09B

description:
NP1131_7C_09
Samples run across two lanes and pooled

tag: quality


title: NP1131_2C_09B

description:
NP1131_2C_09
Samples run across two lanes and pooled

data_processing:
Multiplexing barcode: ATGTCA
Cut and adapt the barcodes and remove poly A and T. Using Galaxy: Cutadapt: Removes sequences of 10 As or Ts along with barcodes.  Max error rate=.11, Matchtimes=1, Min Overlap length=9, Min length =36, Max length = 0,
Run Tophat2. Using Galaxy: Tophat2: Full parameter list: Max realign edit dist=1000, max edit dist =2, library type = FR Unstranded, Final read mismatches = 2, Use bowtie-n-mode = no, Anchor length = 8, max number mismatches in anchor region = 0, min length intron =70, max intron length = 500000, allow indel search = no, max number of alignments = 1, min intron length found during split-segment = 50, Max intron length found during split-segment = 500000, number of mismatches allowed in each segment alignment for reads mapped independently=2, Min length read segements= 25, Use own junctions = yes, Use Gene annotation model = Yes, Use raw junctions = no, Only look for supplied junctions = yes, Use coverage search= No, Use Microexon search = no, Do Fusion search = no, Set Bowtie2 settings = no, Specify read group = No
Run HTseqCounts. Using Galaxy: htseq-counts: Mode: Intersection Strict, Feature type: exon, ID Attribute: gene_id
DESEQ2. Using R: Deseq2 Version 1.4
Genome_build: ensembl_dmel_bdgp5.25; Drosophila_melanogaster.BDGP5.74.gtf
Supplementary_files_format_and_content: Htseq counts reported in .txt file.
Supplementary_files_format_and_content: A total of 4 files linked as supplementary files to the Series record:  One is an overall target file describing each sample in the combined data files and whether that sample was removed due to quality issues.  2nd file is the combined raw counts (HTseq-Count) for each sample we sequenced and set up so the rows are the genes and columns are the sample names.  3rd file is a file converting all gene counts to counts per million mapped reads (CPM). This file was used for z-scoring and removing genes with less than 2 CPM.  4th File is combined data normalized using DESeq2 and regularized log transformed, this file removed 5 samples (ab KC technicals, Brain samples and one G386 sample).  All genes for each cell type with <2CPM in half samples were replaced with zeros.


title: sample 51_RNA_GT_ILC2_rpt1

source_name: Group 2 innate lymphoid cells

value: Small intestine lamina propria

value: Group 2 innate lymphoid cells