title: X19407_H9

city: Pasadena

first: Wen

last: Zhou

state: California

address: 1200 E California Blvd, Mail Code 250-86

department: BBE

institute: California Institute of Technology

description:
FPKM_C1_table.txt
Sample_19407_H9

data_processing:
Prepared using ENCODE long-rna-seq pipeline. Briefly, genomic and transcriptome alignment was performed using STAR(v2.4.0), followed by sort-samtools and index-samtools to sort and index Transcriptome BAM file. Then, generation of bedgraph of reads was performed using bedgraph-star, and RSEM(v1.2.25) was used to generate transcriptome counts and FPKM output. Genome build: mm10
Genome_build: mm10
Supplementary_files_format_and_content: bulk_RNAseq_processed.txt; matrix.mtx with accompanying genes.tsv and barcodes.tsv; FPKM_C1_table.txt

source_name: Thymus

growth_protocol: primary cells isolated from C57BL/6 mice

extract_protocol: C1-Fluidigm 96 and Smartseq2 v4

value: WT

value: Thymus

tag: facs purification gate

value: Lin- 7AAD- CD44+ Kit+


title: ATAC-seq_Pan-BC_1

status: Public on Oct 16 2019

type: SRA

city: Saint Louis

first: Daniel

last: Murphy

state: MO

address: 660 S. Euclid

country: USA

institute: Washington University School of Medicine

library_source: genomic

data_processing:
Alignment (ATAC-seq): Paired-end reads were aligned to mm10 using Bowtie2 (v2.2.5) with a maximum insert size of 2000 (-X 2000). Alignment (RNA-seq): Single-end RNA-seq reads were aligned to mm10 using STAR (v2.7.0d) (index prepared for mm10 with 50 bp reads and RefSeq gene model included in the iGenomes mm10 Annotations).
Sort (ATAC-seq): alignments were sorted in coordinate order using Picard (v2.19.0) SortSam
Merge (ATAC-seq): alignments for individual libraries run on multiple sequencing lanes were merged using Picard (v2.19.0) MergeSamFiles.
Filter (ATAC-seq): alignments were filtered using SAMtools (v1.3) view to retain only properly paired reads (-f 0x0002) with minimum mapping quality 30 (-q 30) not aligning to unlocalized contigs, unassembled contigs, the mitochondrial genome, or ENCODE blacklist regions (-L <POSITION FILE>).
Remove PCR Duplicates (ATAC-seq): PCR duplicates were marked with Picard (v2.19.0) MarkDuplicates and removed with SAMtools (v1.3) view (-F 0x0400).
Filter for nucleosome-free reads(ATAC-seq): alignments were filtered for fragments with an insert size less than 100 using SAMtools (v1.3) view and awk.
Generate bedGraph (ATAC-seq): bedgraph files were generated using HOMER (v4.8) makeUCSCfile (-style DNase -fsize 5e8). Generate bedGraph (RNA-seq): bedgraph files were generated using HOMER (v4.8) makeUCSCfile (-fragLength given).
Call Peaks (ATAC-seq): consensus peaks for each pair of ATAC-seq biological replicates (filtered nucleosome-free reads) were generated using MACS2 (v2.1.1) callpeak (--nomodel --shift -100 --extsize 200 --keep-dup all --pvalue 1e-2 --call-summits) followed by thresholding using the irreproducible discovery rate (IDR) framework.
Feature Counts (ATAC-seq): 200 bp intervals centered on peak summits were merged across peak call sets from this study as well as identically processed peak call sets from photoreceptors (GSE83312) using bedops (v2.4.14), to produce a reference set of photoreceptor and bipolar cell ATAC-seq peaks. Each of the resulting intervals was then scored for coverage using bedtools (v2.24.0) coverageBed to generate the ATAC-seq count table used for differential accessibility analysis. Feature Counts (RNA-seq): RNA-seq counts overlapping RefSeq genes were generated for each biological replicate from this study, as well as identically processed biological replicates from photoreceptors (GSE83312) using HTSeq (v1.9) htseq-count (-f sam -m union -r pos -i gene_name -a 10 --stranded=no). The resulting RNA-seq count table was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (RNA-seq): files generated from normalized RNA-seq reads per genomic interval (3' bases are dropped from reads flanking exon-intron junctions)
Supplementary_files_format_and_content: bedGraph (ATAC-seq): files generated from filtered, nucleosome-free alignment of normalized ATAC-seq reads per genomic interval.
Supplementary_files_format_and_content: ATAC-seq_count_table.txt: Count table of normalized ATAC-seq reads for each biological replicate from photoreceptors (GSE83312) and bipolar cells (this study).
Supplementary_files_format_and_content: RNA-seq_count_table.txt: Count table of normalized RNA-seq reads for each biological replicate from photoreceptors (GSE83312) and bipolar cells (this study).
Supplementary_files_format_and_content: narrowPeak (ATAC-seq): consensus peaks for each replicate.

molecule: genomic DNA

organism: Mus musculus

source_name: FACs sorted retinal cells

extract_protocol:
Retinas were harvested from 6-8 week-old mice, dissociated with papain and treated with DNAse prior to resuspension  in FACS buffer (2.5 mM EDTA, 25 mM HEPES, 1% BSA in HBSS ). Populations of interest were identified by the intensity of GFP-fluorescence and isolated via FACS. For RNA-seq, RNA was isolated with Trizol reagent. For ATAC-seq, taransposition reactions were carried out using the standard protocol (Buenrostro et al. Nature Methods 2013)
ATAC-seq libraries were prepared using the standard protocol (Buenrostro et al. Nature Methods, 2013). RNA-seq libraries were prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing-HV (Clonetech).

tag: tissue

value: retina

tag: cell type

value: bipolar

tag: age (post-natal day)

tag: genotype

value: Otx2-GFP+/-; Grm6-YFP+/+

tag: facs

value: Single Sort


title: ATAC-seq_singleSort_rod_1_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199332

value: rod photoreceptors

value: Nrl-eGFP


title: ATAC-seq_Pan-BC_2


title: X19407_H8

description:
FPKM_C1_table.txt
Sample_19407_H8

library_source: transcriptomic

molecule: polyA RNA

tag: strain


title: X19407_H11

description:
FPKM_C1_table.txt
Sample_19407_H11


title: X19407_H5

description:
FPKM_C1_table.txt
Sample_19407_H5


title: X19407_H2

description:
FPKM_C1_table.txt
Sample_19407_H2


title: X19407_H12

description:
FPKM_C1_table.txt
Sample_19407_H12


title: X19407_H6

description:
FPKM_C1_table.txt
Sample_19407_H6


title: X19406_G9

description:
FPKM_C1_table.txt
Sample_19406_G9


title: X19407_H4

description:
FPKM_C1_table.txt
Sample_19407_H4


title: X19407_H7

description:
FPKM_C1_table.txt
Sample_19407_H7


title: X19407_H3

description:
FPKM_C1_table.txt
Sample_19407_H3


title: ATAC-seq_ON-BC_2


title: IL2_IL7_CGRP0.4ug_rep2

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
bulk RNA-Seq: A14
full-length
rsem.genes.counts.matrix

data_processing:
bulk RNAseq: Bcl2fastq was used to generate fastq files
bulk RNAseq: map to mm10 using Bowtie 2 with default parameters
bulk RNAseq: RSEM were used for calculating counts
scRNA-seq data: the 10x Genomics Cell Ranger Single Cell Software Suite 2.0.1 was used to perform sample demultiplexing and single cell UMI counting
Genome_build: mm10
Supplementary_files_format_and_content: For bulkRNAseq data: tab-delimited text files include counts values for each sample.
Supplementary_files_format_and_content: For scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: For scRNA-seq data: barcodes.tsv, cell names (colname names of the count matrix)
Supplementary_files_format_and_content: For scRNA-seq data: genes.tsv, gene names (row names of the count matrix)
Supplementary_files_format_and_content: For scRNA-seq data: matrix.tsv, the coordinates of cells form projecting cells measured from single-cell RNA-sequencing to the bulk ImmGen dataset

molecule: total RNA

source_name: small intestine

growth_protocol: for bulk RNA-seq, 250 flow sorted-KLRG1+ ILC2s were incubated in RPMI supplemented with 10% FCS, 10mM Hepes, 1mM sodium pyruvate, 10% FBS, 80μm 2-mercaptoethanol, 2mM glutamine, 100U/ml penicillin, 100μg/ml streptomycin, 100 ng/ml IL-2 and 100 ng/ml IL-7 in 96-well round bottom plates at 37°C and 5% CO2. As indicated, the culture was supplemented with 100 ng/ml IL-25 and/or 0.4 μg/ml α-CGRP for 3 hours.

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)
10x single cell RNA-seq, Smart-seq 2

value: BALB/cJ

tag: age

value: 8 weeks

tag: Sex

value: female

tag: sample type

value: wild type


title: IL2_IL7_CGRP0.4ug_rep4

description:
bulk RNA-Seq: A16
full-length
rsem.genes.counts.matrix


title: X19407_H1

description:
FPKM_C1_table.txt
Sample_19407_H1


title: IL2_IL7_CGRP0.4ug_rep1

description:
bulk RNA-Seq: A13
full-length
rsem.genes.counts.matrix


title: X19406_G8

description:
FPKM_C1_table.txt
Sample_19406_G8


title: X19406_G7

description:
FPKM_C1_table.txt
Sample_19406_G7


title: X19406_G6

description:
FPKM_C1_table.txt
Sample_19406_G6


title: IL2_IL7_IL25_CGRP0.4ug_rep2

description:
bulk RNA-Seq: A22
full-length
rsem.genes.counts.matrix


title: X19406_G5

description:
FPKM_C1_table.txt
Sample_19406_G5


title: IL2_IL7_IL25_CGRP0.4ug_rep1

description:
bulk RNA-Seq: A21
full-length
rsem.genes.counts.matrix


title: X19406_G4

description:
FPKM_C1_table.txt
Sample_19406_G4


title: IL2_IL7_IL25_rep3

description:
bulk RNA-Seq: A8
full-length
rsem.genes.counts.matrix


title: X19406_G3

description:
FPKM_C1_table.txt
Sample_19406_G3


title: IL2_IL7_CGRP0.4ug_rep3

description:
bulk RNA-Seq: A15
full-length
rsem.genes.counts.matrix


title: IL2_IL7_IL25_rep1

description:
bulk RNA-Seq: A6
full-length
rsem.genes.counts.matrix


title: X19406_G12

description:
FPKM_C1_table.txt
Sample_19406_G12


title: X19406_G11

description:
FPKM_C1_table.txt
Sample_19406_G11


title: IL2_IL7_rep2

description:
bulk RNA-Seq: A3
full-length
rsem.genes.counts.matrix


title: IL2_IL7_rep1

description:
bulk RNA-Seq: A2
full-length
rsem.genes.counts.matrix


title: KO3

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Replicate 3 of Keratinocytes in InvEE DKer HMGB1 mice

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

source_name: Keratinocytes in InvEE Dker HMGB1 mice

extract_protocol: All Methods listed in Hoste et al.  Epithelial HMGB1 delays skin wound healing and drives tumor initiation by priming neutrophils for NET formation. Cell Reports. 2019.

value: CBA x C57Bl/6J

value: InvEE K5 Cre+ HMGB1 fl/fl

value: skin

value: keratinocytes


title: KO4

description: Replicate 4 of Keratinocytes in InvEE DKer HMGB1 mice


title: IL2_IL7_IL25_CGRP0.4ug_rep3

description:
bulk RNA-Seq: A23
full-length
rsem.genes.counts.matrix


title: KO1

description: Replicate 1 of Keratinocytes in InvEE DKer HMGB1 mice


title: X19405_F8

description:
FPKM_C1_table.txt
Sample_19405_F8

value: WT


title: X19405_F7

description:
FPKM_C1_table.txt
Sample_19405_F7

value: Thymus


title: X19405_F9

description:
FPKM_C1_table.txt
Sample_19405_F9

value: Lin- 7AAD- CD44+ Kit+


title: X19405_F6

description:
FPKM_C1_table.txt
Sample_19405_F6


title: X19406_G1

description:
FPKM_C1_table.txt
Sample_19406_G1


title: WT4

description: Replicate 4 of Keratinocytes in InvEE HMGB1 fl/fl mice

source_name: Keratinocytes isolated from InvEE HMGB1 fl/fl mice

value: InvEE K5 Cre- HMGB1 fl/fl


title: X19405_F5

description:
FPKM_C1_table.txt
Sample_19405_F5


title: KO2

description: Replicate 2 of Keratinocytes in InvEE DKer HMGB1 mice


title: WT2

description: Replicate 2 of Keratinocytes in InvEE HMGB1 fl/fl mice


title: X19405_F3

description:
FPKM_C1_table.txt
Sample_19405_F3


title: IL2_IL7_IL25_rep2

description:
bulk RNA-Seq: A7
full-length
rsem.genes.counts.matrix


title: X19406_G2

description:
FPKM_C1_table.txt
Sample_19406_G2


title: WT3

description: Replicate 3 of Keratinocytes in InvEE HMGB1 fl/fl mice


title: X19405_F4

description:
FPKM_C1_table.txt
Sample_19405_F4


title: X19406_G10

description:
FPKM_C1_table.txt
Sample_19406_G10


title: X19405_F12

description:
FPKM_C1_table.txt
Sample_19405_F12


title: WT1

description: Replicate 1 of Keratinocytes in InvEE HMGB1 fl/fl mice


title: X19405_F2

description:
FPKM_C1_table.txt
Sample_19405_F2


title: P1393H

city: San Francisco

first: Karim

last: Mahiddine

state: CA

address: 513 Parnassus avenue

department: Laboratory medicine

institute: University of Califiornia San Francisco

data_processing:
Reads were aligned  to the mouse genome using the Splice-aware STAR aligner STAR_2.4.2a
Raw counts were determined using STAR_2.4.2a
Reads uniquely mapped to known mRNAs were used to identify genes with differential expression (FDR<0.05) using DESeq2 R v1.16.1 software
Genome_build: Ensembl Mouse GRCm38.78
Supplementary_files_format_and_content: tab-delimited text file of raw counts

source_name: Polymorphonuclear neutrophils sorted from total uterus

extract_protocol:
PMNs (CD45+ Ly6Ghi CD11b+ cells) from enzymatically disaggregated uteri were sorted on a 18-color 4-laser BD ARIA2. RNA was then isolated using an RNeasy Micro Kit.
RNA libraries were prepared according to Illumina's instructions, using an Ovation/NexteraXT kit

treatment_protocol: PRPL (Pgrcre/+ Ptenlox/lox) mice were maintained at ambient O2 ("normoxia" conditions), or housed in an environmental chamber set at 60% oxygen ("hyperoxia" conditions), from P18 to P28, at which point the mice were sacrificed.

value: Pgrcre/+ Ptenlox/lox ("PRPL")

value: Polymorphonuclear neutrophils

value: Total uterus

tag: tumor stage

value: 4 week-old mice (i.e. postnatal day [P] 28)

tag: condition

value: Hyperoxia housing P18-P28


title: P1491H


title: X19405_F11

description:
FPKM_C1_table.txt
Sample_19405_F11


title: IL2_IL7_rep3

description:
bulk RNA-Seq: A4
full-length
rsem.genes.counts.matrix

value: BALB/cJ


title: P1373

value: Normoxia housing


title: P1374


title: X19405_F1

description:
FPKM_C1_table.txt
Sample_19405_F1


title: P1371


title: X19405_F10

description:
FPKM_C1_table.txt
Sample_19405_F10


title: X19404_E7

description:
FPKM_C1_table.txt
Sample_19404_E7


title: X19404_E9

description:
FPKM_C1_table.txt
Sample_19404_E9


title: X19404_E8

description:
FPKM_C1_table.txt
Sample_19404_E8


title: X19404_E6

description:
FPKM_C1_table.txt
Sample_19404_E6


title: single cell 10x rep1

data_processing:
Cellranger 2.0 is run on the FASTQ files to generate matrix, genome build: mm10
Genome_build: mm10
Supplementary_files_format_and_content: bulk_RNAseq_processed.txt; matrix.mtx with accompanying genes.tsv and barcodes.tsv; FPKM_C1_table.txt

extract_protocol: 10x Chromium v2


title: 11292017_IgDnegSI_nonTBSI_v2_Ctrl_nonTB

description:
scRNA-seq
3'-end
PP_LP_mm10_count_matrix.mtx, PP_LP_mm10_count_gene.tsv, PP_LP_mm10_count_barcode.tsv

source_name: Lamina propria

value: 10 weeks

value: female


title: X19404_E4

description:
FPKM_C1_table.txt
Sample_19404_E4


title: X19404_E3

description:
FPKM_C1_table.txt
Sample_19404_E3


title: Antibody sample tag library for ETP subpop

data_processing:
Read 1 includes cell barcode, UMI; read 2 includes cDNA/HTO read. Valid cell barcodes identified in Cellranger pipeline from cDNA library data were used as cell IDs, and the HTO sequences were mapped to a 15 bases reference HTO list, count was quantified by UMI.
Genome_build: mm10
Supplementary_files_format_and_content: matrix file output from 10X single cell RNAseq CellRanger pipeline; HTO count table of individual cell barcode

source_name: ETP subpop tag

extract_protocol: single cell droplet performed with 10x Chromium v3

tag: facs purification gates

value: Subpop1-Hashtag1:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3+ Ly6d- HSA-; Subpop2-Hashtag2:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3+ HSA+; Subpop3-Hashtag3:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3- Ly6d- HSA-; Subpop4-Hashtag4:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3- Ly6d+; Subpop_CTRL-Hashtag5:Lin- 7AAD- Kit+

tag: molecule subtype

value: polyA HTO


title: X19404_E5

description:
FPKM_C1_table.txt
Sample_19404_E5


title: 11292017_IgDnegSI_nonTBSI_v2_Allergy_nonTB

value: Food Allergy


title: X19404_E12

description:
FPKM_C1_table.txt
Sample_19404_E12


title: 10172017_ctrl_allergy_nonPP_nonTB_v2_Ctrl_2

value: wild type


title: X19404_E11

description:
FPKM_C1_table.txt
Sample_19404_E11

value: WT


title: 10172017_ctrl_allergy_nonPP_nonTB_v2_Ctrl_1


title: 11292017_IgDnegSI_nonTBSI_v2_Allergy_IgDLow


title: X19404_E1

description:
FPKM_C1_table.txt
Sample_19404_E1

value: Thymus


title: 10172017_ctrl_allergy_nonPP_nonTB_v2_Allergy_2


title: X19403_D9

description:
FPKM_C1_table.txt
Sample_19403_D9

value: Lin- 7AAD- CD44+ Kit+


title: X19403_D8

description:
FPKM_C1_table.txt
Sample_19403_D8


title: single cell 10x rep2


title: 09012017_PP_WT_Allergy_v2_Control_2

source_name: Peyer's patch


title: 10172017_ctrl_allergy_nonPP_nonTB_v2_Allergy_1


title: 09012017_PP_WT_Allergy_v2_Allergy_2


title: X19403_D7

description:
FPKM_C1_table.txt
Sample_19403_D7


title: X19403_D6

description:
FPKM_C1_table.txt
Sample_19403_D6


title: 11292017_IgDnegSI_nonTBSI_v2_Ctrl_IgDLow


title: X19404_E2

description:
FPKM_C1_table.txt
Sample_19404_E2


title: 07142017_PP_WT_Allergy_v2_Control


title: 09012017_PP_WT_Allergy_v2_Allergy_1


title: X19403_D3

description:
FPKM_C1_table.txt
Sample_19403_D3


title: X19403_D2

description:
FPKM_C1_table.txt
Sample_19403_D2


title: 07142017_PP_WT_Allergy_v2_Allergy


title: 06132017_PP_WT_Allergy_v2_ctrl


title: 06132017_PP_WT_Allergy_v2_allergy


title: X19404_E10

description:
FPKM_C1_table.txt
Sample_19404_E10


title: X19403_D12

description:
FPKM_C1_table.txt
Sample_19403_D12


title: 05152017_PP_location_WTAllergy_v2_CJ


title: 05152017_PP_location_WTAllergy_v2_CI


title: X19403_D10

description:
FPKM_C1_table.txt
Sample_19403_D10


title: 05152017_PP_location_WTAllergy_v2_CD


title: P1353H


title: X19403_D1

description:
FPKM_C1_table.txt
Sample_19403_D1


title: 09012017_PP_WT_Allergy_v2_Control_1


title: 05152017_PP_location_WTAllergy_v2_AJ


title: 05152017_PP_location_WTAllergy_v2_AI


title: X19403_D5

description:
FPKM_C1_table.txt
Sample_19403_D5


title: X19403_C12

description:
FPKM_C1_table.txt
Sample_19403_C12


title: X19402_C9

description:
FPKM_C1_table.txt
Sample_19402_C9


title: 05152017_PP_location_WTAllergy_v2_AD


title: 04242017_PP_location_WT_Allergy_v2_CI


title: X19402_C6

description:
FPKM_C1_table.txt
Sample_19402_C6


title: 04242017_PP_location_WT_Allergy_v2_CJ


title: 04242017_PP_location_WT_Allergy_v2_CD


title: X19402_C7

description:
FPKM_C1_table.txt
Sample_19402_C7


title: X19402_C3

description:
FPKM_C1_table.txt
Sample_19402_C3


title: X19402_C4

description:
FPKM_C1_table.txt
Sample_19402_C4


title: X19403_D11

description:
FPKM_C1_table.txt
Sample_19403_D11


title: 04242017_PP_location_WT_Allergy_v2_AJ


title: 04242017_PP_location_WT_Allergy_v2_AI


title: X19402_C10

description:
FPKM_C1_table.txt
Sample_19402_C10


title: X19403_D4

description:
FPKM_C1_table.txt
Sample_19403_D4


title: X19402_C1

description:
FPKM_C1_table.txt
Sample_19402_C1


title: X19402_C11

description:
FPKM_C1_table.txt
Sample_19402_C11


title: X19401_B8

description:
FPKM_C1_table.txt
Sample_19401_B8


title: X19401_B7

description:
FPKM_C1_table.txt
Sample_19401_B7


title: X19401_B6

description:
FPKM_C1_table.txt
Sample_19401_B6


title: X19401_B4

description:
FPKM_C1_table.txt
Sample_19401_B4


title: X19402_C8

description:
FPKM_C1_table.txt
Sample_19402_C8


title: X19401_B2

description:
FPKM_C1_table.txt
Sample_19401_B2


title: X19401_B12

description:
FPKM_C1_table.txt
Sample_19401_B12


title: X19401_B3

description:
FPKM_C1_table.txt
Sample_19401_B3


title: X19401_B11

description:
FPKM_C1_table.txt
Sample_19401_B11


title: X19401_B10

description:
FPKM_C1_table.txt
Sample_19401_B10


title: X19401_B1

description:
FPKM_C1_table.txt
Sample_19401_B1


title: X19400_A9

description:
FPKM_C1_table.txt
Sample_19400_A9


title: X19400_A8

description:
FPKM_C1_table.txt
Sample_19400_A8


title: S4 HSBS

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
ChIP-seq data were aligned to hg38 using BWA aln 0.7.4, requiring minimal mapping quality of 10. HSBS data were aligned to hg38 by methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014), utilizing BWA mem 0.7.12, removing reads of mapping qualty 0. HiC and HiChIP were aligned to hg38 using HiC-Pro. RNA-seq reads were aligned using STAR 2.5.3 to the hg19 human reference.
PCR duplicates were removed with picard tools 2.9.2 for all data except CTCF ChIP-seq and RNA-seq
ChIP-Seq density tracks were generated by ‘igvtools count --includeDuplicates --minMapQuality 10' and than converted to BigWig format by igvtools tdftobedgraph and bedGraphToBigWig.
HSBS methylation data were called with methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014)
Gene expression was estimated by featureCounts 1.6.2. TPM values were calculated as described in (Wagner GP, Kin K, Lynch VJ, Theory Biosci. 2012)
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq: bigwigs
Supplementary_files_format_and_content: Methylation at CpGs was called by methylCtools 0.9.4. Column 5 represent counts supporting methylated (i.e. not converted) DNA, column 6 represent unmethylated (i.e. converted) DNA at any given loci
Supplementary_files_format_and_content: RNA-seq: TPM values are in a file on the series record, sdhd_tumors_tpm.csv
Supplementary_files_format_and_content: HiC: .hic files and text file with all valid pairs.

organism: Homo sapiens

source_name: GIST S4

growth_protocol: GIST-T1 cell line was obtained from Cosmo Biosciences.  Cells were passaged in DMEM with 10% serum, 1X antibiotics and 1X Glutamax (Life Technologies).

extract_protocol: For hybrid-selection bisulfite-sequencing, total genomic DNA was isolated using the DNAeasy Blood & Tissue Kit (Qiagen) and sheared using the Covaris LE220. Ampure XP beads (Agencourt) were then used to size select gDNA fragments within 150-320bp and sheared distribution was verified via BioAnalyzer (Agilient) prior to continuation. 1 microgram of gDNA was then generated into a sequencing library via end repair, 3’ A base tailing (KAPA Hyper Prep Kit #KK8502) and sequencing adapter ligation (Roche SeqCap Epi Enrichment System). Post-ligation clean-up was performed using Ampure XP beads. Following bead clean-up, DNA library was then bisulfite converted using the EZ DNA Methylation-Lightning Kit (Zymo Research) and amplified via PCR using KAPA HiFi U+ HotStart ReadyMix (KAPA #KK2800). Equal concentration of each bisulfite-converted library was then combined in sets of either three or four libraries/per pool along with SeqCap Epi universal & indexing oligos and bisulfite capture enhancer (SeqCap Epi Accessory Kit). Each pool was subsequently lyophilized using TOMY Micro-Vac (MV100) and resuspended in hybridization buffer (SeqCap Epi Hybridization and Wash Kit) prior to being hybridized to SeqCap Epi Probe Pool (Roche) for 72 hours at 47C in a thermocycler with a heated lid at 57C. Following the 72-hour incubation, captured bisulfite-converted libraries were recovered (SeqCap Pure Capture Bead Kit) at 47C in a thermocycler for 45 minutes, with intermediate vortexing every 15 minutes.  Capture beads were then washed (SeqCap Hybridization and Wash Kit) in a 47C water bath and room temperature, respectively.

value: Localized GIST

tag: chip antibody

tag: sdh status

value: Deficient


title: X19400_A7

description:
FPKM_C1_table.txt
Sample_19400_A7


title: X19402_C5

description:
FPKM_C1_table.txt
Sample_19402_C5


title: S2 HSBS

source_name: GIST S2

value: Metastatic GIST


title: X19400_A5

description:
FPKM_C1_table.txt
Sample_19400_A5


title: S3 HSBS

source_name: GIST S3


title: X19400_A6

description:
FPKM_C1_table.txt
Sample_19400_A6


title: X19401_B9

description:
FPKM_C1_table.txt
Sample_19401_B9


title: S1 HSBS

source_name: GIST S1


title: X19400_A3

description:
FPKM_C1_table.txt
Sample_19400_A3


title: 04242017_PP_location_WT_Allergy_v2_AD


title: S6 HSBS

source_name: GIST S6


title: X19402_C2

description:
FPKM_C1_table.txt
Sample_19402_C2


title: X19401_B5

description:
FPKM_C1_table.txt
Sample_19401_B5


title: X19400_A2

description:
FPKM_C1_table.txt
Sample_19400_A2


title: X19400_A4

description:
FPKM_C1_table.txt
Sample_19400_A4


title: X19400_A12

description:
FPKM_C1_table.txt
Sample_19400_A12


title: PDGFRA2 HSBS

source_name: GIST PDGFRA2

value: Intact


title: X19400_A11

description:
FPKM_C1_table.txt
Sample_19400_A11


title: X19400_A10

description:
FPKM_C1_table.txt
Sample_19400_A10


title: X19400_A1

description:
FPKM_C1_table.txt
Sample_19400_A1


title: PDGFRA1 HSBS

source_name: GIST PDGFRA1


title: NSM1 HSBS

value: Normal stomach muscle


title: NSM2 HSBS


title: X19293_H4

description:
FPKM_C1_table.txt
Sample_19293_H4


title: X19293_G6

description:
FPKM_C1_table.txt
Sample_19293_G6


title: KIT9 HSBS

source_name: GIST KIT9


title: X19293_G12

description:
FPKM_C1_table.txt
Sample_19293_G12

source_name: Thymus


title: KIT7 HSBS

source_name: GIST KIT7


title: X19407_H10

description:
FPKM_C1_table.txt
Sample_19407_H10


title: KIT6 HSBS

source_name: GIST KIT6


title: X19293_F2

description:
FPKM_C1_table.txt
Sample_19293_F2


title: X19293_F10

description:
FPKM_C1_table.txt
Sample_19293_F10


title: X19293_E9

description:
FPKM_C1_table.txt
Sample_19293_E9


title: KIT3 HSBS

source_name: GIST KIT3


title: S5 HSBS

source_name: GIST S5


title: X19293_D2

description:
FPKM_C1_table.txt
Sample_19293_D2


title: KIT5 HSBS

source_name: GIST KIT5


title: KIT1 HSBS

source_name: GIST KIT1


title: KIT2 HSBS

source_name: GIST KIT2


title: KIT4 HSBS

source_name: GIST KIT4


title: X19293_C7

description:
FPKM_C1_table.txt
Sample_19293_C7


title: X19293_B3

description:
FPKM_C1_table.txt
Sample_19293_B3


title: RNA-seq_Act.5 h + A-FOS _rep1

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

description: BioWardrobe ID: 5356

data_processing:
Basecalls performed following illumina pipeline.
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
RNA-Seq data: Fastq files from Illumina pipeline were aligned by STAR (version STAR_2.4.0c PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 --outFilterMismatchNmax 2”. RefSeq annotation from UCSC genome browser (11/2012 PMID: 23155063) for hg19 genome was used. The --outFilterMultimapNmax parameter is used to allow uniq alignment only and --outFilterMismatchNmax parameter is used to allow at max 2 errors.
RPKM values were calculated by BioWardrobe
For ChIP-Seqand ATAC-Seq, fastq files produced by Illumina pipeline were aligned by Bowtie (version 1.0.0 PMID: 19261174) with maximum one allowed error in a sequence and no more than one  of hit was allowed. MACS2 (version 2.1.0.20140616 PMID: 18798982) was used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less than 0.2. To visualize the data it were uploaded to UCSC genome browser and fragment coverage were used with estimated fragment size from MACS2 output.
Genome_build: hg19
Supplementary_files_format_and_content: Table contains RPKM values produced by BioWardrobe

source_name: RNA-seq_Act.5 h + A-FOS

growth_protocol: Human naive CD4 T cells were purified from PBMC by Stem cell kit and cultured in RPMI media supplemented with 10%FBS and 2-ME.

extract_protocol:
Total RNA was isolated with the Aurum™ Total RNA Mini Kit (BIO-RAD, cat#7326820) including on-column DNaseI digest.
PolyA selection and fragmentation of RNA were performed according to the TruSeqTM Stranded polyA RNA Sample Preparation Guide from Illumina. The fragmented RNA was subjected to first-strand cDNA synthesis. For second-strand cDNA synthesis and adapter ligation, the IP-Star® Compact automation system was used. After that, library construction was performed according to the Illumina protocol.

treatment_protocol:
Naïve T cells are pulsed wit A-FOS protein by Neon electroporator and activated
Activation was performed with Anti-CD3 and -CD28 beads for  5, 24, and 60h

tag: subject status

value: healthy donor

value: peripheral blood

value: primary naive CD4 T cells

tag: activation

value: Act. 5 h with anti-CD3 and -CD28 antibodies

tag: rna stranded

value: RNA-Seq Illumina platform dUTP


title: X19293_B2

description:
FPKM_C1_table.txt
Sample_19293_B2

tag: tissue

tag: facs purification gate


title: X19293_C1

description:
FPKM_C1_table.txt
Sample_19293_C1

tag: genotype


title: RNA-seq_Act.5 h + GFP_rep2

description: BioWardrobe ID: 5358

source_name: RNA-seq_Act.5 h + GFP

treatment_protocol:
Naïve T cells are pulsed wit GFP protein by Neon electroporator and activated
Activation was performed with Anti-CD3 and -CD28 beads for  5, 24, and 60h

tag: cell type


title: X18909_G3_mm10

description:
FPKM_C1_table.txt
Sample_18909_G3

tag: strain


title: RNA-seq_Naïve + No protein_rep2

description: BioWardrobe ID: 5420

source_name: RNA-seq_Naïve + No protein

treatment_protocol:
Naïve T cells are pulsed without protein by Neon electroporator
Activation was performed with Anti-CD3 and -CD28 beads for  5, 24, and 60h

value: No activation


title: RNA-seq_Act.5 h + A-FOS _rep2

description: BioWardrobe ID: 5416


title: RNA-seq_Naïve + No protein_rep1

description: BioWardrobe ID: 5354


title: KIT8 HSBS

source_name: GIST KIT8


title: X18909_G10_mm10

description:
FPKM_C1_table.txt
Sample_18909_G10


title: X18909_E7_mm10

description:
FPKM_C1_table.txt
Sample_18909_E7


title: RNA-seq_Act.5 h + GFP_rep1

description: BioWardrobe ID: 5355


title: X18909_F3_mm10

description:
FPKM_C1_table.txt
Sample_18909_F3


title: X18909_F6_mm10

description:
FPKM_C1_table.txt
Sample_18909_F6


title: X18909_E11_mm10

description:
FPKM_C1_table.txt
Sample_18909_E11


title: RNA-seq_Act.60 h_without_CD28_rep1

description: BioWardrobe ID: 2025

source_name: RNA-seq_Act.60 h_without_CD28

treatment_protocol: Activation was performed with Anti-CD3 and -CD28 beads for  5, 24, and 60h

value: Act. 60 h with anti-CD3 antibody


title: RNA-seq_Act.24 h_without_CD28_rep1

description: BioWardrobe ID: 2028

source_name: RNA-seq_Act.24 h_without_CD28

value: Act. 24 h with anti-CD3 antibody


title: X18909_B8_mm10

description:
FPKM_C1_table.txt
Sample_18909_B8


title: RNA-seq_Act.60 h_without_CD28_rep2

description: BioWardrobe ID: 4378


title: RNA-seq_Act.24 h_without_CD28_rep2

description: BioWardrobe ID: 4338


title: X18909_B6_mm10

description:
FPKM_C1_table.txt
Sample_18909_B6


title: RNA-seq_Act.5 h_without_CD28_rep2

description: BioWardrobe ID: 4336

source_name: RNA-seq_Act.5 h_without_CD28

value: Act. 5 h with anti-CD3 antibody


title: X18909_D12_mm10

description:
FPKM_C1_table.txt
Sample_18909_D12

value: WT


title: RNA-seq_Act.5 h_without_CD28_rep1

description: BioWardrobe ID: 2026


title: X18909_D4_mm10

description:
FPKM_C1_table.txt
Sample_18909_D4

value: Thymus


title: X18909_A8_mm10

description:
FPKM_C1_table.txt
Sample_18909_A8

value: Lin- 7AAD- CD44+ Kit+


title: RNA-seq_Act.60 h_rep2

description: BioWardrobe ID: 4379

source_name: RNA-seq_Act.60 h

value: Act. 60 h with anti-CD3 and -CD28 antibodies


title: RNA-seq_Act.60 h_rep1

description: BioWardrobe ID: 2032


title: X18908_H7_mm10

description:
FPKM_C1_table.txt
Sample_18908_H7

source_name: Thymus


title: RNA-seq_Act.24 h_rep2

description: BioWardrobe ID: 4339

source_name: RNA-seq_Act.24 h

value: Act. 24 h with anti-CD3 and -CD28 antibodies


title: X18908_H10_mm10

description:
FPKM_C1_table.txt
Sample_18908_H10


title: X19293_A6

description:
FPKM_C1_table.txt
Sample_19293_A6


title: RNA-seq_Act.5 h_rep2

description: BioWardrobe ID: 4337

source_name: RNA-seq_Act.5 h


title: X18908_H9_mm10

description:
FPKM_C1_table.txt
Sample_18908_H9


title: RNA-seq_Act.24 h_rep1

description: BioWardrobe ID: 2035


title: X18908_G12_mm10

description:
FPKM_C1_table.txt
Sample_18908_G12


title: RNA-seq_Act.5 h_rep1

description: BioWardrobe ID: 2200


title: X18908_G10_mm10

description:
FPKM_C1_table.txt
Sample_18908_G10


title: RNA-seq_Naïve_rep2

description: BioWardrobe ID: 4335


title: X18908_F1_mm10

description:
FPKM_C1_table.txt
Sample_18908_F1


title: X18908_D8_mm10

description:
FPKM_C1_table.txt
Sample_18908_D8


title: ATAC-seq_Act.5 h + A-FOS _rep2

description: Naïve T cells are pulsed wit A-FOS protein by Neon electroporator and activated

data_processing:
Basecalls performed following illumina pipeline.
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
RNA-Seq data: Fastq files from Illumina pipeline were aligned by STAR (version STAR_2.4.0c PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 --outFilterMismatchNmax 2”. RefSeq annotation from UCSC genome browser (11/2012 PMID: 23155063) for hg19 genome was used. The --outFilterMultimapNmax parameter is used to allow uniq alignment only and --outFilterMismatchNmax parameter is used to allow at max 2 errors.
RPKM values were calculated by BioWardrobe
For ChIP-Seqand ATAC-Seq, fastq files produced by Illumina pipeline were aligned by Bowtie (version 1.0.0 PMID: 19261174) with maximum one allowed error in a sequence and no more than one  of hit was allowed. MACS2 (version 2.1.0.20140616 PMID: 18798982) was used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less than 0.2. To visualize the data it were uploaded to UCSC genome browser and fragment coverage were used with estimated fragment size from MACS2 output.
Genome_build: hg19
Supplementary_files_format_and_content: List of islands called by MACS2

source_name: ATAC-seq_Act.5 h + A-FOS

extract_protocol:
Nucleic DNA was processed with nextera transposome (illumina), and purified according to the protocol in Buenrostro et al (PMID: 24097267).
Libraries were prepared according to  the protocol in Buenrostro et al. Briefly, purified DNA was amplified with P5 and P7 primers in PCR, and 200-400 bp DNA was isolated by Ampure DNA purification beads.


title: X18908_B6_mm10

description:
FPKM_C1_table.txt
Sample_18908_B6


title: X18908_A8_mm10

description:
FPKM_C1_table.txt
Sample_18908_A8


title: X18908_A7_mm10

description:
FPKM_C1_table.txt
Sample_18908_A7


title: ATAC-seq_Act.5 h + GFP _rep2

description: Naïve T cells are pulsed wit GFP protein by Neon electroporator and activated

source_name: ATAC-seq_Act.5 h + GFP


title: ATAC-seq_Act.5 h + A-FOS _rep1


title: X18908_B4_mm10

description:
FPKM_C1_table.txt
Sample_18908_B4


title: X18908_G9_mm10

description:
FPKM_C1_table.txt
Sample_18908_G9


title: X18310_H8_mm10

description:
FPKM_C1_table.txt
Sample_18310_H8


title: ATAC-seq_Act.5 h + GFP _rep1


title: ATAC-seq_Act.24 h_without_CD28_rep2

description: BioWardrobe ID: 4438

source_name: ATAC-seq_Act.24 h_without_CD28


title: ATAC-seq_Act.60 h_without_CD28_rep2

description: BioWardrobe ID: 4440

source_name: ATAC-seq_Act.60 h_without_CD28


title: ATAC-seq_Naïve + No protein

description: Naïve T cells are pulsed without protein by Neon electroporator

source_name: ATAC-seq_Naïve + No protein


title: ATAC-seq_Act.60 h_without_CD28_rep1

description: BioWardrobe ID: 4255


title: X18310_H6_mm10

description:
FPKM_C1_table.txt
Sample_18310_H6


title: X18310_H5_mm10

description:
FPKM_C1_table.txt
Sample_18310_H5


title: X18310_H7_mm10

description:
FPKM_C1_table.txt
Sample_18310_H7


title: RNA-seq_Naïve_rep1

description: BioWardrobe ID: 2037


title: X18310_H4_mm10

description:
FPKM_C1_table.txt
Sample_18310_H4


title: X18310_H3_mm10

description:
FPKM_C1_table.txt
Sample_18310_H3


title: ATAC-seq_Act.5 h_without_CD28_rep2

description: BioWardrobe ID: 4435

source_name: ATAC-seq_Act.5 h_without_CD28


title: X18310_H12_mm10

description:
FPKM_C1_table.txt
Sample_18310_H12


title: ATAC-seq_Act.5 h_without_CD28_rep1

description: BioWardrobe ID: 4196


title: ATAC-seq_Act.60 h_rep1

description: BioWardrobe ID: 4199

source_name: ATAC-seq_Act.60 h


title: X18310_H2_mm10

description:
FPKM_C1_table.txt
Sample_18310_H2


title: ATAC-seq_Act.60 h_rep2

description: BioWardrobe ID: 4439


title: X18310_H9_mm10

description:
FPKM_C1_table.txt
Sample_18310_H9


title: ATAC-seq_Act.24 h_rep3

description: BioWardrobe ID: 5274

source_name: ATAC-seq_Act.24 h


title: ATAC-seq_Act.24 h_rep2

description: BioWardrobe ID: 4437


title: X18310_H11_mm10

description:
FPKM_C1_table.txt
Sample_18310_H11


title: X18310_H10_mm10

description:
FPKM_C1_table.txt
Sample_18310_H10


title: ATAC-seq_Act.5 h_rep2

description: BioWardrobe ID: 4436

source_name: ATAC-seq_Act.5 h


title: ATAC-seq_Act.24 h_without_CD28_rep1

description: BioWardrobe ID: 4198


title: ATAC-seq_Act.24 h_rep1

description: BioWardrobe ID: 4197


title: X18309_G9_mm10

description:
FPKM_C1_table.txt
Sample_18309_G9


title: ATAC-seq_Act.5 h_rep3

description: BioWardrobe ID: 5273


title: ATAC-seq_Act.5 h_rep1

description: BioWardrobe ID: 4195


title: X18309_G8_mm10

description:
FPKM_C1_table.txt
Sample_18309_G8


title: X18309_G7_mm10

description:
FPKM_C1_table.txt
Sample_18309_G7


title: ATAC-seq_Naïve_rep2

description: BioWardrobe ID: 4434


title: X18309_G6_mm10

description:
FPKM_C1_table.txt
Sample_18309_G6


title: ATAC-seq_Naïve_rep3

description: BioWardrobe ID: 5272


title: ChIP-seq_NFƘB_Act.5 h_rep2

description: BioWardrobe ID: 2019

source_name: ChIP-seq_NFƘB_Act.5 h

extract_protocol:
Chromatin was immunoprecipitated with antibody and tagmented with nextera transposome (illumina) according to the ChIPmentation protocol in Schmidl et al (PBMD: 26280331).
Libraries were prepared by chipmentation.

value: NFƘB p50 Cell Signaling #12540


title: ATAC-seq_Naïve_rep1

description: BioWardrobe ID: 4370


title: ChIP-seq_NFƘB_Act.5 h_rep1

description: BioWardrobe ID: 4037


title: X18309_G3_mm10

description:
FPKM_C1_table.txt
Sample_18309_G3


title: ChIP-seq_cMYC_Act.5 h

description: BioWardrobe ID: 4103

source_name: ChIP-seq_cMYC_Act.5 h

value: cMYC Cell Signaling #2250


title: X18309_G4_mm10

description:
FPKM_C1_table.txt
Sample_18309_G4


title: X18309_G2_mm10

description:
FPKM_C1_table.txt
Sample_18309_G2


title: ChIP-seq_JUNB_Act.5 h

description: BioWardrobe ID: 4454

source_name: ChIP-seq_JUNB_Act.5 h

value: JUNB Cell Signaling #3753


title: X18309_G12_mm10

description:
FPKM_C1_table.txt
Sample_18309_G12


title: X18309_G10_mm10

description:
FPKM_C1_table.txt
Sample_18309_G10


title: ChIP-seq_NFAT2_Act.5 h_rep2

description: BioWardrobe ID: 2017

source_name: ChIP-seq_NFAT2_Act.5 h

value: healthy donor

value: NFAT2 Cell Signaling #8032


title: X18310_H1_mm10

description:
FPKM_C1_table.txt
Sample_18310_H1


title: ChIP-seq_NFAT2_Act.5 h_rep1

description: BioWardrobe ID: 4031

value: peripheral blood

value: primary naive CD4 T cells


title: X18309_G1_mm10

description:
FPKM_C1_table.txt
Sample_18309_G1


title: X18308_F9_mm10

description:
FPKM_C1_table.txt
Sample_18308_F9


title: ChIP-seq_NFAT1_Act.5 h_without_CD28_rep2

description: BioWardrobe ID: 2016

source_name: ChIP-seq_NFAT1_Act.5 h_without_CD28

value: NFAT1 Cell Signaling #5861


title: ChIP-seq_NFAT1_Act.5 h_without_CD28_rep1

description: BioWardrobe ID: 4034


title: X18308_F7_mm10

description:
FPKM_C1_table.txt
Sample_18308_F7

source_name: Thymus


title: X18308_F8_mm10

description:
FPKM_C1_table.txt
Sample_18308_F8


title: X18309_G5_mm10

description:
FPKM_C1_table.txt
Sample_18309_G5


title: ChIP-seq_NFAT1_Act.5 h_rep1

description: BioWardrobe ID: 4033

source_name: ChIP-seq_NFAT1_Act.5 h

value: Act. 5 h with anti-CD3 and -CD28 antibodies


title: X18308_F6_mm10

description:
FPKM_C1_table.txt
Sample_18308_F6


title: ChIP-seq_H3K4me3_Act.24 h

description: BioWardrobe ID: 2756

source_name: ChIP-seq_H3K4me3_Act.24 h

value: H3K4me3 Millipore #17-614


title: ChIP-seq_H3K4me3_Act.24 h_without_CD28

description: BioWardrobe ID: 2759

source_name: ChIP-seq_H3K4me3_Act.24 h_without_CD28

value: Act. 24 h with anti-CD3 antibody


title: X18308_F4_mm10

description:
FPKM_C1_table.txt
Sample_18308_F4


title: ChIP-seq_H3K4me3_Act.5 h

description: BioWardrobe ID: 2755

source_name: ChIP-seq_H3K4me3_Act.5 h


title: ChIP-seq_H3K4me3_Act.5 h_without_CD28

description: BioWardrobe ID: 2758

source_name: ChIP-seq_H3K4me3_Act.5 h_without_CD28

value: Act. 5 h with anti-CD3 antibody


title: X18308_F3_mm10

description:
FPKM_C1_table.txt
Sample_18308_F3

value: WT


title: ChIP-seq_cFOS_Act.5 h

description: BioWardrobe ID: 4030

source_name: ChIP-seq_cFOS_Act.5 h

value: cFOS Cell Signaling #2250


title: ChIP-seq_H3K4me3_Naïve

description: BioWardrobe ID: 2979

value: No activation


title: X18308_F2_mm10

description:
FPKM_C1_table.txt
Sample_18308_F2

value: Thymus

value: Lin- 7AAD- CD44+ Kit+


title: X18309_G11_mm10

description:
FPKM_C1_table.txt
Sample_18309_G11


title: ChIP-seq_H3K27Ac_Act.24 h_without_CD28

description: BioWardrobe ID: 2765

source_name: ChIP-seq_H3K27Ac_Act.24 h_without_CD28

value: H3K27Ac Diagenode, pAb-196-050


title: ChIP-seq_H3K27Ac_Act.24 h

description: BioWardrobe ID: 2762

source_name: ChIP-seq_H3K27Ac_Act.24 h

value: Act. 24 h with anti-CD3 and -CD28 antibodies


title: X18308_F11_mm10

description:
FPKM_C1_table.txt
Sample_18308_F11


title: X18308_F12_mm10

description:
FPKM_C1_table.txt
Sample_18308_F12


title: ChIP-seq_H3K27Ac_Act.5 h_without_CD28

description: BioWardrobe ID: 2764

source_name: ChIP-seq_H3K27Ac_Act.5 h_without_CD28


title: X18308_F1_mm10

description:
FPKM_C1_table.txt
Sample_18308_F1


title: X18308_F10_mm10

description:
FPKM_C1_table.txt
Sample_18308_F10


title: X18307_E9_mm10

description:
FPKM_C1_table.txt
Sample_18307_E9


title: ChIP-seq_NFAT1_Act.5 h_rep2

description: BioWardrobe ID: 2015


title: X18307_E7_mm10

description:
FPKM_C1_table.txt
Sample_18307_E7


title: X18307_E8_mm10

description:
FPKM_C1_table.txt
Sample_18307_E8


title: ChIP-seq_H3K27Ac_Act.5 h

description: BioWardrobe ID: 2761

source_name: ChIP-seq_H3K27Ac_Act.5 h


title: X18308_F5_mm10

description:
FPKM_C1_table.txt
Sample_18308_F5


title: ChIP-seq_H3K27Ac_Naïve

description: BioWardrobe ID: 2980


title: GEN1C sgDDX6

first: Kendell

last: Clement

address: 7 Divinity Ave.

institute: Harvard University

description: GEN1C sgDDX6

data_processing:
Preprocessing: 10bp were trimmed from the beginning of each read to remove possible adapter contamination
Alignment: Reads were aligned using Bsmap with the following flags: -v 0.05 -s 16 -w 100 -S 1 -p 8 -
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent*1000

source_name: human induced pluripotent stem cells

growth_protocol: Conventional primed iPSCs (GEN1C) were maintained on Matrigel (Corning) coated dishes in mTeSR edium (Stem Cell Technologies) and passaged using gentle cell dissociation reagent (Stem Cell Technologies). For maintenance, cells were passaged every 4-5 days.

extract_protocol:
gDNA was extracted using the Qiagen DNeasy Blood and Tissue kit
Libraries were created using the Nugen Ovation bisulfite kit.

treatment_protocol: Cells were harvested following acutase treatment and processed for total RNA extraction

value: primed hiPSCs


title: X18307_E5_mm10

description:
FPKM_C1_table.txt
Sample_18307_E5


title: RNA-seq_OFF-BC_3

source_name: FACs sorted retinal cells

value: retina

value: bipolar

tag: age (post-natal day)

value: Otx2-GFP+/-; Grm6-YFP+/+

tag: facs

value: Double Sort


title: X18307_E6_mm10

description:
FPKM_C1_table.txt
Sample_18307_E6


title: X18307_E4_mm10

description:
FPKM_C1_table.txt
Sample_18307_E4


title: H9 microglia

city: Leuven

first: Mark

last: Fiers

address: Herestraat 49

department: Center for Brain and Disease

institute: VIB

description:
RM37
H9 microglia naive
processed data file: chimera_human_h9.tsv.gz

data_processing:
Cellranger (version 2.1.1).
Genome_build: Human hg38 (GRCh38), Ensembl version 84; mouse mm10 (GRCm38), Ensembl version 84.
Supplementary_files_format_and_content: *.tsv.gz: Raw gene expression counts per cell in a gzipped tab-separated values file.

source_name: H9 (WiCell Research Institute WA09) Transplanted ESC derived microglia

extract_protocol:
Flow Cytometry or MACS.
10X Genomics V2 chemistry.

value: Microglia

tag: human gender

value: Female


title: In vitro microglia

description:
H9_MG
processed data file: invitro_mh_mc.tsv.gz

source_name: H9 (WiCell Research Institute WA09) ESC derived microglia


title: RNA-seq_OFF-BC_2


title: RNA-seq_OFF-BC_1


title: X18307_E2_mm10

description:
FPKM_C1_table.txt
Sample_18307_E2


title: X18307_E3_mm10

description:
FPKM_C1_table.txt
Sample_18307_E3


title: Human Sample 7

description:
RM102
processed data file: human_patient.tsv.gz

source_name: Temporal cortex

tag: human age

value: 20 years


title: RNA-seq_ON-BC_2

value: Single Sort


title: In vitro monocytes

description:
H9_MNC
processed data file: invitro_mh_mc.tsv.gz

source_name: H9 (WiCell Research Institute WA09) ESC derived monocytes

value: Monocytes


title: Human Sample 6

description:
RM101
processed data file: human_patient.tsv.gz

value: 50 years


title: RNA-seq_ON-BC_3


title: RNA-seq_ON-BC_1


title: Human Sample 5

description:
RM95
processed data file: human_patient.tsv.gz

value: 24 years


title: RNA-seq_Pan-BC_2


title: GEN1C sgCTRL

description: GEN1C sgCTRL


title: X18307_E11_mm10

description:
FPKM_C1_table.txt
Sample_18307_E11

source_name: Thymus

value: WT


title: RNA-seq_Pan-BC_3


title: X18307_E12_mm10

description:
FPKM_C1_table.txt
Sample_18307_E12

value: Thymus


title: Human Sample 4

description:
RM77
processed data file: human_patient.tsv.gz

value: 7 years

value: Male


title: RNA-seq_Pan-BC_1


title: Human Sample 3

description:
RM67
processed data file: human_patient.tsv.gz

value: 48 years


title: X18307_E1_mm10

description:
FPKM_C1_table.txt
Sample_18307_E1

value: Lin- 7AAD- CD44+ Kit+


title: X18306_D9_mm10

description:
FPKM_C1_table.txt
Sample_18306_D9


title: Human Sample 2

description:
RM66
processed data file: human_patient.tsv.gz

value: 38 years


title: Human Sample 1

description:
RM65
processed data file: human_patient.tsv.gz

value: 45 years


title: X18306_D8_mm10

description:
FPKM_C1_table.txt
Sample_18306_D8


title: X18306_D7_mm10

description:
FPKM_C1_table.txt
Sample_18306_D7


title: X18306_D6_mm10

description:
FPKM_C1_table.txt
Sample_18306_D6


title: UnDiff_1

city: Munich

first: Veit

last: Hornung

address: Feodor-Lynen-Straße 25

country: Germany

institute: LMU

data_processing:
Sequenced reads were trimmed for adaptor sequence with trimmomatic and aligned with STAR softare
The TPM (Transcripts Per Million) was quantified with RSEM
Genome_build: Ensembl release 91
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Cell Line

growth_protocol: BLaER1 cells were cultured in RPMI Medium 1640, supplemented with 10% (v/v) FCS, L-glutamine and 100 U/ml Penicillin-Streptomycin.

extract_protocol:
Undifferentiated as well as differentiated BLaER1 cells were lysed in Trizol (2x106/1ml) and total RNA was purified using the Zymo Direct-zol RNA Miniprep.
Total RNA was used to generate stranded RNA sequencing libraries using the Encore Complete RNA-Seq™ library system of NuGEN.

treatment_protocol: BLaER1 cells were trans-differentiated for 5-6 day in medium containing 10 ng/ml hrIL-3, hr-CSF-1 (M-CSF) (both MPI of Biochemistry, Munich) and 100 nM b-Estradiol.

tag: cell line

tag: Stage

value: Un-differentiaed


title: Diff_1

value: Differentiaed


title: X18306_D4_mm10

description:
FPKM_C1_table.txt
Sample_18306_D4


title: X18307_E10_mm10

description:
FPKM_C1_table.txt
Sample_18307_E10


title: Diff_2


title: X18306_D5_mm10

description:
FPKM_C1_table.txt
Sample_18306_D5


title: X18306_D3_mm10

description:
FPKM_C1_table.txt
Sample_18306_D3


title: X18306_D2_mm10

description:
FPKM_C1_table.txt
Sample_18306_D2


title: X18306_D12_mm10

description:
FPKM_C1_table.txt
Sample_18306_D12


title: JUNB_Act.5 h_with_fly_DNA

description: Immunoprecipitated DNA was added with drosophila genomic DNA before library amplification.

value: Primary naive CD4 T cells from peripheral blood

tag: treatment

value: Act. 5 h with anti-CD3 and -CD28 antibodies

tag: passages

value: Primary

tag: donor

value: healthy donor

value: JUNB Cell Signaling #3753

tag: biowardrobe id


title: JUNB_Act.5 h_with_fly_DNA_without_CD28

value: Act. 5 h with anti-CD3 antibody

tag: chip antibody


title: NFAT1_Act.5 h_with_fly_DNA_without_CD28

value: NFAT1 Cell Signaling #5861


title: NFAT1_Naive_with_fly_DNA

value: No activation


title: NFAT1_Act.5 h_with_fly_DNA


title: Retinal tissue, biological rep5

type: RNA

city: Groningen

first: Youhai

last: Li

state: Groningen

address: Hanzeplein 1

department: Dept. Pathology and Medical Biology

country: Netherlands

institute: University Medical Center Groningen (UMCG)

hyb_protocol: Following fragmentation, 5.5 ug of  ss-cDNA were hybridized for 16 hr at  on the Genechip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChips were scanned using the Genechip Scanner 7G (Affymetrix)

data_processing: These raw CEL files were normalized using the Affymetrix® Expression Console Software (version 4.0, Affymetrix) and the adjusted intensity values were transformed to log2 format

label: biotin

organism: Rattus norvegicus

source_name: Whole retinal tissue

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneChip WT Pico protocol from 1 ng total RNA

growth_protocol: The retinae and brain hemisphere from individual rat was cryosectioned. 2-3 cryosections from each organs were collected as whole tissues samples. The left crysections were used for microvessels isolation.

extract_protocol: Total RNA was obtained with RNeasy Plus Micro kit (Qiagen, Germany)

treatment_protocol: Under ico-cold condition, the retinal and brain crysections were homogenated and centrifuged. The microvessels samples were captured by filtering the homogenate with nylon mesh.

value: Wistar

tag: Sex

value: Whole retinal tissue


title: Retinal tissue, biological rep2

value: Male

tag: tissue


title: X18306_D11_mm10

description:
FPKM_C1_table.txt
Sample_18306_D11

value: WT

value: Thymus

tag: facs purification gate


title: cFOS_Act.5 h_with_fly_DNA

value: cFOS Santa Cruz Biotechnology #sc-7202


title: Retinal tissue, biological rep6


title: Retinal tissue, biological rep4


title: Retinal tissue, biological rep3


title: JUNB_Naive_with_fly_DNA


title: cFOS_Act.5 h_with_fly_DNA_without_CD28


title: UnDiff_2


title: Retinal microvessels, biological rep4

source_name: Retinal microvessels

value: Retinal microvessels


title: X18306_D10_mm10

description:
FPKM_C1_table.txt
Sample_18306_D10

tag: genotype

value: Lin- 7AAD- CD44+ Kit+


title: JunB_Act.5 h + A-FOS_with_fly_DNA

description: Naïve T cells are pulsed wit GFP protein by Neon electroporator and activated. Immunoprecipitated DNA was added with drosophila genomic DNA before library amplification.

tag: cell type


title: Retinal tissue, biological rep1

tag: strain


title: X18305_C9_mm10

description:
FPKM_C1_table.txt
Sample_18305_C9


title: JunB_Act.5 h + GFP_with_fly_DNA


title: X18305_C8_mm10

description:
FPKM_C1_table.txt
Sample_18305_C8


title: Retinal microvessels, biological rep3


title: Retinal microvessels, biological rep2


title: Retinal microvessels, biological rep1


title: Brain tissue, biological rep6

source_name: Whole brain tissue

value: Whole brain tissue


title: Retinal microvessels, biological rep5


title: Retinal microvessels, biological rep6


title: Brain tissue, biological rep3


title: Brain tissue, biological rep4


title: WM852_3

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC
Counts per gene from STAR were used as input to generate normalised gene expression matrix using EdgeR {Robinson, 2010 }.
Genome_build: hg38
Supplementary_files_format_and_content: edgeR normalised gene expression as logCPM

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with 100U/ml penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Libraries were prepared using recommended Illumina protocols
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

value: melanoma cell line


title: TS603H2

type: genomic

city: Bethesda

first: Mioara

last: Larion

state: Maryland

address: 37 Convent Drive, Building 37

department: NCI, CCR

institute: National Institutes of Health

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: DNA methylation of cultured cells was performed using Infinium EPIC array. We performed noob  (Normal-exponential convolution using out-of-band probes) background correction (37) and dye bias correction using the minfi package (38). The DNA methylation score for each locus is presented as a beta (  ) value (   = (M/(M+U)) in which M and U indicate the mean methylated and unmethylated signal intensities for each locus, respectively.   -values range from zero to one, with scores of zero indicating no DNA methylation and scores of one indicating complete DNA methylation. A detection p-value also accompanies each data point and compares the signal intensity difference between the analytical probes and a set of negative control probes on the array. Any data point with a corresponding p-value greater than 1x10-16 is deemed not to be statistically significantly different from background and was thus masked as    NA   . The genomic location of the EPIC probes was classified into those within CpG islands (CGI), in CGI shores (4kb regions flanking CGIs), or in open seas (> 4kb to the nearest CGIs) using UCSC genome table browser (hg38) CGI genomic annotation.

label: Cy3, Cy5

source_name: grade III oligodendroglioma

label_protocol: Standard Illumina protocol

growth_protocol: Cells were seeded in DMEM F12 media supplemented with N2, EGF, FGF and Heparin sulphate for 3 days.

extract_protocol: DNA methylation of cultured cells was performed using Infinium EPIC 850 array

treatment_protocol: Cell lines were grown either in normoxia (N) or hypoxia( H) for at least 3 days before collecting.

value: Glioma stem cells

value: IDH1 mutant

tag: stress

value: hypoxia (H)


title: X18306_D1_mm10

description:
FPKM_C1_table.txt
Sample_18306_D1

extract_protocol: C1-Fluidigm 96 and Smartseq2 v4


title: cFOS_Naive_with_fly_DNA

value: Primary naive CD4 T cells from peripheral blood

value: Primary

value: healthy donor


title: Brain microvessels, biological rep6

source_name: Brain microvessels

value: Brain microvessels


title: WM852_2


title: X18305_C5_mm10

description:
FPKM_C1_table.txt
Sample_18305_C5


title: cFOS_Act.5 h + A-FOS_with_fly_DNA

value: Act. 5 h with anti-CD3 and -CD28 antibodies


title: TS603N2

value: normoxia (N)


title: Brain microvessels, biological rep4

value: Wistar

value: Male


title: TS603H3


title: Brain tissue, biological rep2


title: BT142H2

source_name: grade III oligoastrocytoma


title: WM852_1


title: cFOS_Act.5 h + GFP_with_fly_DNA


title: Brain microvessels, biological rep3


title: BT142N1


title: X18305_C7_mm10

description:
FPKM_C1_table.txt
Sample_18305_C7

value: WT

value: Thymus


title: Brain microvessels, biological rep5


title: A375M_3


title: X18305_C3_mm10

description:
FPKM_C1_table.txt
Sample_18305_C3


title: X18305_C6_mm10

description:
FPKM_C1_table.txt
Sample_18305_C6


title: Brain tissue, biological rep5


title: A375M_2


title: hic_minus35.inter_30_10000_blocks

city: Memphis

first: Chunliang

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

data_processing:
Raw sequence data were mapped and processed using Juicer v1.5  with default parameters.
The Hi-C data and MboI cut sites were mapped to hg19. Replicates data were first processed separately.
After confirmation of good reproducibility by HiC-Spector, we merged the replicates and re-processed as combined results.
The data were visualized with the Juicebox. The processed files are TAD called by Arrowhead come with Juicer.
genome build: hg19
processed data files format and content: bed

source_name: blood

growth_protocol: Human B-ALL cells SEM (DSMZ) were grown in RPMI 1640 CONTAINING 10%FETAL BOVINE SERUM (FBS) (Hyclone), 2mM glutamine (Sigma) and 1% penicillin/streptomycin (Invirtogen).  Cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Suspension cells (SEM) cells were collected at 1X107 cells per reaction while adherent cells (IMR90, HCT116 and human iPS) were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction. Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.
Briefly, five million CTCFAID SEM cells (clones 27 and 35) with or without IAA treatment were crosslinked with 1% formaldehyde for 10 min at room temperature, digested with 125 Units of MboI, labeled by biotinylated nucleotides and ligated for proximity ligation. After de-crosslinking, ligated DNA was purified and sheared to 300–500 bps. Ligation junctions were then pulled down with streptavidin beads and prepped as a standard Illumina library. Each library underwent 75-cycle paired-end sequencing on Illumina HiSeq 4000 system. About 100 million reads were obtained for each sample.

treatment_protocol: In situ Hi-C experiments was performed on two CTCF AID homozygous knock-in clones 27 and 35.

value: B-ALL cells SEM (DSMZ)

value: colon

tag: genotype/variation


title: Brain tissue, biological rep1

value: Whole brain tissue


title: TS603H1


title: BT142H1


title: TS603N1


title: hic_minus27.inter_30_10000_blocks


title: A375M_1

value: melanoma cell line


title: BT142N2

value: Glioma stem cells


title: X18305_C12_mm10

description:
FPKM_C1_table.txt
Sample_18305_C12

data_processing:
Prepared using ENCODE long-rna-seq pipeline. Briefly, genomic and transcriptome alignment was performed using STAR(v2.4.0), followed by sort-samtools and index-samtools to sort and index Transcriptome BAM file. Then, generation of bedgraph of reads was performed using bedgraph-star, and RSEM(v1.2.25) was used to generate transcriptome counts and FPKM output. Genome build: mm10
Genome_build: mm10
Supplementary_files_format_and_content: bulk_RNAseq_processed.txt; matrix.mtx with accompanying genes.tsv and barcodes.tsv; FPKM_C1_table.txt

value: Lin- 7AAD- CD44+ Kit+


title: hic_plus35.inter_30_10000_blocks


title: X18305_C4_mm10

description:
FPKM_C1_table.txt
Sample_18305_C4


title: TS603N3

value: IDH1 mutant


title: SkMel30.1_3


title: X18305_C11_mm10

description:
FPKM_C1_table.txt
Sample_18305_C11


title: X18305_C2_mm10

description:
FPKM_C1_table.txt
Sample_18305_C2


title: SkMel30.1_2


title: X18305_C10_mm10

description:
FPKM_C1_table.txt
Sample_18305_C10


title: HBL-100_2


title: Brain microvessels, biological rep2


title: Brain microvessels, biological rep1


title: SkMel30.1_1


title: SP_D-MT_3

city: Seoul

first: Kang-Yell

last: Choi

state: State...

address: 50 Yonsei Ro, Seodemun-Gu Seoul 120-749, Korea

country: South Korea

institute: Yonsei University

description: replicate 3

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)   Array probes transformed by logarithm and normalized by quantile method.

source_name: Spheroid DLD-1 CRC cells harboring homogeneous mutant KRAS 3

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: D-WT or D-MT cells obtained from Dr. B. Vogelstein (Johns Hopkins Oncology Center, Baltimore, MD) were grown in McCoy's 5A (Modified) medium containing 10% heat inactivated fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: D-WT or D-MT cells were grown in adherent condition or spheroid condition for 3 days. Adherent condition: McCoy's 5A (Modified) medium containing 10% heat inactivated fetal bovine serum and 1% penicillin-streptomycin. Cells were plated at a density of 1×106 cells per dish in 100 mm culture dish. Spheroid condition: DMEM/F12 (1:1) medium containing 1×B27 supplement, EGF (100 ng/ml), bFGF (50 ng/ml), heparin (4 μg/ml), and 1% penicillin-streptomycin. Cells were plated at a density of 2×105 cells per dish in 90 mm petri dish.

value: colon cancer

value: homogeneous mutant KRAS


title: X18304_B7_mm10

description:
FPKM_C1_table.txt
Sample_18304_B7


title: SP_D-WT_1

description: replicate 1

source_name: Spheroid DLD-1 CRC cells harboring homogeneous wild-type KRAS 1

value: homogeneous wild-type KRAS


title: hic_plus27.inter_30_10000_blocks


title: X18305_C1_mm10

description:
FPKM_C1_table.txt
Sample_18305_C1


title: SP_D-MT_2

description: replicate 2

source_name: Spheroid DLD-1 CRC cells harboring homogeneous mutant KRAS 2


title: SP_D-WT_3

description: replicate 3

source_name: Spheroid DLD-1 CRC cells harboring homogeneous wild-type KRAS 3


title: SP_D-MT_1

description: replicate 1

source_name: Spheroid DLD-1 CRC cells harboring homogeneous mutant KRAS 1


title: SP_D-WT_2

description: replicate 2

source_name: Spheroid DLD-1 CRC cells harboring homogeneous wild-type KRAS 2


title: HBL-100_3


title: X18304_B8_mm10

description:
FPKM_C1_table.txt
Sample_18304_B8


title: HBL-100_1


title: X18304_B6_mm10

description:
FPKM_C1_table.txt
Sample_18304_B6


title: IGR39_2


title: IGR39_3


title: X18304_B9_mm10

description:
FPKM_C1_table.txt
Sample_18304_B9


title: AD_D-MT_3

description: replicate 3

source_name: Adherent DLD-1 CRC cells harboring homogeneous mutant KRAS 3


title: AD_D-MT_2

description: replicate 2

source_name: Adherent DLD-1 CRC cells harboring homogeneous mutant KRAS 2


title: AD_D-MT_1

description: replicate 1

source_name: Adherent DLD-1 CRC cells harboring homogeneous mutant KRAS 1


title: IGR39_1


title: AD_D-WT_2

description: replicate 2

source_name: Adherent DLD-1 CRC cells harboring homogeneous wild-type KRAS 2


title: AD_D-WT_3

description: replicate 3

source_name: Adherent DLD-1 CRC cells harboring homogeneous wild-type KRAS 3


title: IGR37_3


title: X18304_B5_mm10

description:
FPKM_C1_table.txt
Sample_18304_B5

source_name: Thymus


title: IGR37_1


title: X18304_B12_mm10

description:
FPKM_C1_table.txt
Sample_18304_B12


title: X18304_B4_mm10

description:
FPKM_C1_table.txt
Sample_18304_B4


title: X18304_B3_mm10

description:
FPKM_C1_table.txt
Sample_18304_B3


title: IGR37_2


title: X18304_B11_mm10

description:
FPKM_C1_table.txt
Sample_18304_B11


title: X18304_B2_mm10

description:
FPKM_C1_table.txt
Sample_18304_B2


title: SKNO-1 control 1

city: M

first: L

last: D

state: M

address: District

department: Department of Hematology

institute: Hospital

description: SAMPLE 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: control

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: leukemic cell line

value: wild type; control


title: HBL_2

source_name: HBL

value: HBL


title: X18304_B10_mm10

description:
FPKM_C1_table.txt
Sample_18304_B10


title: HBL_1


title: M800_1112_R_T4

city: Boston

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

data_processing:
RNA-seq data was processed by Bcbio_nextgen pipeline (https://github.com/bcbio/bcbio-nextgen). Briefly, alignment was performed using TopHat2 against mouse genome assembly mm10 with default settings. Bioconductor package ‘Rsubread’ was used to generate gene-level read counts, which were further used for differential expression analysis by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: text file contains gene-level read counts.

source_name: leukemia stem cells

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy plus Mini or Micro kit (Qiagen). Quality of the RNA was checked by an Agilent 2100 Bioanalyzer. Genomic DNA was extracted using QIAamp DNA Mini or Micro kit (Qiagen) according to manufacturer’s instruction.
For RNA sequencing, poly-A selection and cDNA synthesis were performed, followed by library preparation using Illumina TruSeq RNA Sample Prep Kit, sequencing (75-bp paired reads), and sample identification for quality control.

value: leukemia stem cells

tag: leukemic burden

tag: mouse id

tag: color

value: iRFP

tag: time point

tag: infection


title: H29_AN08784_ASD/Autism

city: New York

first: Michael

last: Corley

state: NY

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

hyb_protocol: Illumina Infinium protocol.

scan_protocol: Illumina Infinium protocol. Scanned using Illumina HiScan System.

data_processing: IDAT Data loaded into R using RnBeads 0.99.10 Pipeline, background subtracted using methylumi, and normalized using swan. (http://bioconductor.org/packages/release/bioc/html/RnBeads.html)

label: Cy5 and Cy3

source_name: postmortem brain

label_protocol: Illumina Infinium protocol. Cy5 and Cy3

extract_protocol: Genomic DNA was obtained from fresh frozen brain tissue using the Qiagen Allprep Universal DNA/RNA kit according to manufacturer's instructions for difficult tissues. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

value: postmortem brain

tag: gender

value: male

tag: age

value: 65 years

tag: disease state

value: ASD/Autism

tag: postmortem interval (hours)

tag: brain region

value: subventricular zone of lateral ventricles


title: M800_1113_R_T4


title: SKNO-1 control 2

description: SAMPLE 5

tag: cell line


title: SKNO-1 siEZH1

description: SAMPLE 6

source_name: Ezh1 knock down

value: Ezh1 knock down


title: SKNO-1 siAE

description: SAMPLE 2

source_name: AML1-ETO konck down

value: AML1-ETO konck down


title: M800_1115_R_T4


title: H46_UMB1866_Control

tag: tissue

value: 32 years 319 days

value: Control


title: X18304_B1_mm10

city: Pasadena

first: Wen

last: Zhou

address: 1200 E California Blvd, Mail Code 250-86

institute: California Institute of Technology

description:
FPKM_C1_table.txt
Sample_18304_B1

tag: genotype

value: WT

value: Thymus

tag: facs purification gate

value: Lin- 7AAD- CD44+ Kit+


title: 501mel_3

tag: cell type

value: melanoma cell line


title: M800_1111_R_T4


title: H44_UMB5342_Control

value: 22 years 355 days


title: H23_AN06420_ASD/Autism

value: 39 years


title: X18303_A9_mm10

description:
FPKM_C1_table.txt
Sample_18303_A9

tag: strain


title: 501mel_2


title: M800_1106_R_T3

value: leukemia stem cells


title: X18303_A8_mm10

description:
FPKM_C1_table.txt
Sample_18303_A8


title: AD_D-WT_1

description: replicate 1

source_name: Adherent DLD-1 CRC cells harboring homogeneous wild-type KRAS 1

value: colon cancer

tag: genotype/variation

value: homogeneous wild-type KRAS


title: M800_1103_R_T3

tag: leukemic burden

value: iRFP


title: H41_UMB4999_ASD/Autism

value: postmortem brain

value: male

value: 20 years 274 days


title: 501mel_1


title: H45_UMB5297_ASD/Autism

value: 33 years 83 days

value: ASD/Autism

value: subventricular zone of lateral ventricles


title: M800_1102_R_T3

tag: mouse id


title: H40_UMB1322_Control

value: 16 years 209 days

value: Control


title: X18303_A6_mm10

description:
FPKM_C1_table.txt
Sample_18303_A6

value: WT

value: Thymus


title: IGR37_siSCD_2_t48h_R13

description: processed data file: edgeR_SCD_normalised_count_Log.txt

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC as well as mouse-Mitf
Counts per gene from STAR were used as input for differential gene expression analysis using EdgeR {Robinson, 2010 }.
Reads for each sample set were first filtered for genes whose expression is count-per-million prior to glmQLFTest.
Genome_build: hg38
Supplementary_files_format_and_content: edgeR normalised, differential gene expression using glmQLFTest

growth_protocol: IGR37 and 501mel were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with 100U/ml penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

treatment_protocol:
For siRNA treatment, cells were treated with 20nM of the indicated siRNA for 48h
For  SCD inhibitor treatment, cells were treated with A939372 at 1 uM for 48 h.

value: melanoma cell line

tag: treatment

value: 20nM siSCD#2 48h


title: HBL_3

value: HBL


title: H38_UMB4669_Control

value: 16 years 125 days


title: IGR37_siSCD_2_t48h_R2


title: H42_UMB4786_Control

value: 22 years 189 days


title: M800_1101_R_T3

value: leukemia stem cells

tag: color

tag: time point


title: IGR37_siSCD_2_t48h_R1

description:
siSCD1_DGE.xlsx @IGR37siSCD#2_vs_siCTR-tab
processed data file: edgeR_SCD_normalised_count_Log.txt


title: X18303_A5_mm10

description:
FPKM_C1_table.txt
Sample_18303_A5

value: Lin- 7AAD- CD44+ Kit+


title: H37_AN02639_ASD/Autism

value: postmortem brain

tag: gender

value: 21 years


title: M800_1097_R_T2

value: iRFP

tag: infection


title: H37_AN13287_ASD/Autism

value: male

tag: age

value: 43 years

tag: disease state


title: H43_UMB5176_ASD/Autism

value: 22 years 199 days

value: ASD/Autism

tag: postmortem interval (hours)

tag: brain region

value: subventricular zone of lateral ventricles


title: M800_1098_R_T2


title: IGR37_siSCD_1_t48h_R3

description: processed data file: edgeR_siSCD1_normalised_count_Log.txt

tag: cell line

value: 20nM siSCD#1 48h


title: X18303_A4_mm10

description:
FPKM_C1_table.txt
Sample_18303_A4

tag: genotype

value: WT

tag: tissue

value: Thymus


title: M800_1095_R_T2

tag: cell type


title: X18303_A2_mm10

description:
FPKM_C1_table.txt
Sample_18303_A2

tag: strain

tag: facs purification gate


title: X18303_A7_mm10

description:
FPKM_C1_table.txt
Sample_18303_A7


title: H36_UMB1405_Control

value: 21 years 1 day

value: Control


title: H35_AN00764_ASD/Autism

value: 20 years


title: H39_UMB5403_ASD/Autism

value: 16 years 266 days


title: M800_1092_R_T2

value: leukemia stem cells

tag: leukemic burden


title: M800_1093_R_T2

tag: mouse id


title: X18303_A11_mm10

description:
FPKM_C1_table.txt
Sample_18303_A11

value: Lin- 7AAD- CD44+ Kit+


title: X18303_A12_mm10

description:
FPKM_C1_table.txt
Sample_18303_A12


title: IGR37_siSCD_1_t48h_R1

description:
siSCD1_DGE.xlsx @IGR37siSCD#1_vs_siCTR-tab
processed data file: edgeR_siSCD1_normalised_count_Log.txt

value: melanoma cell line

tag: treatment


title: M798_1971_G_T3

tag: color

value: GFP


title: X18303_A10_mm10

description:
FPKM_C1_table.txt
Sample_18303_A10


title: H33_UMB5303_ASD/Autism

value: postmortem brain

value: 67 years 120 days


title: IGR37_siCTR_t48h_R3

value: 20nM siCTRL 48h


title: X18303_A1_mm10

description:
FPKM_C1_table.txt
Sample_18303_A1


title: IGR37_siCTR_t48h_R2


title: IGR37_siCTR_t48h_R1


title: M798_1970_G_T3

tag: time point


title: H32_UMB5498_Control

tag: gender

value: male

value: 51 years 109 days


title: H34_UMB5452_Control

value: 67 years 188 days

value: subventricular zone of lateral ventricles


title: IGR37_siCTR_1_t48h_R3


title: M798_1692_R_T3

value: iRFP

tag: infection


title: DN2a_Bcl11bpos_SMARTseq_rep

description:
bulk_RNAseq_processed.txt
20588_2A-YFP_plus_S1
Bulk_RNAseq_DN2a_Bcl11bpos_SMARTseq

data_processing:
FASTQ files were mapped onto the mouse genome build GRCm38(mm10) with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings ?--output-genome-bam --sampling-for-bam? was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build GRCm38(mm10) together with the Ensembl gene model file Mus_musculus.GRCm38.gtf.The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with ?keepAll setting). For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the ?noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bulk_RNAseq_processed.txt; matrix.mtx with accompanying genes.tsv and barcodes.tsv; FPKM_C1_table.txt

extract_protocol: SMART-Seq v4 Ultra Low Input+Nextera XT library prep

value: Thymus

value: Lin- 7AAD- CD44+ Kit+ CD25+ YFP+


title: IGR37_siCTR_1_t48h_R2


title: IGR37_siCTR_1_t48h_R1


title: M798_1691_R_T3


title: M798_1689_R_T3


title: DN2a_Bcl11bpos_rep1

description:
bulk_RNAseq_processed.txt
16675_GATCAG
Bulk_RNAseq_DN2a_Bcl11bpos_1

extract_protocol: NEBNext Ultra RNA


title: H31_UMB5115_ASD/Autism

tag: age

value: 46 years 135 days

value: ASD/Autism


title: H28_UMB1135_Control

value: 42 years 110 days

tag: disease state

value: Control


title: IGR37_SCDi_A93_t48h_R3


title: DN2a_Bcl11bneg_SMARTseq_rep

description:
bulk_RNAseq_processed.txt
20589_2A-YFP-_S2
Bulk_RNAseq_DN2a_Bcl11bneg_SMARTseq

value: Lin- 7AAD- CD44+ Kit+ CD25+ YFP-


title: M798_1665_R_T2

value: leukemia stem cells


title: IGR37_SCDi_A93_t48h_R2

value: melanoma cell line


title: M798_1661_R_T2


title: DN2a_Bcl11bneg_rep2

description:
bulk_RNAseq_processed.txt
20721_ACTGAT
Bulk_RNAseq_DN2a_Bcl11bneg_2


title: IGR37_SCDi_A93_t48h_R1

description:
siSCD1_DGE.xlsx @IGR37SCDi_vs_DMSO-tab
processed data file: edgeR_SCD_normalised_count_Log.txt


title: IGR37_siSCD_1_t48h_R2

value: 20nM siSCD#1 48h


title: M798_1657_R_T2


title: DN2a_Bcl11bneg_rep1

description:
bulk_RNAseq_processed.txt
16676_TAGCTT
Bulk_RNAseq_DN2a_Bcl11bneg_1


title: IGR37_DMSO_t48h_R3

value: DMSO


title: H24_AN01410_Control

value: postmortem brain

value: 27 years 62 days

tag: postmortem interval (hours)


title: M798_1650_S_T3

value: Sapphire


title: Flt3neg_ETP_SMARTseq_rep

description:
bulk_RNAseq_processed.txt
20590_Fneg-ETP_S3
Bulk_RNAseq_Flt3neg_ETP_SMARTseq

value: Lin- 7AAD- CD44+ Kit+ CD25- Flt3-


title: H25_AN09714_ASD/Autism

value: male

value: 60 years 40 days

tag: brain region

value: subventricular zone of lateral ventricles


title: DN2a_Bcl11bpos_rep2

description:
bulk_RNAseq_processed.txt
20722_ATTCCT
Bulk_RNAseq_DN2a_Bcl11bpos_2

value: Thymus

value: Lin- 7AAD- CD44+ Kit+ CD25+ YFP+


title: H20_AN08873_ASD/Autism

value: 5 years

value: ASD/Autism


title: M798_1649_S_T3


title: Flt3pos_ETP_SMARTseq_rep

description:
bulk_RNAseq_processed.txt
20591_Fpos-ETP_S4
Bulk_RNAseq_Flt3pos_ETP_SMARTseq

value: Lin- 7AAD- CD44+ Kit+ CD25- Flt3+


title: H26_AN10723_Control

value: 60 years

value: Control


title: X18303_A3_mm10

description:
FPKM_C1_table.txt
Sample_18303_A3

value: WT

value: Lin- 7AAD- CD44+ Kit+


title: IGR37_DMSO_t48h_R2

tag: cell line

value: melanoma cell line

value: DMSO


title: M798_1645_S_T3

value: leukemia stem cells


title: total_ETP_rep2

description:
bulk_RNAseq_processed.txt
20719_CGTACG
Bulk_RNAseq_ETP_2

tag: genotype

value: Lin- 7AAD- CD44+ Kit+ CD25-


title: 501mel_siSCD_2_t48h_R3

value: 20nM siSCD#2 48h


title: IGR37_DMSO_t48h_R1


title: H18_UMB4332_Control

tag: tissue

value: postmortem brain

value: male

value: 5 years 241 days


title: H19_UMB5408_Control

value: 6 years 309 days

value: subventricular zone of lateral ventricles


title: H30_UMB4326_Control

value: 46 years 73 days


title: M798_1643_S_T2

tag: cell type

value: Sapphire


title: M798_1641_S_T2


title: Flt3neg_ETP_rep1

description:
bulk_RNAseq_processed.txt
16674_ACTTGA
Bulk_RNAseq_Flt3neg_ETP

tag: strain

value: Thymus

value: Lin- 7AAD- CD44+ Kit+ CD25- Flt3-


title: H17_UMB5391_Control

value: 8 years 286 days

value: Control


title: 501mel_siSCD_2_t48h_R1

description:
siSCD1_DGE.xlsx @501melsiSCD#2_vs_siCTR-tab
processed data file: edgeR_SCD_normalised_count_Log.txt


title: M798_1633_S_T2


title: 501mel_siSCD_2_t48h_R2


title: total_ETP_rep1

description:
bulk_RNAseq_processed.txt
20720_GAGTGG
Bulk_RNAseq_ETP_1

tag: facs purification gate


title: 501mel_siSCD_1_t48h_R3

value: 20nM siSCD#1 48h


title: M798_1197_G_T3

tag: leukemic burden

value: GFP


title: H16_UMB4721_ASD/Autism

value: 8 years 304 days

value: ASD/Autism


title: 554299A12 - Mtefd_nodules_11dpi_BR3 vs WT_nodules_11dpi_BR4

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Identification of genes affected by a KO mutation in a transcription factor involved in root and nodule development, MtEFD1.

hyb_protocol: WT_nodules_11dpi_BR4 Cy5 / Mtefd_nodules_11dpi_BR3 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Medicago truncatula

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - Media=aeroponic caisson medium hygrometry Temperature=20°C Light=400 µmol/m²/s

treatment_protocol: Name:rhizobium inoculation 11 days - inoculation - rhizobacteria inoculation,rhizobium:time 11day . Plants grown in aeroponic conditions were nitrogen-starved for four days then inoculated with Sinorhizobium meliloti. Root systems were harvested just before inoculation, then isolated nodules were collected at indicated times.

value: WT

value: nodules

tag: time

tag: cultivar

value: Mtefd


title: 501mel_siSCD_1_t48h_R2

value: melanoma cell line

tag: treatment


title: H14_UMB4849_ASD/Autism

value: postmortem brain

value: male

value: 7 years 17 days


title: M798_1196_G_T3

value: leukemia stem cells

tag: mouse id

tag: color

tag: time point


title: H13_UMB1674_Control

tag: gender

tag: age

value: 8 years 339 days

value: subventricular zone of lateral ventricles


title: 501mel_siSCD_1_t48h_R1

description:
siSCD1_DGE.xlsx @501melsiSCD#1_vs_siCTR-tab
processed data file: edgeR_siSCD1_normalised_count_Log.txt


title: M798_1195_G_T3

tag: infection


title: 554299A10 - Mtefd_nodules_11dpi_BR1 vs WT_nodules_11dpi_BR2

hyb_protocol: WT_nodules_11dpi_BR2 Cy5 / Mtefd_nodules_11dpi_BR1 Cy3 : 30pmol.


title: 554299A11 - WT_nodules_11dpi_BR3 vs Mtefd_nodules_11dpi_BR4

hyb_protocol: Mtefd_nodules_11dpi_BR4 Cy5 / WT_nodules_11dpi_BR3 Cy3 : 30pmol.


title: M798_1194_G_T2


title: H11_UMB4231_ASD/Autism

value: 8 years 300 days

tag: disease state

tag: postmortem interval (hours)

tag: brain region


title: 501mel_siCTR_t48h_R2

description: processed data file: edgeR_SCD_normalised_count_Log.txt

tag: cell line

value: 20nM siCTRL 48h


title: CTRL-E1

city: Nagoya

first: Ian

last: Baudi

state: Aichi

address: Kawasumi, Mizuho

department: Virology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description: Gene expression 24hr after IFNa treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes .Cy3-labelled cRNA were then hybridized on Mouse SurePrint 3 v2.0 chips for 17 hours at 65°C in a rotating Agilent hybridization oven at 10rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with Buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Detection, data extraction, and pre-analysis were performed using a G2505C Agilent microarray scanner, Feature Extraction v10.10.1.1. and GeneSpring GX v14.8.0 software.

source_name: Liver Interferon-alpha- 24hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick-Amp Labeling Kit, one color Cy3 protocol (Agilent Technologies, Santa Clara, CA, USA)

extract_protocol: RNA was isolated from snap-frozen liver tissue obtained at selected time points using Isogen (Nippon Gene, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: HBsAg transgenic and control mice were intravenously injected with 5MU/kg recombinant mouse IFN alpha and then sacrificed  2,4,8 and 24 hours later. Non treated mice were sacrificed as time point 0hr. Liver samples were snap frozen in liquid nitrogen at sacrifice for RNA extraction at a later time point.

tag: tissue

value: Liver

tag: genotype

value: non-transgenic

value: Male

tag: time (hr)


title: CTRL-E2


title: 501mel_siCTR_t48h_R3

tag: cell type


title: M798_1193_G_T2

tag: leukemic burden

value: GFP


title: H12_UMB1349_ASD/Autism

value: 5 years 220 days

value: ASD/Autism


title: 554299A07 - WT_nodules_4dpi_BR3 vs Mtefd_nodules_4dpi_BR4

hyb_protocol: Mtefd_nodules_4dpi_BR4 Cy5 / WT_nodules_4dpi_BR3 Cy3 : 30pmol.

treatment_protocol: Name:rhizobium inoculation 4 days - inoculation - rhizobacteria inoculation,rhizobium:time 4day . Plants grown in aeroponic conditions were nitrogen-starved for four days then inoculated with Sinorhizobium meliloti. Root systems were harvested just before inoculation, then isolated nodules were collected at indicated times.

value: nodules

tag: time

tag: cultivar

value: WT


title: 501mel_siCTR_t48h_R1

value: melanoma cell line

tag: treatment


title: M798_1192_G_T2

tag: mouse id

tag: color


title: 501mel_siCTR_1_t48h_R3

description: processed data file: edgeR_siSCD1_normalised_count_Log.txt


title: CTRL-D1

description: Gene expression 8hr after IFNa treatment

source_name: Liver Interferon-alpha- 8hr

tag: gender


title: 554299A06 - Mtefd_nodules_4dpi_BR1 vs WT_nodules_4dpi_BR2

hyb_protocol: WT_nodules_4dpi_BR2 Cy5 / Mtefd_nodules_4dpi_BR1 Cy3 : 30pmol.

value: Mtefd


title: 554299A09 - WT_nodules_11dpi_BR1 vs Mtefd_nodules_11dpi_BR2

hyb_protocol: Mtefd_nodules_11dpi_BR2 Cy5 / WT_nodules_11dpi_BR1 Cy3 : 30pmol.


title: 501mel_siCTR_1_t48h_R2


title: CTRL-C2

description: Gene expression 4hr after IFNa treatment

source_name: Liver Interferon-alpha- 4hr


title: M784_4823_S4_T4

value: Sapphire

tag: time point


title: 554299A08 - Mtefd_nodules_4dpi_BR3 vs WT_nodules_4dpi_BR4

hyb_protocol: WT_nodules_4dpi_BR4 Cy5 / Mtefd_nodules_4dpi_BR3 Cy3 : 30pmol.


title: 554299A05 - WT_nodules_4dpi_BR1 vs Mtefd_nodules_4dpi_BR2

hyb_protocol: Mtefd_nodules_4dpi_BR2 Cy5 / WT_nodules_4dpi_BR1 Cy3 : 30pmol.


title: H15_UMB4337_Control

value: postmortem brain

value: male

tag: age

value: 8 years 90 days

value: Control


title: M798_1191_G_T2

value: leukemia stem cells

tag: infection


title: M784_4822_S4_T4


title: CTRL-C1


title: 501mel_SCDi_A93_t48h_R2


title: 501mel_SCDi_A93_t48h_R1

description:
siSCD1_DGE.xlsx @501melSCDi_vs_DMSO-tab
processed data file: edgeR_SCD_normalised_count_Log.txt


title: 501mel_siCTR_1_t48h_R1

value: 20nM siCTRL 48h


title: M784_4806_G_T3


title: 501mel_SCDi_A93_t48h_R3


title: 554299A04 - Mtefd_roots_0dpi_BR3 vs WT_roots_0dpi_BR4

hyb_protocol: WT_roots_0dpi_BR4 Cy5 / Mtefd_roots_0dpi_BR3 Cy3 : 30pmol.

treatment_protocol: no treatment

value: roots


title: CTRL-B2

description: Gene expression 2hr after IFNa treatment

source_name: Liver Interferon-alpha- 2hr

value: Liver

value: non-transgenic


title: CTRL-A1

description: Gene expression in non treated liver

source_name: Liver Interferon-alpha- 0hr

value: Male


title: M784_4824_S4_T4


title: CTRL-D2


title: Tg-E2

value: HBsAg transgenic


title: 554299A02 - Mtefd_roots_0dpi_BR1 vs WT_roots_0dpi_BR2

hyb_protocol: WT_roots_0dpi_BR2 Cy5 / Mtefd_roots_0dpi_BR1 Cy3 : 30pmol.


title: Sorted 4 ETP subpopulations and ETP-DN2 controls

data_processing:
Cellranger 3.0 is run on the FASTQ files to generate matrix, genome build: mm10
Genome_build: mm10
Supplementary_files_format_and_content: matrix file output from 10X single cell RNAseq CellRanger pipeline; HTO count table of individual cell barcode

source_name: ETP subpop cDNA_lib

extract_protocol: single cell droplet performed with 10x Chromium v3

tag: strain

value: Thymus

tag: facs purification gates

value: Subpop1-Hashtag1:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3+ Ly6d- HSA-; Subpop2-Hashtag2:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3+ HSA+; Subpop3-Hashtag3:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3- Ly6d- HSA-; Subpop4-Hashtag4:Lin- 7AAD- Kit+ CD25- Bcl11b- Flt3- Ly6d+; Subpop_CTRL-Hashtag5:Lin- 7AAD- Kit+

tag: molecule subtype

value: polyA RNA


title: CTRL-B1

tag: tissue


title: CTRL-A2

description: Gene expression in non treated liver

tag: genotype


title: 554299A01 - WT_roots_0dpi_BR1 vs Mtefd_roots_0dpi_BR2

hyb_protocol: Mtefd_roots_0dpi_BR2 Cy5 / WT_roots_0dpi_BR1 Cy3 : 30pmol.

value: WT


title: M784_4804_G_T3

value: GFP


title: 554226A01 - WT_nodules_6dpi_BR1 vs Mtefd_nodules_6dpi_BR2

hyb_protocol: Mtefd_nodules_6dpi_BR2 Cy5 / WT_nodules_6dpi_BR1 Cy3 : 30pmol.

treatment_protocol: Name:rhizobium inoculation 6 days - inoculation - rhizobacteria inoculation,rhizobium:time 6day . Plants grown in aeroponic conditions were nitrogen-starved for four days then inoculated with Sinorhizobium meliloti. Root systems were harvested just before inoculation, then isolated nodules were collected at indicated times.

value: Mtefd

value: nodules


title: 554226A04 - Mtefd_nodules_6dpi_BR3 vs WT_nodules_6dpi_BR4

hyb_protocol: WT_nodules_6dpi_BR4 Cy5 / Mtefd_nodules_6dpi_BR3 Cy3 : 30pmol.


title: 501mel_DMSO_t48h_R2

tag: cell line

value: melanoma cell line

value: DMSO


title: M784_4805_G_T3

tag: cell type


title: M784_4802_G_T2

tag: leukemic burden


title: Tg-E1

tag: time (hr)


title: 501mel_DMSO_t48h_R1


title: scRNA-Seq_Normal mouse small intestine (2)

city: Tianjin

first: Ming

last: Wei

address: 94 Weijin road

department: Department of Immunology, Nankai University School of Medicine

country: China

institute: Nankai University

data_processing:
Initially, raw base call (BCL) files generated by Illumina sequencers was demultiplexed into FASTQ files
After barcode processing, sequencing reads per cell barcode were then aligned to the UCSC mm10 transcriptome with STAR (version 2.5.1b).
Prior to single-cell 3ʹgene counting, duplicates were filtered based on unique molecular identifiers (UMIs), and finally single cell information (gene expression matrix) of each individual sample was generated.
In this study, outputs of samples from different runs of cellranger count were merged together, facilitated by cellranger aggr pipeline which normalized those runs to the same sequencing depth among libraries.As calculated by Cell Ranger, the post-normalization mean reads per cell from all libraries was >70,000.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations

source_name: LP tissues from small intestines of normal mice

extract_protocol:
Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad)  at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

treatment_protocol: Dextran sodium sulfate (DSS) induced colitis was performed according to the previous method (Cell Rep 14, 695-707). Briefly, mice (7-8 weeks old, male) received 2.5% (wt/vol) DSS (40,000 kDa; ICN Biochemicals) or indicated doses in their drinking water for 7 days, then switched to regular drinking water.For pan-antibotics treated mice, C57BL/6 mice (7-8 weeks old, male) were with pan-antibiotics (ampicillin (A, 1 g/L, Sigma), vancomycine (V, 0.5g/L, Sigma), neomycin sulfate (N, 1 g/L, Sigma), and metronidazole (M, 1g/L, Sigma) via the drinking water for one week (sometime longer than one week).

value: LP cells from small intestines

tag: cell population

tag: background strain

value: wildtype

value: 7-8 weeks

tag: Sex

value: male


title: M784_4801_G_T2

value: leukemia stem cells

tag: mouse id

tag: color


title: 554226A02 - Mtefd_nodules_6dpi_BR1 vs WT_nodules_6dpi_BR2

hyb_protocol: WT_nodules_6dpi_BR2 Cy5 / Mtefd_nodules_6dpi_BR1 Cy3 : 30pmol.

tag: time

tag: cultivar


title: 554226A03 - WT_nodules_6dpi_BR3 vs Mtefd_nodules_6dpi_BR4

hyb_protocol: Mtefd_nodules_6dpi_BR4 Cy5 / WT_nodules_6dpi_BR3 Cy3 : 30pmol.


title: Tg-D2

value: Liver

tag: gender


title: scRNA-Seq_GF/Colon  (2)

source_name: colonic LP tissues of germ-free (GF) mice (8 weeks old, male)

value: colonic LP cells

tag: age


title: IGR37_NLS-CTNNB1-24h_dox_R2.gz

description: Doxycycline-induced-nuclear-localised-Beta-catenin replicate 2

growth_protocol: IGR37 were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with 100U/ml penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

treatment_protocol: CTNNB1 inducible cell line was treated with 20ng/ml Doxycycline for 24h before harvest.

value: melanoma

tag: treatment


title: scRNA-Seq_Pan-antibiotics/Colon

source_name: colonic LP tissues of pan-antibiotics-treated SPF mice (8 weeks old, male)

tag: treated with

value: pan-antibiotics


title: scRNA-Seq_Normal mouse small intestine (1)


title: M784_4799_G_T4

tag: time point

tag: infection


title: M784_4710_G_T2


title: IGR37_NLS-CTNNB1-24h_dox_R3.gz

description: Doxycycline-induced-nuclear-localised-Beta-catenin replicate 3

tag: cell line


title: scRNA-Seq_GF/Colon  (1)

tag: cell type

tag: genotype


title: Flt3pos_ETP_rep1

description:
bulk_RNAseq_processed.txt
16673_CAGATC
Bulk_RNAseq_Flt3pos_ETP

source_name: Thymus

tag: strain

tag: tissue

value: Thymus

tag: facs purification gate

value: Lin- 7AAD- CD44+ Kit+ CD25- Flt3+


title: IGR37_NLS-CTNNB1-24h_dox_R1.gz

description: Doxycycline-induced-nuclear-localised-Beta-catenin replicate 1


title: Tg-D1

value: HBsAg transgenic

value: Male

tag: time (hr)


title: Tg-C2


title: Tg-C1


title: M784_4800_G_T4

tag: leukemic burden

tag: mouse id

value: GFP


title: 554299A03 - WT_roots_0dpi_BR3 vs Mtefd_roots_0dpi_BR4

hyb_protocol: Mtefd_roots_0dpi_BR4 Cy5 / WT_roots_0dpi_BR3 Cy3 : 30pmol.

value: Mtefd

value: roots

tag: time

value: WT


title: scRNA-Seq_NLRC4/DSS

source_name: colonic LP tissues of DSS-treated Nlrc4 KO mice

tag: cell population

tag: background strain

value: Nlrc4 deficient

value: DSS

tag: Sex


title: M784_1417_S_T3

tag: color

value: Sapphire


title: IGR37_NLS-CTNNB1-0h_dox_R2.gz

description: Negative control, no Doxycycline replicate 2

tag: treatment

value: Negative control, no Doxycycline


title: M784_1416_S_T3

value: leukemia stem cells

tag: time point


title: scRNA-Seq_WTDSS/Colon

source_name: colonic LP tissues of DSS-treated SPF mice

value: wildtype

tag: treated with

tag: age

value: 7-8 weeks

value: male


title: scRNA-Seq_WTC /Colon  (2)

source_name: colonic LP tissues of SPF mice (8 weeks old, male)

tag: cell type

value: colonic LP cells


title: IGR37_NLS-CTNNB1-0h_dox_R1.gz

description: Negative control, no Doxycycline replicate 1

value: melanoma

tag: cell line


title: M784_1415_S_T3

source_name: leukemia stem cells

tag: infection


title: Tg-B2

tag: tissue

value: Liver

tag: genotype

tag: gender


title: Tg-B1

value: HBsAg transgenic

tag: time (hr)