title: Trop2-positive luminal Young Rep 2

city: Los Angeles

first: Andrew

middle: Scott

last: Goldstein

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

description:
Y-Trop2-plus-Lum
processed data file: TMM_normalized_reads_count_per_million.xlsx

data_processing:
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M values) was used to normalize the gene expression.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.genes.results: Tab-delimited text files include TPM and FPKM values.
Supplementary_files_format_and_content: TMM_normalized_reads_count_per_million.xlsx: Excel file includes TMM (trimmed mean of M values) normalized reads count per million.

source_name: Prostate

extract_protocol:
Sorted cells were pelleted and flash frozen on dry ice. RNA was extracted from the pellets using the RNeasy Mini Kit (QIAGEN) following the manufactural instruction.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit (Roche). The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

value: 3 months

value: prostate

value: luminal Trop2+


title: mESC_WT_LIF_exp1_rep1

status: Public on Aug 01 2019

type: SRA

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description:
trim71_diff_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF mES W

library_source: transcriptomic

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads from mouse samples were aligned to the mm10 genome assembly using the qAlign function from the QuasR R package (v. 1.20.0) with default settings, or using the STAR aligner with the following settings: —outFileterType BySJout, —outFilterMultimapNmax 20, —outMultimapperOrder Random, —outSAMmultNmax 1, —alignSJoverhangMin 8, —alignSJDBoverhangMin 1,  —alignIntronMin 20, —alignIntronMax 1000000
Reads from human samples were aligned to the hg19 genome assembly using the STAR aligner, with the same settings as above.
Gene expression was quantified using Ensembl annotations for mouse and UCSC known Gene annotations for human, downloaded from Bioconductor (“TxDb.Mmusculus.UCSC.mm10.ensGene” and “TxDb.Hsapiens.UCSC.hg19.knownGene”). The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Ensembl identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample. HuH7 file: first column contains Entrez IDs, second column contains gene symbols, following columns as in other files.

molecule: total RNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells (129xC57BL/6 Rosa26Cre-ERT2/BirA-V5 [cMB063 (Ostapcuk et al., 2018)]) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.   Ne4C cells (ATCC® CRL-2925™ (Schlett and Madarasz, 1997)) were cultured on poly-l-lysine coated dishes in Ne4C medium (DMEM [Gibco; 11885084] supplemented with 10% fetal bovine serum [Sigma], 2mM L-glutamine [Gibco; 25030081], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032]) at 37 °C in 5% CO2.   Huh-7 cells (JCRB0403 (Nakabayashi et al., 1982)) were cultured in Huh-7 medium (DMEM [Gibco; 31966021] supplemented with 10% fetal bovine serum [Sigma] 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032]) at 37 °C in 5% CO2.

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input)

tag: cell type

value: mESC

tag: strain

tag: genotype


title: ND, CBL sample 95--02

type: genomic

city: Tempe

first: Danielle

middle: Lisa

last: Brokaw

state: AZ

address: Biodesign Institute Building C, 1001 S McAllister Ave

department: Center for Neurodegeneration, Biodesign

country: USA

institute: Arizona State University

description:
control CBL sample
CBL 95--02

hyb_protocol: Samples were randomly assigned to one of nine Illumina 450K plates and hybridized according to protocol.

scan_protocol: iScan System according to user protocol

data_processing:
Data was analyzed in R (version 3.4.2) using minfi (1.23.4) and SVA (3.26.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis. NOOB and functional normalization were performed using the minfi package according author guidelines. Confounding variables were detected using SVA and, alongside batch/plate effects, were accounted for using the ComBat algorithm.
Normalized Average betas included as supplementary files (processedSamples*.txt) on the Series record.
Methylated and unmethylated signal intensities included as supplementary files (signalIntensities*.txt) on the Series record.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: CBL sample 95--02

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue was incubated in lysis buffer (100 mM Tris HCL pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 100 ug/mL Proteinase K) overnight at 55°C.  and disassembled using a pestle. Disassociated tissue was treated with 4 uL of Rnase A for 30 minutes at RT and then treated with ethanol overnight at -20°C. 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

tag: plate

tag: bead chip

tag: well position

tag: tissue

value: brain

tag: brain region

value: CBL

tag: gender

value: M

tag: age

tag: diagnosis

value: ND


title: ND, CBL sample 98--23

description:
control CBL sample
CBL 98--23

source_name: CBL sample 98--23


title: mESC_Trim71NHL_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
WN2

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
ScriptSeq Illumina Total RNA-seq (stranded - high input)

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 TRIM71R738A/R738A


title: mESC_Trim71NHL_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
WN1


title: mESC_Trim71RING_rep3

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
WR3

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 TRIM71C12AC15A/C12AC15A


title: Trop2-negative luminal Young Rep 2

state: CA

description:
Y-Trop2-minus-Lum
processed data file: TMM_normalized_reads_count_per_million.xlsx

tag: strain/background

value: luminal Trop2-


title: ND, CBL sample 98--33

description:
control CBL sample
CBL 98--33

source_name: CBL sample 98--33

value: F


title: ND, CBL sample 95--40

description:
control CBL sample
CBL 95--40

source_name: CBL sample 95--40


title: mESC_Trim71RING_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
WR1


title: Trop2-positive luminal Young Rep 1

description:
Y-Trop2-plus
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: mESC_Trim71KO_rep3

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
K3

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 TRIM71-/-

value: Rosa26Cre-ERT2/BirA-V5 TRIM71-/-


title: Trop2-negative luminal Young Rep 1

description:
Y-Trop2-minus
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: mESC_Trim71RING_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
WR2


title: ND, CBL sample 95--39

description:
control CBL sample
CBL 95--39

source_name: CBL sample 95--39


title: mESC_Trim71KO_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
K1


title: Stromal Young Rep 3

description:
Y3-Stromal
processed data file: TMM_normalized_reads_count_per_million.xlsx

value: stromal


title: mESC_Trim71KO_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
K2


title: ch12_Med23mm_mRNA_spikein_br2

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: ercc-spike-in

data_processing:
base calling: illumina CASAVA 1.8.2
Promter Capture HiC-Seq: alignment: bowtie 2.3.4.3 with default parameter to hg19
Promter Capture HiC-Seq: alignment and filter: HiCUP v0.5.9
Promter Capture HiC-Seq: Normalization: randomly selecting enough reads in order to obtain 73 million read pairs in cis and >10 b apart from each bait
Promter Capture HiC-Seq: Interaction call: with default parameter by using CHiCAGO 1.10.1
BSseq:triming: remove first 8nt with cutadapt program
BSseq:alignment: aliged to mm9 with default parameter using Bismark
BSseq:filter: low quality sequences and PCR duplicates are removed by BSseeker2
BSseq:bedgraph generation: bismark_methylation_extractor in Bismark pacakge
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Promter Capture HiC-Seq: .txt file generated by CHiCAGO for significant interaction calls
Supplementary_files_format_and_content: BSseq:bedgraph to show the methylation %

source_name: CH12 B cell line

extract_protocol:
Promoter Capture  HiC-Seq:  we used the same protocol at Montefiori et al., (Elife, 2018 Jul 10; 7)                                                                                BS-seq: Genomic DNA was isolated from 3×106 cells using Qiagen DNeasy blood and tissue kit (Cat #: 69506). The bisulfite conversion was performed using the EZ DNA Methylation-Gold™ Kit (Cat #: D5005) from Zymo Research. Whole-genome bisulfite sequencing libraries were prepared from 50 ng converted DNA using Illumina TruSeq® DNA Methylation Kit (Cat #: EGMK91324), which was performed following the manufacturer’s protocol.
Promoter Capture HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 3000 (Illumina).                                                                                BS-seq: standard RNA-Seq   library   preparation   was performed following  the genomic DNA protocol with 20% PhiX. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina)

value: lymphoma cell line


title: mESC_WT_rep3

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
W3


title: ND, CBL sample 02--33

description:
control CBL sample
CBL 02--33

source_name: CBL sample 02--33


title: mESC_Trim71KO_batch2_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
2K2

extract_protocol:
TriZol, RNEasy Mini kit [Quiagen: 74104] with on-column DNAse digestion
ScriptSeq Illumina Total RNA-seq (stranded - high input)


title: ND, CBL sample 04--05

description:
control CBL sample
CBL 04--05

source_name: CBL sample 04--05


title: mESC_Trim71NHL_rep3

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
WN3


title: mESC_WT_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
W1


title: Trop2-positive luminal Old Rep 2

description:
O-Trop2-plus-Lum
processed data file: TMM_normalized_reads_count_per_million.xlsx

value: 24 months


title: mESC_WT_batch2_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
2W2


title: Stromal Young Rep 1

description:
Y1-Stromal
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: ND, CBL sample 03--58

description:
control CBL sample
CBL 03--58

source_name: CBL sample 03--58


title: mESC_WT_batch2_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
2W1


title: mESC_Trim71KO_batch2_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
2K1


title: ND, CBL sample 01--36

description:
control CBL sample
CBL 01--36

source_name: CBL sample 01--36


title: Trop2-positive luminal Old Rep 1

description:
O-Trop2-plus
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: mESC_Trim71KO_batch1_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
1K2


title: mESC_Trim71KO_batch1_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
1K1

treatment_protocol: mES (129xC57BL/6)  Rosa26Cre-ERT2/BirA-V5 TRIM71-/-


title: ND, CBL sample 02--04

description:
control CBL sample
CBL 02--04

source_name: CBL sample 02--04


title: Stromal Young Rep 2

description:
Y2-Stromal
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Trop2-negative luminal Old Rep 1

description:
O-Trop2-minus
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: ND, CBL sample 01--14

description:
control CBL sample
CBL 01--14

source_name: CBL sample 01--14


title: Trop2-negative luminal Old Rep 2

description:
O-Trop2-minus-Lum
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: mESC_WT_batch1_rep1

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
1W1


title: HFD_Nurr_1

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
Quality assessment of the RNA-seq data was done using the NGS-QC-Toolkit. Reads with more than 30% nucleotide with phred quality scores less than 20 were removed from further analysis.
Quality filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the tophat (v 2.0.12) aligner using default setting except for –library-type = fr-firststrand.  (v1.4.6) (71) per gene ID.
Aligned reads were counted using feature count
Differential gene expression analysis was done using the R package edgeR (82)(v 3.8.6).
For each comparison, genes were required to have 1 cmp in at least 3 samples to be considered as expressed. They were used for normalization factor calculation. Differential gene expression analysis was performed using the GLM approach following edgeR official documentation.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Counts per million per sample per gene.

growth_protocol: Wild type (WT) or Nurr1 transgenic (Nurr1-mTg) mice were on High Fat Diet (HFD) or normal chow (NC) diet for a period of 10 weeks.

extract_protocol:
RNA was isolated from mouse tissues using TRIzol reagent (Invitrogen).
Illumina RNA-seq analysis was performed by the University of Texas Southwestern Microarray Core Facility. SE-50 Per Lane; Library preparation was performed by the core.

treatment_protocol: Wild type (WT) mice maintained on normal chow and HFD for 10 weeks provided AQ in the drinking water ad libitum.

tag: biological replicate

tag: group

tag: diet

value: High Fat Diet

value: Nurr1 transgenic

value: skeletal muscle


title: HFD_Nurr_2


title: Stromal Old Rep 3

description:
O3-Stromal
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: HFD_Nurr_3


title: ND, CBL sample 03--15

description:
control CBL sample
CBL 03--15

source_name: CBL sample 03--15


title: Stromal Old Rep 2

description:
O2-Stromal
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: HFD_WT_3

value: HFD-WT

value: wild type-transgenic control


title: ND, CBL sample 07--72

description:
control CBL sample
CBL 07--72

source_name: CBL sample 07--72


title: HFD_WT_1


title: HFD_WT_2


title: mESC_WT_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
W2


title: ND, CBL sample 06--21

description:
control CBL sample
CBL 06--21

source_name: CBL sample 06--21


title: Luminal Old Rep 3

data_processing:
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M values) was used to normalize the gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: TMM (trimmed mean of M values) normalized reads count per million

value: prostate

value: luminal


title: Stromal Old Rep 1

description:
O1-Stromal
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: WT_NC_AQ_3

value: WT-NC-AQ

value: Normal Chow with DRUG AQ

value: wild type


title: ND, CBL sample 06--57

description:
control CBL sample
CBL 06--57

source_name: CBL sample 06--57

value: brain

value: CBL

value: M

value: ND


title: WT_NC_AQ_1


title: Luminal Old Rep 2

source_name: Prostate


title: ND, CBL sample 04--38

description:
control CBL sample
CBL 04--38

source_name: CBL sample 04--38

value: F


title: Luminal Old Rep 1


title: WT_HFD_3

value: WT-HFD


title: ND, CBL sample 99--04

description:
control CBL sample
CBL 99--04

source_name: CBL sample 99--04


title: ND, CBL sample 99--02

description:
control CBL sample
CBL 99--02

source_name: CBL sample 99--02


title: WT_HFD_AQ_3

value: WT-HFD-AQ

value: High Fat Diet with DRUG AQ


title: ND, CBL sample 99--46

description:
control CBL sample
CBL 99--46

source_name: CBL sample 99--46


title: Luminal Young Rep 2

value: 3 months


title: WT_NC_3

value: WT-NC

value: Normal Chow

value: skeletal muscle


title: WT_HFD_AQ_1


title: WT_HFD_AQ_2


title: Luminal Young Rep 1

value: prostate


title: WT_HFD_1

value: High Fat Diet


title: ND, CBL sample 97--10

description:
control CBL sample
CBL 97--10

source_name: CBL sample 97--10


title: WT_NC_1


title: WT_NC_AQ_2

value: WT-NC-AQ


title: WT_HFD_2


title: WT_NC_2


title: Basal Old Rep 3

value: 24 months

value: basal


title: Cbfb-cKO_CD103-CD11b+_rep1

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were quality and adapter trimmed by trim_galore, then mapped to mm10 whole genome using STAR v2.7 with a gtf file from EMBL-EBI (GRCm38.92)
Reads on each gene were counted using htseq-count with -s no option and a GTF file from EMBL-EBI (GRCm38.92)
Genome_build: mm10

source_name: Intestinal Dendritic Cells

extract_protocol:
Single cell suspensions from mouse intestine were prepared using EDTA and collagenase IV with agitations. Dendritic cells were flow-sorted into buffer TCL (QIAGEN) by FACS Aria and RNA were isolated using Agencourt RNAClean XP beads (Beckman Coulter).
RNA libraries were prepared for sequencing applying scRNA-seq procedure with modofications

tag: genotype/variation

value: Cbfb-cKO

value: mixed background

value: gut

tag: cell types

value: Dendritic cell


title: Cbfb-cKO_CD103-CD11b+_rep3


title: Cbfb-cKO_CD103-CD11b+_rep2


title: ND, CBL sample 97--37

description:
control CBL sample
CBL 97--37

source_name: CBL sample 97--37

value: brain

value: CBL

value: M

value: ND


title: Cbfb-cKO_CD103+CD11b-_rep3


title: Basal Old Rep 1

tag: cell type


title: Luminal Young Rep 3

tag: strain

value: 3 months

value: luminal


title: Cbfb-cKO_CD103+CD11b-_rep2


title: ND, CBL sample 97--19

description:
control CBL sample
CBL 97--19

source_name: CBL sample 97--19


title: Cbfb-cKO_CD103+CD11b-_rep1


title: Basal Young Rep 3


title: ND, CBL sample 08--81

description:
control CBL sample
CBL 08--81

source_name: CBL sample 08--81

value: F


title: WT_CD103-CD11b+_rep2

value: wild type


title: WT_CD103-CD11b+_rep3


title: Basal Young Rep 2

value: prostate


title: ND, CBL sample 96--45

description:
control CBL sample
CBL 96--45

source_name: CBL sample 96--45


title: WT_CD103-CD11b+_rep1


title: Basal Young Rep 1


title: ND, CBL sample 96--06

description:
control CBL sample
CBL 96--06

source_name: CBL sample 96--06


title: ND, CBL sample 08--72

description:
control CBL sample
CBL 08--72

source_name: CBL sample 08--72


title: WT_CD103+CD11b-_rep2


title: Basal Old Rep 2


title: WT_CD103+CD11b-_rep1


title: mESC_WT_batch1_rep2

description:
trim71_total_mRNA_counts.tab
sample name in processed data file:
1W2

value: mESC

tag: genotype


title: ch12_wt_chipseq_Rad21_br2

library_source: genomic

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
ATAC-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragment and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer running with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer between the end of the primer and the restriction sites used in the corresponding experiment.
4C-Seq: mapping: bowtie-1.1.1/bowtie -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to NlaIII/CSP6i fragment (human) or DpnII/CSP6i fragment (mouse)to calculate fraction of restriction fragments for which 4C reads were found
CRISPR screen: Build artificial genome with primer and sgRNA constructs and make index with bowtie
CRISPR screen: alignment: bowtie -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: filtering and sort: samtools view -S -b -F4 | samtools sort -@ 2
CRISPR screen: samtools idxstats on aligned file
CRISPR screen: calculate frequency of each sgRNAs in each pool
CRISPR screen: samtools idxstats on aligned file
Genome_build: mm9 (MGSCv37), hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh.
Supplementary_files_format_and_content: 4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window.
Supplementary_files_format_and_content: mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: CRISPRscreen: summarized text file on each codition, replicates, gene, sgRNAs.

source_name: CH12 B cell line

growth_protocol: Cas9 expressing cells: Primary CD4+ cells expressing Cas9 were isolated from a Cas9 expressing mouse (Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh) (Platt et al., Cell, 2014). Spleen was triturated in DMEM, supernatant was filtered and immediately processed according to the MACS mouse CD4+ T Cell Isolation Kit (Miltenyi Biotec, Cologne, Germany), following the manufacturer’s protocol. Isolated cells were seeded in a six-well plate that was previously coated with aCD3 and aCD28 at a final concentration of 10 ug/mL in 1.6 mL of PBS. The plate was incubated at 37°C for a minimum of 30 min. The PBS was then removed and the cells added to the plate. Cas9 expression in E14 ES cells was obtained through infection with lentiCas9-blast virus (Addgene plasmid #52962). After Blasticidin selection (7.5 ug/mL), clones expressing Cas9 were isolated and expanded to be used for the multiCRISPR screen for essential Mediator subunits. Cas9 expression was assessed by Western blot analysis and cutting efficiency after transfection with sgRNA plasmids.

extract_protocol:
Extraction protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with MNase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or MNase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x10^7 resting and activated B cells were digested with 24 different concentrations of MNaseI. After an initial RT-qPCR analysis and curve-fitting, the MNaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MNaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MNaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: We used the same protocol for in situ HiC libraries as Rao et al., (Cell, 2014 Dec; 159:1-16).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA was religated in a 7 ml volume (1,000 U T4 DNA Ligase, Roche). Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C. Bait was amplified with inverse PCR primers as follows: 3RR with DpnII: _4C 5′- GCTTATCTGTAAAGAATGGGTC-3′, 3RR_Csp6i 5′-GGCCTTAGAAGGCTCTGTAC-3′. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 10^6 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated. ERCC-spike-in was added on some samples for quantitative comparison between two conditions.
ATACseq: One hundred thousand cultured cells were harvested for each point. Cell lysis and Transposition reaction were immediately performed according to Greenleaf’s group protocol (Corces et al., Nat Meth 2017; Buenrostro et al., Nat Meth 2013). Transposed DNA was immediately purified and stored at -20C before library preparation according to the above protocol.
CRISPRscreen: Cells were harvested at an early reference time-point (second day after infection) and two late time-points (14 and 21 days after infection). DNA was extracted using DNeasy Blood and tissue kit according to the manufacturer’s instructions (#69506, Qiagen).
Library construction protocol:
ChIP-Seq  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2500 or 3000 (Illumina).
HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
4C-seq: DNA was prepared for paired-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on HiSeq 2000, 2500 or 3000 (Illumina).
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).
CRISPRscreen: DNA was prepared for single-end Illumina sequencing using staggered GeCKO readout primers (Shalem et al. 2013). 80 cycles of sequencing data were acquired on the MiSeq (Illumina).

treatment_protocol: CRISPR infection: The viral libraries which contain sgRNAs were used to infect Cas9 expressing E14 ES cells and primary CD4+ T cells isolated from the Rosa26-Cas9 expressing mice. Two hundred thousand cells were seeded in a six-well plate the day before infection. Concentrated viruses were added to the media in presence of Polybrene (6 ug/mL). The amount of virus was adjusted according to the viral titer to obtain a MOI of 0.3. Cells were transduced by spinfection at 1,350g for 90 min and 28-32°C. Infected cells were selected 24h after infection, using Puromycin at a final concentration of 1 ug/ml for ES cells and 2 ug/mL for CD4+ T cells.

tag: cell line

value: lymphoma cell line

value: WT

tag: chip antibody

value: Abcam, ab992


title: Trim71_RING_mutant_CRAC_rep2

first: Alex

middle: Charles

last: Tuck

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description: in-line barcode L5Ac (NNNNGCGCAGC)

data_processing:
Library strategy: CRAC-seq
Sequencing reads were preprocessed for standard analyses (and bigWig file generation) as follows:
(i) The 3’ adapter was removed (if present) using Trimmomatic-0.32 with settings ILLUMINACLIP:adapters_file.fa:2:30:4
(ii) Low quality reads were removed using fastq_quality_filter -q 25 -p 100 -Q 33
(iii) Reads with identical sequence and 5’ inline unique molecule identifier, UMI, were collapsed, as they are likely to arise from duplication during PCR.
(iv) Low complexity regions were trimmed from the 3’ end of reads (regions of 2 nt or more where 80 % or more of the sequence comprises one nucleotide). This is to enable RNA fragments to be mapped even if they have non-templated nucleotides added at the 3' end (e.g. poly(A) tail).
(v) Homopolymers and dinucleotide-rich sequences were removed using prinseq-lite, with settings -min_len 18 -lc_threshold 20 -lc_method dust.
To generate the bigWig files provided here, reads were aligned using bowtie2 --sensitive mode, and filtered for those with a mapping quality (column 5 in the SAM output) value of 8 or higher.
To obtain a high quality set of reads mapping uniquely to transcripts and filter out reads arising from repeats or non-coding RNAs (e.g. tRNA, snoRNA or rRNA), we applied a stringent set of criteria. First, we used bowtie2-2.3.4.1 (settings --local -p 10 -a --very-sensitive) to map all reads to three indexes:
(i) Genome: mm10 genomic sequence.
(ii) Gencode non-coding RNAs: Gencode release M16 Mt_rRNA, Mt_tRNA, miRNA, rRNA, scRNA, snoRNA, sRNA, scaRNA and snRNA features from the file gencode.vM16.annotation.gtf, and predicted tRNAs from the file gencode.vM16.tRNAs.gtf, and a repeat-masked version of the mouse pre-rRNA sequence BK000964 from GenBank.
(iii) Gencode mRNAs/lincRNAs: Gencode release M16 protein_coding and lincRNA features from the file gencode.vM16.annotation.gtf.
We then assigned reads as “repeats/ncRNAs” if they mapped best or equally well to Gencode non-coding RNAs, or if they mapped best or equally well to regions of the genome overlapping RepeatMasker repeats (downloaded from UCSC table browser, version 2012-02-07). Excluding these repeats/ncRNAs, we then extracted reads mapping better or equally well to Gencode mRNA/lincRNAs as to the genome. We then filtered these for unique protein-coding transcript mappers, by mapping (bowtie2-2.3.4.1 --local -p 10 -a --very-sensitive) to an index containing one transcript isoform per protein-coding gene (we selected the APPRIS isoform with the longest 3’ UTR for each gene, selecting one at random in case of a tie), and selecting reads for which (i) the second best match score (if detected) was < 0.8 times the best match score and (ii) the MAPQ score was at least 8. We removed any reads for which the 5’ end was soft-clipped, and collapsed reads with identical UMIs and 5’ end mapping positions (retaining one read at random).
Genome_build: mm10

source_name: mouse embryonic stem cell

growth_protocol: Cells were cultured on gelatin-coated dishes in serum+LIF medium (DMEM, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, 15 % (v/v) fetal bovine serum, 0.1 mM beta-mercaptoethanol, 50 μg/ml penicillin, 80 μg/ml streptomycin and home-made LIF conditioned medium)

extract_protocol:
For each CRAC-seq sample, 2 x 15-cm dishes of cells were washed twice with PBS, removing the second wash, and crosslinked in a Strategen Stratalinker oven at 254 nm (using the 400 mJ/cm2). Cells were lysed at 4 °C by the addition of 5 ml TN150 (50 mM Tris-HCl [pH 7.8], 150 mM NaCl, 0.1 % [v/v] Nonidet P40 substitute, 1x cOmplete Protease Inhibitor Cocktail) supplemented with additional Nonidet P40 substitute to 0.5 % (v/v), incubating for 10 min before scraping cells and transferring the suspension to a 15 ml tube. Debris was removed by centrifuging at 6,500 g for 20 min at 4 °C. The supernatant was incubated rotating overnight at 4 °C with anti-FLAG M2 magnetic beads ([Sigma; M8823]; 100 µl of slurry; beads washed twice in TN150). The beads were washed briefly three times with TN150 (wash volume is always 1 ml), then RNPs eluted twice by rotating for 3 h at 4 °C with 750 μl TN150 + 0.3 mg/ml 3xFLAG peptide + 5 mM ß-mercaptoethanol. The two elutions were pooled, then incubated rotating overnight at 4 °C with Dynabeads M-280 Streptavidin ([Thermo Fisher Scientific; 11205D]; 50 µl slurry washed twice in 100 mM NaOH, 50 mM NaCl then once in TN150). Beads were washed twice with TN600 (as for TN150, except 600 mM NaCl) then twice with TN150. A limited RNase digestion was performed by incubating beads for 4 min at 37 °C with 500 μl TN150 supplemented with 1 μl of 0.1 U diluted RNace-IT and 5 mM β-mercaptoethanol), quenching by capturing beads on a magnetic rack and replacing the solution with wash buffer I (WBI; 50 mM Tris–HCl [pH 7.8], 300 mM NaCl, 0.1% Nonidet P40 substitute, 5 mM β-mercaptoethanol, and 4.0 M guanidine hydrochloride). Beads were washed an additional two times with WBI, then three times with 1 x PNK buffer (50 mM Tris–HCl [pH 7.8], 10 mM MgCl2, 0.5% Nonidet P40 substitute, and 5 mM β-mercaptoethanol).
To prepare cDNA libraries, a series of enzymatic steps were carried out on-bead. Reactions volumes were always 80 μL, and beads were washed once with WBI and three times with 1 x PNK buffer between each reaction:
(i) Alkaline phosphatase treatment: 8 U TSAP and 80 U RNasIN; incubating 30 min at 37 °C.
(ii) Ligation of the 3’ linker: 0.1 nmol miRCat-33 DNA linker, 40 U T4 RNA Ligase 1, 80 U RNasIN, and 12.5% (v/v) PEG8000; incubating overnight at 16 °C.
(iii) Phosphorylation of the 5’ RNA end: 40 U T4 PNK and 2 μl rATP; incubating 1 h at 37 °C.
(iv) Ligation of the 5’ linker: 0.2 nmol 5′ linker, 40 U T4 RNA Ligase 1, 1.25 mM rATP, 80 U RNasIN, and 12.5% (v/v) PEG8000; incubating overnight at 16 °C.
Beads were washed three times with WBI then three times with WBII (50 mM Tris–HCl [pH 7.8], 50 mM NaCl, 0.1% Nonidet P40 substitute, and 5 mM β-mercaptoethanol). To release RNA fragments, beads were incubated for 2 h at 55 °C (shaking at 800 rpm) in 400 μl WBII containing 200 μg Proteinase K. RNA was then extracted using phenol:chloroform (adding 50 μl 3 M sodium acetate [pH 5.2] + 500 μl 1:1 phenol:chloroform, mixing vigorously, then centrifuging at ~15,000 g for 20 min). The aqueous phase (upper phase) was transferred to a new tube, and RNA precipitated with 1 ml ethanol and 20 μg glycogen (incubating at -20 °C overnight before centrifuging at full speed for 1 h at 4 °C, then washing the pellet with 70 % ethanol).
For reverse transcription using Superscript III (Thermo Fisher Scientific), the RNA pellet was resuspended in 11 μl H2O, 1 μl miRCat RT oligo (10 μM) and 1 μl 10 mM dNTP mix. The sample was heated to 80 °C for 3 min, then snap cooled on ice for 5 min. After spinning to collect condensation, 4 μl first strand buffer, 1 μl 100 mM DTT and 1 μl rRNasIN® [Promega; N2511] were added, then the sample mixed, incubated for 3 min at 50 °C, and 1 μl Superscript III added. The sample was incubated for a further 60 min at 50 °C, then for 15 min at 65 °C to inactivate Superscript III. RNA was degraded by adding 2 μl RNase H [NEB; M0297] and incubating for 30 min at 37 °C. This produces approximately 20 μl of cDNA.
Libraries were then amplified by preparing 10 x 50 μl LA Takara Taq PCR reactions, each containing 2 μl of cDNA, 10 pmol P5, 10 pmol PE and 12.5 nmol each dNTP. PCR reactions were then pooled, cleaned up using a QIAgen PCR purification kit (eluting in 30 µl elution buffer), and resolved on a 3 % Metaphor agarose gel in 0.5 × TBE. The DNA smear from ~120-300 bp was then cut out (taking care not to cut the prominent adapter dimer band just below) and extracted using a QIAgen MinElute Gel Extraction kit, eluting in 20 µl elution buffer. Samples were sequenced on an Illumina HiSeq2500 platform (50 nt single-end reads).

tag: strain background

value: CB9 (Cast/EiJ x C57BL/6J)

value: mouse embryonic stem cell

value: RING mutant


title: ND, CBL sample 95--26

description:
control CBL sample
CBL 95--26

source_name: CBL sample 95--26

tag: plate

tag: bead chip

tag: well position

tag: tissue


title: Trim71_NHL_mutant_CRAC_rep2

description: in-line barcode L5Ab (NNNNATTAGC)

value: NHL mutant


title: Trim71_CRAC_rep4

description: in-line barcode L5Aa (NNNNTAAGC)

value: Trim71 wild-type


title: ch12_wt_chipseq_Rad21_br1


title: ND, CBL sample 95--21

description:
control CBL sample
CBL 95--21

source_name: CBL sample 95--21

value: brain

tag: brain region

value: CBL

tag: gender

tag: age

tag: diagnosis


title: Trim71_CRAC_rep3

description: in-line barcode L5Bb (NNNNGTGAGC)


title: Trim71_NHL_mutant_CRAC_rep1

description: in-line barcode L5Bc (NNNNCACTAGC)


title: ND, CBL sample 01--23

description:
control CBL sample
CBL 01--23

source_name: CBL sample 01--23

value: ND


title: ND, CBL sample 03--28

description:
control CBL sample
CBL 03--28

source_name: CBL sample 03--28

value: M


title: ch12_wt_chipseq_polII_br2

value: Abcam, ab817


title: Trim71_CRAC_rep2

description: in-line barcode L5Ab (NNNNATTAGC)


title: WT_CD103+CD11b-_rep3

value: mixed background

value: gut

value: Dendritic cell


title: ND, CBL sample 03--39

description:
control CBL sample
CBL 03--39

source_name: CBL sample 03--39


title: Trim71_CRAC_rep1

description: in-line barcode L5Ad (NNNNCGCTTAGC)


title: ch12_wt_chipseq_polII_br1


title: ND, CBL sample 02--06

description:
control CBL sample
CBL 02--06

source_name: CBL sample 02--06

value: F


title: Trim71_RING_mutant_CRAC_rep1

description: in-line barcode L5Bd (NNNNTCTCTAGC)


title: 14637X5 4-OH-Tam

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 87.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.16.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

growth_protocol: Preadipocytes were isolated from minced inguinal white adipose tissue of Tcf7l2 F/F mice by digestion with Collagenase type II (Sigma). Cells from the stromal vascular fraction were then resuspended in HBSS and stained with Biotin CD31 (Biolegend), Biotin CD45 (Biolegend), Biotin Ter-119 (Biolegend), FITC Streptavidin (Biolegend), PE CD34 (BD Biosciences), V500 Sca1 (BD Biosciences), PE/Cy7 CD29 (Biolegend), and Sytox Blue (Thermo Fisher). Dead cells were excluded by uptake of Sytox blue and lineage positive cells were excluded by FITC Streptavidin. Preadipocytes were positively selected for by CD34, Sca1, and CD29 staining. Cells were sorted on a BD FACS Aria cell sorter and analyzed with BD FACSDiva software. Isolated preadipocytes were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10%FBS(RMBIO) and maintained in a 5% CO2 atmosphere and were then immortalized by retroviral expression of the SV40 large T antigen using a hygromycin selection marker. To generate an inducible knockout cell line immortalized cells were then infected with retroviral vector pMSCV CreERT2 using a puromycin selection marker.  For differentiation cells were plated, grown to confluence, and then stimulated with differentiation media (1M dexamethasone, 0.5mM isobutylmethylxanthine, and 5g/mL insulin) for two days. The cells were maintained in 10% FBS DMEM with 5g/mL insulin.

extract_protocol:
cells were harvested with trizol and RNA was prepeed with Qiagen easy miniprep columns
Library preps were made with Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold

treatment_protocol: Cells were treated with either EtOH or 4-hydroxytamoxifen for 24 hours 2 days prior to induction of differentiation

tag: animal age

value: 3 month old mice

tag: differentiation strategy

value: cells were differentiated until day 8 with DMI + 5 nM W1933

value: Tcf7l2 Knock out cells


title: ch12_wt_chipseq_PolII_APR48h

value: lymphoma cell line

tag: genotype/variation

value: WT

tag: treatment


title: 14637X3 EtOH

tag: strain

tag: cell type

value: cells were differentiated until day 8 with DMI + 5 nM W1931

value: wild type


title: 14637X6 4-OH-Tam

value: cells were differentiated until day 8 with DMI + 5 nM W1934

tag: genotype


title: ch12_wt_chipseq_Nipbl_br2

tag: cell line

tag: chip antibody

value: Bethyl, A301-779A


title: 14637X2 EtOH

value: cells were differentiated until day 8 with DMI + 5 nM W1930


title: 14637X1 EtOH

value: cells were differentiated until day 8 with DMI + 5 nM W1929


title: ch12_wt_chipseq_Nipbl_br1


title: 14513X6 WT_TCF7L2_ ChIP_2

data_processing:
Basecalls performed using CASAVA version 1.4
FASTQ sequences were aligned to the mouse genome (UCSC build mm10) with Novocraft Novoalign (version 3.7, http://www.novocraft.com). For multi-mapping alignments, one random alignment was retained.
ChIPSeq calls were made with Macs2 (version 2.1.1.20160309) using a multi-replicate wrapper (https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq, version 2). Duplicate reads were subsampled to a maximum depth of 30 with the application bam_partial_dedup. Fragment coverage was generated with an extension of 200 bp, excluded the mitochondrial chromosome and Encode black list regions, depth-normalized to 1 million reads, and averaged over the replicates. Enrichment was generated with local lambda (small 1000 bp, large 10000 bp). Peaks were called with a q-value threshold of 2, minimum peak length of 250 bp, and a peak gap length of 100 bp.
ChIP peaks were annotated with the R package ChIPSeeker (version 1.12.1) using UCSC knownGene transcript and Ensembl annotation tables.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP samples represent fragment coverage, extended 200 bp, depth normalized to 1 million reads. Input samples represent calculated control_lambda from Macs2.

growth_protocol: Preadipocytes were isolated from minced inguinal white adipose tissue of Tcf7l2 F/F mice by digestion with Collagenase type II (Sigma). Cells from the stromal vascular fraction were then resuspended in HBSS and stained with Biotin CD31 (Biolegend), Biotin CD45 (Biolegend), Biotin Ter-119 (Biolegend), FITC Streptavidin (Biolegend), PE CD34 (BD Biosciences), V500 Sca1 (BD Biosciences), PE/Cy7 CD29 (Biolegend), and Sytox Blue (Thermo Fisher). Dead cells were excluded by uptake of Sytox blue and lineage positive cells were excluded by FITC Streptavidin. Preadipocytes were positively selected for by CD34, Sca1, and CD29 staining. Cells were sorted on a BD FACS Aria cell sorter and analyzed with BD FACSDiva software. Isolated preadipocytes were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10%FBS(RMBIO) and maintained in a 5% CO2 atmosphere and were then immortalized by retroviral expression of the SV40 large T antigen using a hygromycin selection marker. To generate an inducible knockout cell line immortalized cells were then infected with retroviral vector pMSCV CreERT2 using a puromycin selection marker.

extract_protocol:
Lysates were clarified from sonicated nuclei and TCF7L2-DNA complexes were isolated with antibody.
Libraries were prepared according to DNA SMART ChIP-Seq Kit (Takara #634865)  Briefly,  a priming site is first added to the 3’ end of the DNA template using the Terminal Deoxynucleotidyl Transferase. This is followed by annealing of a proprietary DNA SMART Poly(dA) Primer, which anneals to the T-tail added by the Terminal Deoxynucleotidyl Transferase. This primer is then used by the SMARTScribeTM Reverse Transcriptase (RT) to copy the DNA strand. When the SMARTScribe RT reaches the 5’ end of the DNA template, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the newly synthesized DNA. The carefully designed DNA SMART Oligonucleotide base-pairs with these additional non-template nucleotides and creates an extended template, enabling the SMARTScribe RT to continue replicating to the end of the oligonucleotide. Sequencing libraries are then generated by PCR-mediated addition of Illumina adapters using primers compatible with regions on the DNA SMART Poly(dA) Primer and the DNA SMART Oligonucleotide

treatment_protocol: Cells were treated with either EtOH or 500 nM 4-hydroxy-tamoxifen for 24 hours before induction to differntiate with DMEM containing 10% FBS, 1 μM dexamethasone, 0.5 mM isobutylmethylxanthine, and 5 μg/ml insulin, 5 nM GW1929 for 2 days, followed by 5 μg/ml insulin and 5nM GW alone, and cells were harvested on Day 8

value: immortalized primary preadiocytes

tag: passages

value: TCF7L2 (Cell signaling #2569 lot#4)


title: ch12_wt_chipseq_PolIIS5P_APR48h

value: Millipore, 05-623


title: ND, CBL sample 02--01

description:
control CBL sample
CBL 02--01

source_name: CBL sample 02--01

tag: plate

tag: bead chip

value: brain

value: CBL

value: ND


title: 14513X5 WT_TCF7L2_ ChIP_1


title: 14513X4 WT input


title: ch12_wt_chipseq_Med26_br2

value: Cell Signaling Technology, 13641S


title: 14513X3 KO_TCF7L2_ ChIP_2

value: Tcf7l2 KO


title: ND, CBL sample 04--21

description:
control CBL sample
CBL 04--21

source_name: CBL sample 04--21

tag: well position

tag: tissue

value: M


title: 14513X2 KO_TCF7L2_ ChIP_1


title: ND, CBL sample 02--08

description:
control CBL sample
CBL 02--08

source_name: CBL sample 02--08

tag: brain region

tag: gender


title: 14513X1 KO input


title: ch12_wt_chipseq_Med26_br1

value: lymphoma cell line


title: 14637X4 4-OH-Tam

value: 3 month old mice

value: cells were differentiated until day 8 with DMI + 5 nM W1932

value: Tcf7l2 Knock out cells


title: ch12_wt_chipseq_Med26_APR48h

value: WT


title: 12376X9 17 TCF7 KO

description:
HFD 12 weeks
12376F9_1

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 87.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 125 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.16.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

source_name: inguinal white adipose tissue

growth_protocol: TCF7L2F/F and TCF7L2F/F; Adp-Cre mice on C57BL/6 background

extract_protocol:
Tissues were harvested and flash frozen in liquid nitrogen and stored at -80°C and RNA was purified using Qiagen RNeasy mini Kit.
Library preps were made with Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold

treatment_protocol: 65% High Fat Diet for 4 monthes

value: inguinal white adipose tissue

tag: age

value: 6 months

value: Adipose Tcf7l2 KO

tag: diet

value: HFD 16 weeks


title: ND, CBL sample 07--18

description:
control CBL sample
CBL 07--18

source_name: CBL sample 07--18

tag: diagnosis


title: 12376X10 11 TCF7 KO

description:
HFD 12 weeks
12376F10_1


title: ch12_wt_chipseq_input_br2

tag: genotype/variation


title: 12376X8 9 TCF7 KO

description:
HFD 12 weeks
12376F8_1


title: 12376X6 1 TCF7 KO

description:
HFD 12 weeks
12376F6_1


title: ch12_wt_chipseq_input_br1


title: 12376X5 3 TCF7 F/F

description:
HFD 12 weeks
12376F5_1

value: Wild type


title: ND, CBL sample 00--53

description:
control CBL sample
CBL 00--53

source_name: CBL sample 00--53

value: F


title: ND, CBL sample 07--63

description:
control CBL sample
CBL 07--63

source_name: CBL sample 07--63

value: brain


title: ND, CBL sample 08--52

description:
control CBL sample
CBL 08--52

source_name: CBL sample 08--52

value: CBL


title: 12376X3 16 TCF F/F

description:
HFD 12 weeks
12376F3_1


title: ND, CBL sample 07--73

description:
control CBL sample
CBL 07--73

source_name: CBL sample 07--73

value: ND


title: 12376X2 13 TCF7 F/F

description:
HFD 12 weeks
12376F2_1


title: ch12_wt_chipseq_H3K4me3_APR48h

source_name: CH12 B cell line

tag: treatment

value: Abcam, ab8580


title: ch12_wt_chipseq_H3K4me1_br2

value: Abcam, ab8895


title: 12376X1 7 TCF7 F/F

description:
HFD 12 weeks
12376F1_1

tag: strain


title: ND, CBL sample 06--49

description:
control CBL sample
CBL 06--49

source_name: CBL sample 06--49

value: M


title: 4NEP_BM

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1720 2nd Avenue South, NP2540

department: Hematology/Oncology

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 used for basecalling
Raw FASTQ files were trimmed using TrimGalore! Version 0.5.0 with parameters --paired --trim1
Trimmed FASTQ files were then aligned using STAR version 2.5.3 with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
HTSeq count version 0.9.1 with parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 version 1.20.0 was used to normalize and calculate differential expression
Genome_build: GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab-delimited Excel file containing each sample as a column header and rows represent Ensembl Gene ID#s

source_name: LSK cells

growth_protocol: Bone marrow Lin- Sca+ and cKIT+ cells were FACS sorted from cre+ve and cre-ve mice which were induced for CML for a period of 10 weeks.

extract_protocol:
Sequencing libraries were prepared with the SMARTer Ultra Low Input RNA Kit for Sequencing (v4, TaKaRa Clontech, catalog no. 634891) and Nextera XT DNA Library Preparation Kit (96 samples, Illumina, cat no. FC-131-1096).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor stage

value: CML

value: Bone marrow

tag: cell type

value: LSK cells

value: SIRT1 deleted (cre+)


title: ch12_wt_chipseq_H3K4me1_br1

tag: cell line

value: lymphoma cell line

value: WT


title: 4BEP_BM


title: ND, CBL sample 04--64

description:
control CBL sample
CBL 04--64

source_name: CBL sample 04--64


title: 3LEP_BM


title: 1NEP_BM

value: control (cre-)


title: 12376X7 6 TCF7 KO

description:
HFD 12 weeks
12376F7_1

value: inguinal white adipose tissue

value: 6 months

tag: genotype

value: Adipose Tcf7l2 KO


title: 2REP_BM


title: ND, CBL sample 96--30

description:
control CBL sample
CBL 96--30

source_name: CBL sample 96--30


title: 2BEP_BM


title: ND, CBL sample 94--25

description:
control CBL sample
CBL 94--25

source_name: CBL sample 94--25

value: F


title: 4REP_BM


title: ch12_wt_chipseq_H3K27ac_APR48h

tag: chip antibody

value: Abcam. ab4729


title: ch12_wt_chipseq_CTCF_br2

value: Millipore, 07-729


title: ch12_wt_chipseq_CTCF_br1


title: 12376X4 4 TCF7 F/F

description:
HFD 12 weeks
12376F4_1

value: Wild type

value: HFD 16 weeks


title: ND, CBL sample 99--25

description:
control CBL sample
CBL 99--25

source_name: CBL sample 99--25

tag: plate

value: brain

value: CBL

value: ND


title: ch12_Tailless_Hic_br2_tr4

description:
processed data file: ch12_Tailless_Hic_br2_tr4_inter.hic
processed data file: ch12_Tailless_Hic_br2_tr4_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ND, CBL sample 99--31

description:
control CBL sample
CBL 99--31

source_name: CBL sample 99--31

tag: bead chip


title: 2LEP_BM

value: CML

value: Bone marrow


title: Control

city: Guangxi

first: Songqing

last: He

address: No.22 Shuangyong road

country: China

institute: Guangxi Medical University

description: total RNA

data_processing:
Libraries use Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System checking the quality and yield
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, 18nt to 40nt small RNAs were then mapped to mm8 whole genome
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Liver

growth_protocol: Eight- to ten-week-old female mice were fed a control Lieber-DeCarli diet for five days to acclimatize them to a liquid diet, then allowed free access to the Lieber-DeCarli diet containing 5% (v/v) ethanol for 10 days; control groups were pair-fed with an isocaloric control diet. The mice were gavaged with a single dose of ethanol (6 g/kg body weight) or isocaloric dextrin-maltose on the 16th day and euthanized 9 h later.

extract_protocol:
Liver were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: small RNAs profiling of wild-type mice were generated by deep sequencing, using Illumina HiSeq2500.

value: Liver

value: Lieber-DeCarli diet

value: female


title: ch12_Tailless_chipseq_Rad21_br2

value: lymphoma cell line

value: WT

value: Abcam, ab992


title: ch12_Tailless_Hic_br2_tr3

description:
processed data file: ch12_Tailless_Hic_br2_tr3_inter.hic
processed data file: ch12_Tailless_Hic_br2_tr3_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ND, CBL sample 08--90

description:
control CBL sample
CBL 08--90

source_name: CBL sample 08--90

tag: well position

value: M


title: ND, CBL sample 95--38

description:
control CBL sample
CBL 95--38

source_name: CBL sample 95--38

tag: tissue

value: F


title: ch12_Tailless_chipseq_Rad21_br1


title: Et-OH

description: total RNA

value: Lieber-DeCarli diet containing 5% (v/v) ethanol


title: ch12_Tailless_chipseq_polII_br2

value: Abcam, ab817


title: ch12_Tailless_Hic_br2_tr1

description:
processed data file: ch12_Tailless_Hic_br2_tr1_inter.hic
processed data file: ch12_Tailless_Hic_br2_tr1_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ch12_Tailless_chipseq_polII_br1


title: ND, CBL sample 95--27

description:
control CBL sample
CBL 95--27

source_name: CBL sample 95--27

tag: brain region


title: ch12_Tailless_Hic_br1_tr4

description:
processed data file: ch12_Tailless_Hic_br1_tr4_inter.hic
processed data file: ch12_Tailless_Hic_br1_tr4_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ND, CBL sample 95--36

description:
control CBL sample
CBL 95--36

source_name: CBL sample 95--36

tag: gender


title: ch12_Tailless_Hic_br1_tr1

description:
processed data file: ch12_Tailless_Hic_br1_tr1_inter.hic
processed data file: ch12_Tailless_Hic_br1_tr1_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ch12_Tailless_Hic_br1_tr2

description:
processed data file: ch12_Tailless_Hic_br1_tr2_inter.hic
processed data file: ch12_Tailless_Hic_br1_tr2_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ch12_wt_chipseq_PolIIS2P_APR48h

value: Abcam. Ab5095


title: ch12_Tailless_chipseq_Nipbl_br1

value: Bethyl, A301-779A


title: ND, CBL sample 99--47

description:
control CBL sample
CBL 99--47

source_name: CBL sample 99--47

value: brain

tag: age


title: ch12_Tailless_chipseq_Nipbl_br2


title: ch12_wt_chipseq_Rad21_APR60h


title: ch12_Tailless_chipseq_Med26_br2

value: Cell Signaling Technology, 13641S


title: ND, CBL sample 02--24

description:
control CBL sample
CBL 02--24

source_name: CBL sample 02--24

value: CBL

value: ND


title: ch12_wt_chipseq_input_APR60h


title: ch12_Med14Nsmash_chipseq_input_APR60h


title: ch12_Med14Nsmash_chipseq_PolIIS2P_APR48h


title: ch12_Tailless_chipseq_Med26_br1


title: ch12_Tailless_Hic_br2_tr2

description:
processed data file: ch12_Tailless_Hic_br2_tr2_inter.hic
processed data file: ch12_Tailless_Hic_br2_tr2_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ch12_Tailless_chipseq_input_br2


title: ch12_Med24mm25mm_mRNA_c3

description:
mRNA-Seq
mRNA


title: ch12_Tailless_chipseq_input_br1


title: ND, CBL sample 03--26

description:
control CBL sample
CBL 03--26

source_name: CBL sample 03--26


title: ch12_Med14Nsmash_chipseq_H3K4me3_APR48h

value: Abcam, ab8580


title: ch12_Tailless_Hic_br1_tr3

description:
processed data file: ch12_Tailless_Hic_br1_tr3_inter.hic
processed data file: ch12_Tailless_Hic_br1_tr3_inter_30.hic
processed data file: ch12_Tailless_Hic_inter.hic
processed data file: ch12_Tailless_Hic_inter_30.hic


title: ch12_Med24mm25mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: ch12_Tailless_chipseq_H3K4me1_br2

value: Abcam, ab8895


title: ND, CBL sample 02--27

description:
control CBL sample
CBL 02--27

source_name: CBL sample 02--27


title: ND, CBL sample 01--31

description:
control CBL sample
CBL 01--31

source_name: CBL sample 01--31


title: ch12_Med24mm25mm_mRNA_c1

description:
mRNA-Seq
mRNA

source_name: CH12 B cell line


title: ND, CBL sample 00--38

description:
control CBL sample
CBL 00--38

source_name: CBL sample 00--38


title: ch12_Med14Nsmash_chipseq_Rad21_APR60h


title: ch12_Med1mm_mRNA_c3

description:
mRNA-Seq
mRNA


title: ch12_Tailless_chipseq_H3K4me1_br1


title: ch12_Med1mm_mRNA_c4

description:
mRNA-Seq
mRNA


title: ND, CBL sample 03--50

description:
control CBL sample
CBL 03--50

source_name: CBL sample 03--50


title: ch12_Cdk8mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: ch12_Tailless_chipseq_CTCF_br2

value: Millipore, 07-729


title: ch12_Ccncmm_mRNA_c3

description:
mRNA-Seq
mRNA

value: Ccncmm


title: ch12_Cdk8mm_mRNA_c1

description:
mRNA-Seq
mRNA

value: lymphoma cell line


title: ND, CBL sample 08--44

description:
control CBL sample
CBL 08--44

source_name: CBL sample 08--44


title: ch12_Tailless_chipseq_CTCF_br1


title: ch12_Med1mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: ND, CBL sample 05--28

description:
control CBL sample
CBL 05--28

source_name: CBL sample 05--28


title: d12 Adrb2-/- 03

first: J.

middle: David

last: Farrar

address: 5323 Harry Hines Blvd.

department: Immunology

institute: University of Texas Southwestern Medical Center

data_processing:
Quality assessment of the RNA-Seq data was done using NGS-QC-Toolkit.
Reads with more than 30% nucleotide with phred quality scores less than 20 were removed from further analysis.
Quality filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using hisat aligner (v 2.0.1) using default settings except for -library-type = fr-firststrand.
FPKM values were then generated from aligned reads using StringTie(v1.3.2, option -A).
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text with samples as columns and genes as rows, units are provided in FPKM

molecule: polyA RNA

source_name: Purified Clone4-transgenic CD8+ T cells

extract_protocol:
After purification of CD8+ T cells, total RNA was isolated using ARCTURUS® PicoPure® RNA Isolation Kit or Zymogen Quick-RNA™ MiniPrep according to manufacturer's protocols
50 ng of total RNA was used to prepare polyA RNA libraries for Illumina sequencing using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7530S, #E7490S, #E7335S, and using Axygen #MAG-PCR-CL-5) according to manufacturer's protocol ("for use with NEBNext Poly(A) mRNA Magnetic Isolation Module, NEB #E7490 and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530)")

treatment_protocol: Purified naïve CD8+ T cells from Adrb2+/+ or Adrb2-/- Clone4-transgenic mice were transferred intravenously into naïve Balb/cJ male mice at a 1:1 mix (1,000 cells each) and the following day the mice were infected with 10^6 PFU of recombinant Vesicular Stomatitis Virus expressing Influenza PR/8 hemaglutining (VSV-HA). The cells were then FACS-purified at days 4, 5, 7, and 12 post infection, or before transfer for day 0.

value: naive Balb/cJ

tag: agent

tag: days post-infection

tag: index

value: CTTGTA


title: ch12_Ccncmm_mRNA_c1

description:
mRNA-Seq
mRNA

tag: genotype/variation


title: ch12_Ccncmm_mRNA_c2

description:
mRNA-Seq
mRNA


title: ch12_Med14Nsmash_chipseq_PolII_APR48h

tag: treatment


title: ND, CBL sample 06--08

description:
control CBL sample
CBL 06--08

source_name: CBL sample 06--08

value: M

tag: diagnosis


title: d12 Adrb2+/+ 03

tag: strain

value: 10^6 PFU of recombinant Vesicular Stomatitis Virus expressing Influenza PR/8 hemaglutining (VSV-HA)

value: CAGATC


title: d12 Adrb2-/- 02

value: GCCAAT


title: ND, CBL sample 05--10

description:
control CBL sample
CBL 05--10

source_name: CBL sample 05--10


title: d12 Adrb2-/- 01

value: TGACCA


title: ch12_Med1mm_mRNA_c2

description:
mRNA-Seq
mRNA

tag: cell line

tag: cell type


title: d12 Adrb2+/+ 02

tag: genotype

value: ACAGTG


title: ch12_Med14Nsmash_chipseq_H3K27ac_APR48h

tag: chip antibody

value: Abcam. ab4729


title: ch12_Med14Nsmash_chipseq_Med26_APR48h

value: Cell Signaling Technology, 13641S


title: d12 Adrb2+/+ 01

value: CGATGT


title: d7 Adrb2-/- 03


title: ND, CBL sample 06--15

description:
control CBL sample
CBL 06--15

source_name: CBL sample 06--15

tag: plate

tag: bead chip

value: brain

value: CBL

value: F

value: ND


title: d7 Adrb2-/- 01


title: ND, CBL sample 05--18

description:
control CBL sample
CBL 05--18

source_name: CBL sample 05--18

tag: well position

tag: tissue


title: ch12_wt_mRNA_c9

description:
mRNA-Seq
mRNA

value: WT


title: ch12_Med14Nsmash_chipseq_PolIIS5P_APR48h

value: lymphoma cell line

value: Millipore, 05-623


title: ND, CBL sample 00--34

description:
control CBL sample
CBL 00--34

source_name: CBL sample 00--34

tag: brain region

tag: gender


title: d7 Adrb2+/+ 03

value: naive Balb/cJ

tag: agent


title: ND, CBL sample 05--14

description:
control CBL sample
CBL 05--14

source_name: CBL sample 05--14

tag: age


title: d7 Adrb2+/+ 02

tag: days post-infection

tag: index


title: d5 Adrb2-/- 03

value: CTTGTA


title: d7 Adrb2-/- 02

value: 10^6 PFU of recombinant Vesicular Stomatitis Virus expressing Influenza PR/8 hemaglutining (VSV-HA)


title: ch12_wt_mRNA_c7

description:
mRNA-Seq
mRNA

tag: genotype/variation


title: ND, CBL sample 96--22

description:
control CBL sample
CBL 96--22

source_name: CBL sample 96--22

value: M

tag: diagnosis


title: d7 Adrb2+/+ 01

tag: strain


title: ND, CBL sample 94--17

description:
control CBL sample
CBL 94--17

source_name: CBL sample 94--17


title: ch12_wt_mRNA_c8

description:
mRNA-Seq
mRNA

tag: cell line


title: d5 Adrb2-/- 02

value: GCCAAT


title: d5 Adrb2-/- 01

value: TGACCA


title: d5 Adrb2+/+ 03

value: CAGATC


title: ND, CBL sample 94--30

description:
control CBL sample
CBL 94--30

source_name: CBL sample 94--30


title: d5 Adrb2+/+ 01


title: d5 Adrb2+/+ 02

value: ACAGTG


title: ch12_wt_mRNA_c5

description:
mRNA-Seq
mRNA

tag: cell type


title: ch12_wt_mRNA_c4

description:
mRNA-Seq
mRNA


title: ND, CBL sample 99--54

description:
control CBL sample
CBL 99--54

source_name: CBL sample 99--54


title: d4 Adrb2-/- 01

tag: genotype


title: d4 Adrb2-/- 02


title: d4 Adrb2+/+ 02


title: ND, CBL sample 99--27

description:
control CBL sample
CBL 99--27

source_name: CBL sample 99--27


title: ch12_wt_mRNA_c2

description:
mRNA-Seq
mRNA

source_name: CH12 B cell line


title: ch12_wt_mRNA_c1

description:
mRNA-Seq
mRNA


title: d0 Adrb2-/- 03

description: Cells used for transfer prior to infection


title: ND, CBL sample 03--63

description:
control CBL sample
CBL 03--63

source_name: CBL sample 03--63


title: ch12_Med9mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: d0 Adrb2-/- 01


title: ch12_Med9mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: d0 Adrb2+/+ 03


title: d0 Adrb2+/+ 02


title: ch12_wt_mRNA_c6

description:
mRNA-Seq
mRNA


title: ND, CBL sample 99--22

description:
control CBL sample
CBL 99--22

source_name: CBL sample 99--22


title: ND, CBL sample 99--58

description:
control CBL sample
CBL 99--58

source_name: CBL sample 99--58


title: ND, CBL sample 01--46

description:
control CBL sample
CBL 01--46

source_name: CBL sample 01--46


title: d4 Adrb2-/- 03

source_name: Purified Clone4-transgenic CD8+ T cells


title: d0 Adrb2+/+ 01


title: ch12_Med29mm_mRNA_sg2sc3

description:
mRNA-Seq
mRNA


title: ND, CBL sample 08--23

description:
control CBL sample
CBL 08--23

source_name: CBL sample 08--23


title: d4 Adrb2+/+ 03


title: ch12_Med29mm_mRNA_sg1sc3

description:
mRNA-Seq
mRNA


title: ND, CBL sample 00--03

description:
control CBL sample
CBL 00--03

source_name: CBL sample 00--03


title: ch12_Med29mm_mRNA_sg2sc1

description:
mRNA-Seq
mRNA


title: ND, CBL sample 95--30

description:
control CBL sample
CBL 95--30

source_name: CBL sample 95--30


title: H1_MSX2_KO_10_2

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: H1 after MSX2-knockout derived CD31+ cells collected at day 8 after hematopoietic differentiation

growth_protocol: H1 with or without HAND1 overexpression were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 2 days.

extract_protocol:
H1 drived cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line  background

tag: timepoint


title: ch12_Med29mm_mRNA_sg1sc2

description:
mRNA-Seq
mRNA


title: H1_MSX2_KO_7_2

value: at day 8 after hematopoietic differentiation


title: H1_WT_2

source_name: H1 derived cells collected at day 8 after hematopoietic differentiation

value: wild type


title: d4 Adrb2+/+ 01

value: CGATGT


title: ND, CBL sample 06--35

description:
control CBL sample
CBL 06--35

source_name: CBL sample 06--35

tag: plate

tag: bead chip

value: brain

value: CBL


title: ch12_wt_mRNA_c3

description:
mRNA-Seq
mRNA


title: H1_MSX2_KO_10_1


title: ch12_Med29mm_mRNA_sg2sc2

description:
mRNA-Seq
mRNA


title: ND, CBL sample 04--62

description:
control CBL sample
CBL 04--62

source_name: CBL sample 04--62

tag: well position

tag: tissue

value: F

value: ND


title: ch12_Med26mm_mRNA_c1s2

description:
mRNA-Seq
mRNA

value: lymphoma cell line


title: H1_MSX2_KO_7_1


title: ND, CBL sample 04--52

description:
control CBL sample
CBL 04--52

source_name: CBL sample 04--52

tag: brain region

tag: gender


title: H1_WT_1


title: IgG_Low_glucose_ChIPSeq

city: Shanghai

first: Zhaoyu

last: Qin

address: Room 815, Mingdao Building, 131 Dong'an Road

department: Institutes of Biomedical Sciences

institute: Fudan University

data_processing:
Basecalls performed using illumia bcl2fastq2.17
Data were filtered using the following specifications: remove adapter(skewer);  remove low quality reads(FastX-Toolkit,  more than 20% of the bases with Q ≤ 20, Q = -10log[error_ratio]);  remover N bases
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie 1.1.2
peaks were called using MACS14
genome build: hg19
processed data files format and content: Differential binding analysis of peaks was performed by R package DiffBind and differential-binding peaks were annotated by HOMER. The information was listed in the csv files.

source_name: hepatocarcinoma cells

growth_protocol: Cells were cultured in High Glucose Dulbecco's Modified Eagle’s Medium (DMEM) (SH30022.01, Thermo Scientific, Massachusetts, USA) supplemented with 10% fetal bovine serum (SS0415, Biochrome, Berlin, Germany) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and HNF4A-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: To establish the overexpression stable cell lines, the full-length cDNA was sub-cloned into pCDH-CMV-MCS-EF1-puro vector (System Biosciences). The viruses were packaged in 293 T cells using Lipofectamine 2000, and the virus DNA was transduced into HCCLM3 cells.

value: hepatocarcinoma cells


title: HNF4A_Low_glucose_ChIPSeq


title: ND, CBL sample 06--05

description:
control CBL sample
CBL 06--05

source_name: CBL sample 06--05

tag: age


title: d0 Adrb2-/- 02

value: naive Balb/cJ

tag: agent

tag: days post-infection


title: HNF4A_High_glucose_ChIPSeq


title: ND, CBL sample 07--11

description:
control CBL sample
CBL 07--11

source_name: CBL sample 07--11


title: IgG_High_glucose_ChIPSeq


title: ch12_Med26mm_mRNA_c1

description:
mRNA-Seq
mRNA

source_name: CH12 B cell line

tag: genotype/variation


title: ch12_Med26mm_mRNA_c1s1

description:
mRNA-Seq
mRNA


title: ND, CBL sample 05--12

description:
control CBL sample
CBL 05--12

source_name: CBL sample 05--12

tag: diagnosis


title: H3K4Ac_FADU_hypoxia

city: Hangzhou

first: Jian-Qiu

last: Wang

state: Zhejiang

address: No. 16 Xuelin Street

department: Basic Medical Science

institute: Hangzhou Normal University

data_processing:
Raw sequencing reads were mapped to the human genome
(assembly hg19) using Bowtie v2.0.4 algorithm . The
binding regions for H3K4ac were identified by MACS v1.4.2 algorithm with
default parameter.
Genome_build: hg19
Supplementary_files_format_and_content: bed  file for the peak information

source_name: FADU cells

growth_protocol: FADU cell line (ATCC) was maintained in RPMI-1640 media (Invitrogen) supplemented with 10% fetal bovine serum (FBS, GIBCO), penicillin G (100 U/mL), streptomycin (100 µg/mL) in a humidified atmosphere of 5% CO2 at 37°C. Cells were passed with Trypsin/EDTA (Invitrogen) when they reached 80% to 90% confluence.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-H3K4Ac (#17-10050, CS204376, Millipore) antibody or rabbit normal IgG (#17-10050, PP64B, Millipore) .
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For hypoxia, cells were cultured in multi-gas incubators (Astec, Tokyo, Japan). Nitrogen gas was supplied to the chambers in order to induce a reduced percentage (1%) of oxygen for 18 hours. For normoxia, cells were cultured in incubators containing 5% CO2 and atmospheric concentration of O2, approximately 20% O2.

value: pharynx

tag: morphology

value: epithelial

tag: disease

value: squamous cell carcinoma


title: Input_FADU


title: ND, CBL sample 06--02

description:
control CBL sample
CBL 06--02

source_name: CBL sample 06--02

extract_protocol: Tissue was incubated in lysis buffer (100 mM Tris HCL pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 100 ug/mL Proteinase K) overnight at 55°C.  and disassembled using a pestle. Disassociated tissue was treated with 4 uL of Rnase A for 30 minutes at RT and then treated with ethanol overnight at -20°C. 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

value: M


title: H3K4Ac_FADU_normoxia


title: ch12_Med25mm_mRNA_c2

description:
mRNA-Seq
mRNA

tag: cell line

tag: cell type


title: ch12_Med25mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: ch12_Med29mm_mRNA_sg1sc1

description:
mRNA-Seq
mRNA


title: ch12_Med24mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: ch12_Med24mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: ND, CBL sample 92--14

description:
control CBL sample
CBL 92--14

source_name: CBL sample 92--14


title: ND, CBL sample 95--03

description:
control CBL sample
CBL 95--03

source_name: CBL sample 95--03


title: ch12_Med23mm24mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: ch12_Med23mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_245]

type: RNA

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Expression levels were normalized with Actb.
A -deltaCt value normazized to Actb is used as a gene expression level for each gene.

label: FAM

organism: Rattus norvegicus

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

label_protocol: Single cell capture, lysis and RT pre-amplification experiments were performed using C1 Auto Prep System (Fluidigm) according to the manufacturer's instructions. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer.

extract_protocol: Adult hepatocytes were isolated from Wistar rats by two-step collagenase perfusion. NPCs were harvested from the undigested remnant tissue by further digestiong with collagenase-hyaluronidase.

tag: strain

value: Wistar

value: 6 week old

tag: Sex

value: Female


title: 4c Hepatocytes [Hep_4c_239]


title: 4c Hepatocytes [Hep_4c_238]


title: ND, CBL sample 06--03

description:
control CBL sample
CBL 06--03

data_processing:
Data was analyzed in R (version 3.4.2) using minfi (1.23.4) and SVA (3.26.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis. NOOB and functional normalization were performed using the minfi package according author guidelines. Confounding variables were detected using SVA and, alongside batch/plate effects, were accounted for using the ComBat algorithm.
Normalized Average betas included as supplementary files (processedSamples*.txt) on the Series record.
Methylated and unmethylated signal intensities included as supplementary files (signalIntensities*.txt) on the Series record.

source_name: CBL sample 06--03

tag: plate


title: 4c Hepatocytes [Hep_4c_244]


title: 4c Hepatocytes [Hep_4c_242]


title: 4c Hepatocytes [Hep_4c_237]


title: 4c Hepatocytes [Hep_4c_236]


title: ND, CBL sample 97--02

description:
control CBL sample
CBL 97--02

source_name: CBL sample 97--02

tag: bead chip


title: 4c Hepatocytes [Hep_4c_241]


title: 4c Hepatocytes [Hep_4c_243]


title: 4c Hepatocytes [Hep_4c_234]


title: 4c Hepatocytes [Hep_4c_235]


title: ND, CBL sample 96--39

description:
control CBL sample
CBL 96--39

source_name: CBL sample 96--39

tag: well position


title: 4c Hepatocytes [Hep_4c_240]


title: ND, CBL sample 99--29

description:
control CBL sample
CBL 99--29

source_name: CBL sample 99--29

tag: tissue


title: ch12_Med23mm24mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_233]


title: ch12_Med23mm24mm25mm_mRNA_sc2

description:
mRNA-Seq
mRNA


title: Cortex-anti-let7

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: Bioconductor software, RMA normalization log2

label: biotin

source_name: cortex and hippocampus

label_protocol: Total RNA (2 ug) was labeled and hybridized to the Mouse Genome 430 2.0 arrays and hybridized according to manufacturer’s instructions.

extract_protocol: Total RNA was extracted with TriZol reagent (Invitrogen) according to a standard protocol.

value: cortex

tag: treatment


title: ch12_Med23mm24mm25mm_mRNA_sc1

description:
mRNA-Seq
mRNA


title: ND, CBL sample 06--61

description:
control CBL sample
CBL 06--61

source_name: CBL sample 06--61

tag: brain region

tag: gender


title: Hippo-PBS

value: hippocampus

value: PBS


title: ch12_Med23mm24mm25mm16mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: ND, CBL sample 08--85

description:
control CBL sample
CBL 08--85

source_name: CBL sample 08--85

value: brain

tag: age


title: ND, CBL sample 97--53

description:
control CBL sample
CBL 97--53

source_name: CBL sample 97--53

value: CBL


title: Hippo-anti-let7


title: 4c Hepatocytes [Hep_4c_226]


title: Cortex-PBS


title: 4c Hepatocytes [Hep_4c_227]


title: 4c Hepatocytes [Hep_4c_231]


title: ch12_Med23mm24mm25mm16mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: ch12_Med23mm24mm25mm15mm16mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_229]


title: AD, CBL sample 03--59

description:
Alzheimer's CBL sample
CBL 03--59

source_name: CBL sample 03--59

value: AD


title: 4c Hepatocytes [Hep_4c_228]


title: ch12_Med23mm24mm25mm15mm16mm_mRNA_c3

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_232]


title: 4c Hepatocytes [Hep_4c_222]


title: 4c Hepatocytes [Hep_4c_230]


title: ch12_Med20mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: AD, CBL sample 97--20

description:
Alzheimer's CBL sample
CBL 97--20

source_name: CBL sample 97--20

value: F


title: 4c Hepatocytes [Hep_4c_221]


title: 4c Hepatocytes [Hep_4c_220]


title: AD, CBL sample 03--14

description:
Alzheimer's CBL sample
CBL 03--14

source_name: CBL sample 03--14


title: ch12_Med23mm24mm25mm15mm16mm_mRNA_c2

description:
mRNA-Seq
mRNA

source_name: CH12 B cell line

value: lymphoma cell line


title: 4c Hepatocytes [Hep_4c_225]


title: AD, CBL sample 94--20

description:
Alzheimer's CBL sample
CBL 94--20

source_name: CBL sample 94--20


title: 4c Hepatocytes [Hep_4c_219]


title: 4c Hepatocytes [Hep_4c_224]


title: AD, CBL sample 00--12

description:
Alzheimer's CBL sample
CBL 00--12

source_name: CBL sample 00--12


title: ch12_Med20mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_216]


title: 4c Hepatocytes [Hep_4c_223]


title: AD, CBL sample 00--37

description:
Alzheimer's CBL sample
CBL 00--37

source_name: CBL sample 00--37


title: 4c Hepatocytes [Hep_4c_218]


title: 4c Hepatocytes [Hep_4c_214]


title: ch12_Med19mm_mRNA_sg2c2

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_213]


title: 4c Hepatocytes [Hep_4c_217]


title: AD, CBL sample 01--21

description:
Alzheimer's CBL sample
CBL 01--21

source_name: CBL sample 01--21


title: 4c Hepatocytes [Hep_4c_215]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: ch12_Med19mm_mRNA_sg1c3

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_212]


title: ch12_Med19mm_mRNA_sg1c2

description:
mRNA-Seq
mRNA


title: ch12_Med19mm_mRNA_sg2c1

description:
mRNA-Seq
mRNA


title: AD, CBL sample 07--71

description:
Alzheimer's CBL sample
CBL 07--71

source_name: CBL sample 07--71


title: 4c Hepatocytes [Hep_4c_210]


title: ch12_Med19mm_mRNA_sg1c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_209]


title: 4c Hepatocytes [Hep_4c_208]


title: AD, CBL sample 92--16

description:
Alzheimer's CBL sample
CBL 92--16

source_name: CBL sample 92--16


title: AD, CBL sample 97--33

description:
Alzheimer's CBL sample
CBL 97--33

source_name: CBL sample 97--33


title: ch12_Med16mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_206]


title: ch12_Med16mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_207]


title: AD, CBL sample 07--50

description:
Alzheimer's CBL sample
CBL 07--50

source_name: CBL sample 07--50


title: 4c Hepatocytes [Hep_4c_205]


title: AD, CBL sample 98--06

description:
Alzheimer's CBL sample
CBL 98--06

source_name: CBL sample 98--06


title: AD, CBL sample 96--21

description:
Alzheimer's CBL sample
CBL 96--21

source_name: CBL sample 96--21


title: ch12_Med15mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_204]


title: AD, CBL sample 08--48

description:
Alzheimer's CBL sample
CBL 08--48

source_name: CBL sample 08--48


title: 4c Hepatocytes [Hep_4c_202]


title: ch12_Med15mm16mm_mRNA_c3

description:
mRNA-Seq
mRNA


title: AD, CBL sample 97--27

description:
Alzheimer's CBL sample
CBL 97--27

source_name: CBL sample 97--27


title: 4c Hepatocytes [Hep_4c_200]


title: 4c Hepatocytes [Hep_4c_201]


title: ch12_Med15mm16mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_211]


title: AD, CBL sample 97--22

description:
Alzheimer's CBL sample
CBL 97--22

source_name: CBL sample 97--22


title: 4c Hepatocytes [Hep_4c_199]


title: 4c Hepatocytes [Hep_4c_198]


title: 4c Hepatocytes [Hep_4c_197]


title: AD, CBL sample 98--07

description:
Alzheimer's CBL sample
CBL 98--07

source_name: CBL sample 98--07


title: 4c Hepatocytes [Hep_4c_196]


title: 4c Hepatocytes [Hep_4c_195]


title: AD, CBL sample 95--33

description:
Alzheimer's CBL sample
CBL 95--33

source_name: CBL sample 95--33


title: ch12_Med13Lmm_mRNA_c3

description:
mRNA-Seq
mRNA

source_name: CH12 B cell line


title: ch12_Med13Lmm_mRNA_c2

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_194]


title: AD, CBL sample 05--05

description:
Alzheimer's CBL sample
CBL 05--05

source_name: CBL sample 05--05


title: 4c Hepatocytes [Hep_4c_192]


title: ch12_Med13Lmm_mRNA_c1

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_191]


title: AD, CBL sample 04--32

description:
Alzheimer's CBL sample
CBL 04--32

source_name: CBL sample 04--32


title: 4c Hepatocytes [Hep_4c_193]


title: 4c Hepatocytes [Hep_4c_203]


title: 4c Hepatocytes [Hep_4c_190]


title: ch12_Cdk19mm_mRNA_sc3

description:
mRNA-Seq
mRNA


title: AD, CBL sample 06--58

description:
Alzheimer's CBL sample
CBL 06--58

source_name: CBL sample 06--58


title: 4c Hepatocytes [Hep_4c_189]


title: ch12_Cdk19mm_mRNA_sc2

description:
mRNA-Seq
mRNA


title: 4c Hepatocytes [Hep_4c_188]


title: 4c Hepatocytes [Hep_4c_186]


title: AD, CBL sample 06--60

description:
Alzheimer's CBL sample
CBL 06--60

source_name: CBL sample 06--60


title: AD, CBL sample 05--25

description:
Alzheimer's CBL sample
CBL 05--25

source_name: CBL sample 05--25


title: 4c Hepatocytes [Hep_4c_187]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: 4c Hepatocytes [Hep_4c_184]


title: ch12_Med15mm16mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: D.f. extract_TLR3MAVS-DKO6

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description:
Treated_DKO6
TLR3MAVS knockout mouse treated with D.f. extract

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: TLR3MAVS double knockout mouse lung

growth_protocol: 6 to 8 weeks old mouse lungs

extract_protocol:
TRIZol total RNA isolation
Total RNA samples about 1-2 microgram were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 100bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from the lung of  wild type or TLR3MAVS double knockout mice  that were treated with PBS or  HDM (D.f.) extract for  14-16 hours

tag: strain background

value: TLR3MAVS double knockout

tag: treated with

value: HDM (D.f.) extract for 14-16 hrs

value: lung


title: 4c Hepatocytes [Hep_4c_185]


title: ch12_Cdk19mm_mRNA_sc1

description:
mRNA-Seq
mRNA

tag: genotype/variation


title: AD, CBL sample 98--36

description:
Alzheimer's CBL sample
CBL 98--36

source_name: CBL sample 98--36

tag: diagnosis


title: AD, CBL sample 99--21

description:
Alzheimer's CBL sample
CBL 99--21

source_name: CBL sample 99--21


title: D.f. extract_TLR3MAVS-DKO5

description:
Treated_DKO5
TLR3MAVS knockout mouse treated with D.f. extract


title: 4c Hepatocytes [Hep_4c_182]


title: D.f. extract_wild type4

description:
Treated_WT4
wild type mouse treated with D.f. extract

source_name: wild type B6 mouse lung

value: wild type


title: 4c Hepatocytes [Hep_4c_179]


title: 4c Hepatocytes [Hep_4c_178]


title: 4c Hepatocytes [Hep_4c_175]


title: AD, CBL sample 99--34

description:
Alzheimer's CBL sample
CBL 99--34

source_name: CBL sample 99--34


title: 4c Hepatocytes [Hep_4c_176]


title: D.f. extract_wild type3

description:
Treated_WT3
wild type mouse treated with D.f. extract


title: 4c Hepatocytes [Hep_4c_177]


title: AD, CBL sample 01--04

description:
Alzheimer's CBL sample
CBL 01--04

source_name: CBL sample 01--04


title: PBS-TLR3MAVS-DKO-2

description:
Saline_DKO2
TLR3MAVS knockout mouse treated with PBS

value: PBS-control


title: 4c Hepatocytes [Hep_4c_174]


title: PBS-wild type-1

description:
Saline_WT1
wild type mouse treated with PBS


title: 4c Hepatocytes [Hep_4c_172]


title: 4c Hepatocytes [Hep_4c_173]


title: AD, CBL sample 99--61

description:
Alzheimer's CBL sample
CBL 99--61

source_name: CBL sample 99--61

value: M


title: AD, CBL sample 99--33

description:
Alzheimer's CBL sample
CBL 99--33

source_name: CBL sample 99--33


title: 4c Hepatocytes [Hep_4c_183]

value: Wistar


title: 211

city: Basel-Sadt

first: Jordan

middle: Gabriel

last: Loeliger

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University of Basel

data_processing:
RNA seq reads were mapped to the human genome assembly using RNA STAR
Mapping quality was assessed by QuasR
Genome_build: hg38
Supplementary_files_format_and_content: Excel file with all raw read counts and differentially expressed genes

source_name: total PPBL B cells

extract_protocol:
PBMCs were isolated from buffy coats. B cells were enriched by positive selection anti-CD19 beads. Total RNA was isolated and riobsomal RNA depleted. NEBNext Ultra Library prep kit was used for Illumina sequencing using a HiSeq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PPBL patient

value: blood

value: total PPBL B cells

tag: cell markers

value: total, magnetically enriched CD19


title: AD, CBL sample 99--56

description:
Alzheimer's CBL sample
CBL 99--56

source_name: CBL sample 99--56


title: D.f. extract with RNaseIII-6

description:
DF_RsePOS6
wild type mouse treated with D.f. extract plus Rnase III

value: HDM (D.f.) extract with RNaseIII for 14-16 hrs


title: 210


title: D.f. extract with RNaseIII-5

description:
DF_RsePOS5
wild type mouse treated with D.f. extract plus Rnase III


title: AD, CBL sample 00--11

description:
Alzheimer's CBL sample
CBL 00--11

source_name: CBL sample 00--11

value: brain


title: 4c Hepatocytes [Hep_4c_171]

value: 6 week old

value: Female


title: 4c Hepatocytes [Hep_4c_180]


title: AD, CBL sample 01--09

description:
Alzheimer's CBL sample
CBL 01--09

source_name: CBL sample 01--09

value: CBL

value: F

value: AD


title: D.f. extract without RNaseIII-4

description:
DF_RseNEG4
wild type mouse treated with D.f. extract

value: HDM (D.f.) extract without RNaseIII for 14-16 hrs


title: D.f. extract without RNaseIII-3

description:
DF_RseNEG3
wild type mouse treated with D.f. extract

value: lung


title: 4c Hepatocytes [Hep_4c_181]


title: 204

source_name: marginal zone like B cells

value: healthy control

value: marginal zone like B cells


title: AD, CBL sample 01--32

description:
Alzheimer's CBL sample
CBL 01--32

source_name: CBL sample 01--32


title: 209


title: 4c Hepatocytes [Hep_4c_169]


title: 202


title: 4c Hepatocytes [Hep_4c_170]


title: PBS-control-2

description:
SAL_2
wild type mouse treated with PBS

value: wild type

value: PBS-control


title: PBS-control-1

description:
SAL_1
wild type mouse treated with PBS


title: AD, CBL sample 03--36

description:
Alzheimer's CBL sample
CBL 03--36

source_name: CBL sample 03--36

value: M


title: 203

value: blood


title: AD, CBL sample 07--12

description:
Alzheimer's CBL sample
CBL 07--12

source_name: CBL sample 07--12


title: 4c Hepatocytes [Hep_4c_167]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

value: Wistar


title: 4c Hepatocytes [Hep_4c_168]


title: 4c Hepatocytes [Hep_4c_165]


title: 4c Hepatocytes [Hep_4c_166]


title: AD, CBL sample 08--15

description:
Alzheimer's CBL sample
CBL 08--15

source_name: CBL sample 08--15


title: AD, CBL sample 03--32

description:
Alzheimer's CBL sample
CBL 03--32

source_name: CBL sample 03--32


title: PC3 PXNsiRNA_3

city: Rochester

first: Stephen

middle: R

last: Hammes

state: NY

address: 601 Elmwood Ave, Box 693

department: Medicine

institute: University of Rochester

description:
Androgen Receptor negative bone metastasis derived prostate cancer cell line
Transfected with paxillin-targeted siRNAfor 72 hours, replicate 3
5c

data_processing:
Data Formatting - bcltofastq-1.8.4
CLEANING - seqclean-x86_64 (seqclean & cln2qual), fastqc-0.10.1, fastx_toolkit_0.0.13 (fastq_quality_trimmer)
MAPPING - SHRiMP_2_2_3
DIFFERENTIAL EXP. - cufflinks-2.0.2.Linux_x86_64 (cuffdiff2)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw count and FPKM values for each sample

source_name: prostate cancer cell line

growth_protocol: PC3 cells was growing in RPMI 1640 media supplied with 10% FBS and 1% penicillin and strepavidin.

extract_protocol:
mRNA was isolated using Qiagen Rneasy Plus Mini Kit
Illumina TruSeq mRNA

treatment_protocol: PC3 cells were transfected with either Non-specific siRNA or Paxillin-targeted siRNA for  72 hours

tag: cell line

tag: transfection

value: paxillin-targeted siRNA


title: PC3 PXNsiRNA_2

description:
Androgen Receptor negative bone metastasis derived prostate cancer cell line
Transfected with paxillin-targeted siRNAfor 72 hours, replicate 2
4c


title: PC3 PXNsiRNA_1

description:
Androgen Receptor negative bone metastasis derived prostate cancer cell line
Transfected with paxillin-targeted siRNAfor 72 hours, replicate 1
2c


title: 4c Hepatocytes [Hep_4c_163]

tag: strain


title: 4c Hepatocytes [Hep_4c_164]

tag: Sex


title: PC3 NSPsiRNA_3

description:
Androgen Receptor negative bone metastasis derived prostate cancer cell line
Transfected with Non-specific siRNAfor 72 hours, replicate 3
5a

value: non-specific siRNA


title: AD, CBL sample 05--39

first: Danielle

last: Brokaw

address: Biodesign Institute Building C, 1001 S McAllister Ave

institute: Arizona State University

description:
Alzheimer's CBL sample
CBL 05--39

source_name: CBL sample 05--39

tag: plate

value: brain


title: PC3 NSPsiRNA_2

description:
Androgen Receptor negative bone metastasis derived prostate cancer cell line
Transfected with Non-specific siRNAfor 72 hours, replicate 2
4a


title: AD, CBL sample 04--33

description:
Alzheimer's CBL sample
CBL 04--33

source_name: CBL sample 04--33

tag: bead chip


title: 4c Hepatocytes [Hep_4c_161]

value: 6 week old


title: 201

tag: cell type


title: AD, CBL sample 03--54

description:
Alzheimer's CBL sample
CBL 03--54

source_name: CBL sample 03--54

tag: well position

tag: tissue