title: Pdx1_p33tpp_01: p33t_pp_rep1

city: Neuherberg

institute: Helmholtz Zentrum München German Research Center for Environmental Health

source_name: PDX1P33T/+ iPS derived pancreatic precursor cells, biological replicate 1


title: Diffuse Large B-cell Lymphoma patient DLBCL_080

status: Public on Jun 19 2019

type: RNA

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

country: USA

institute: MD Anderson Cancer Center

hyb_protocol: According to affymetrix protocol

scan_protocol: According to affymetrix protocol

data_processing: Raw cel files were RMA normalized using the ExpressionFileCreator module of GenePattern31, and quality checked for batch effects by unsupervised clustering of the 3,000 most variably expressed genes across the dataset.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: biopsy

label_protocol: According to affymetrix protocol

extract_protocol: Trizol or Qiagen RNA extraction kit

tag: diagnosis

value: Diffuse Large B-cell Lymphoma

tag: tissue

value: tumor specimen


title: H3K27ac_SNA_ChIP_rep1

type: SRA

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

description:
H3K27ac_SNA1
H3K27ac_SNA1_CAGATC

library_source: genomic

data_processing:
DNA fragments were aligned to the mm10 reference genome and processed using the Kundaje lab's AQUAS ChIPseq and ATACseq pipelines (https://github.com/kundajelab/chipseq_pipeline and https://github.com/kundajelab/atac_dnase_pipelines).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file plotting the p-value of enrichment over input (ChIPseq) or background (ATACseq) for each condition (replicates pooled together)
Supplementary_files_format_and_content: Peak file showing the peaks identified in multiple replicates of each condition using the 'naïve overlapping' approach from the Kundaje lab's AQUAS ChIPseq and ATACseq pipelines. Encode mm10 blacklist regions have been filtered out.

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
ChIPseq: Chromatin IP was performed according to a previously published protocol (Schmidt et al., 2009) with a few adjustments. Briefly, sciatic L4-L6 DRGs (10 mice/sample) were extracted 24 hours after surgery and crushed using an automatic pestle and chemically cross-linked with a 1% formaldehyde solution containing 50mM Hepes-KOH pH7.5, 100mM NaCl, 1mM EDTA and 0.5mM EDTA, for 15 minutes at room temperature. Nuclear extracts were then sonicated for 30 min using a Bioruptor (Diagenode) and successful chromatin shearing (200-800 bp) was confirmed by agarose gel analysis. Immunoprecipitation was performed overnight with Protein G Dynabeads (Invitrogen) bound to 10 μg of of H3K27ac (Ab4729, Abcam), or H3K9ac (Ab10812, Abcam), or H3K27me3 (C15410195, Diagenode) antibodies. After washing, elution and reverse crosslinking, DNA was treated with RNAse A and Proteinase K and purified using Qiagen PCR purification columns. The concentration of the recovered DNA was quantified with Picogreen assay and the enrichment of the immunoprecipitate calculated with respect to the input and IgG.
ChIPseq: Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit from Illumina (NEW ENGLAND BioLabs) following the manufacturer’s protocol. Briefly, 2 ng of Input and IP DNA were end repaired and adaptor ligated, using a dilution of 1:20 of adaptors. Samples were cleaned to remove unligated adaptors and size selection was performed to select and enrich fragments of 200bp in size. Libraries were amplified by PCR using multiplex oligo following manufacturer’s protocol. Prior to sequencing, libraries were run on an Agilent Bioanalyser for size and quality control checking. Sequencing was performed in an Illumina HiSeq2000, generating 50bp single ended reads.
ATACseq: ATAC-seq was performed according to a previously published protocol (Buenrostro, 2015; Buenrostro, 2013). Briefly, sciatic L4-L6 DRGs (1 mouse/sample) were extracted 24 hours after surgery and crushed using an automatic pestle in Lysis buffer containing 0.1% Igepal (Sigma). 50000 nuclei were used for the transposition reaction with Nextera Tn5 Transposase (Illumina, FC-121-1030). The product was purified using the minElute PCR purification kit (Qiagen).
ATACseq: Transposase-accessible purified DNA was amplified by 11 cycle PCR using barcoded primers. Libraries were run on an Agilent Bioanalyser for size and quality control checking, quantified using Qbit (ThermoFisher), and multiplexed. Sequencing was performed in an Illumina HiSeq4000, generating 75bp pair-ended reads.

treatment_protocol: Mice (6-8 weeks old) underwent the following procedures: a) spinal cord dorsal column axotomy (DCA), b) laminectomy (Lam), c) sciatic nerve axotomy (SNA), and  d) sham sciatic nerve surgery (Sham).

tag: strain

tag: age

value: 6-8 weeks old

value: Dorsal Root Ganglia (DRG)

tag: chip antibody

value: H3K27ac Abcam Ab4729

tag: index sequence

value: CAGATC


title: Diffuse Large B-cell Lymphoma patient DLBCL_085


title: iPSPdx1_p33t_13: p33t_iPS_rep2

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

hyb_protocol: According to the Affymetrix expression protocol

data_processing:
Expression data were RMA normalized using the oligo package (version 1.38.0) together with expression data from GSE106813
Normalized expression data was filtered to retain only the 30562 probe sets with highest expression values

source_name: PDX1P33T/+ iPS cells, biological replicate 2

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: PDX1P33T/+ iPSCs were cultured on 1:100 diluted Matrigel (BD Biosciences) in mTeSR™1 medium (Stem Cell Technologies). At ~70–80% confluency, cultures were rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) followed by incubation with 1× TrypLE Select Enzyme (Life Technology) for 3–5 min at 37 °C. Single cells were rinsed with mTeSR™1 medium, and spun at 1,000 rpm for 3 min. The resulting cell pellet was resuspended in mTeSR™1 medium supplemented with 10 μM Y-27632 (Sigma-Aldrich) and the single cell suspension was seeded at ~1.0 × 105 cells/cm² on Matrigel-coated surfaces. Cultures were fed every day with mTeSR™1 medium and differentiation was initiated 48 h following seeding, resulting in ~90% starting confluency.

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol: PDX1P33T/+ iPSCs plated on 1:100 diluted Matrigel were first rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) and then cultured in RPMI 1640 medium (Invitrogen) further supplemented with 1.2 g/L sodium bicarbonate (Sigma), 0.2% ESC-qualified FBS (Life Technologies), 100 ng/mL Activin-A (R&D Systems), and 20 ng/mL of Wnt3A (R&D Systems) for day 1 only. For the next 2 days, cells were cultured in RPMI with 0.5% FBS, 1.2g/L sodium bicarbonate and 100 ng/mL Activin-A ; Cells were rinsed with 1× DPBS (without Mg2+ and Ca2+) once and then exposed to DMEM-F12 (Life Technologies) medium further supplemented with 2 g/L sodium bicarbonate, 2% FBS and 50 ng/mL of FGF7 (R&D Systems) for 3 days; Cultures were maintained for 4 days in DMEM-HG medium (Life Technologies) supplemented with 0.25 µM SANT-1 (Sigma-Aldrich), 2 µM retinoic acid (RA; Sigma-Aldrich), 100 ng/mL of Noggin (R&D Systems), and 1% B27 (Invitrogen).

tag: cell type

value: PDX1P33T/+ iPS cells


title: Diffuse Large B-cell Lymphoma patient DLBCL_079


title: H3K27ac_Sham_ChIP_rep1

description:
H3K27ac_Sham1
H3K27ac_Sham1_GCCAAT

value: GCCAAT


title: H3K27ac_Sham_ChIP_rep2

description:
H3K27ac_Sham2
H3K27ac_Sham2_CCGTCC

value: CCGTCC


title: H3K27me3_SNA_Input_rep1

description:
H3K27me3_SNAI1
H3K27me3_SNAI1_TGACCA

value: TGACCA


title: APR_T

city: South Bend

first: Qingfei

last: Wang

state: IN

address: 1234 N Notre Dame Ave, Harper Hall A121

department: Harper Cancer Research Institute

institute: University of Notre Dame

library_source: transcriptomic

data_processing:
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat.  The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat.
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene

source_name: Ab+Pal treated resistant/progressive tumor CD45- cells

extract_protocol:
Fresh mammary tumors were enzymatically digested.  Cells for single cell RNA-seq were prepared by density centrifugation using Ficoll-Paque media (GE Healthcare) followed by magnetic-activated cell sorting (Miltenyi) based separation or enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols for Nextera XT DNA sample prep kit

tag: mouse strain

value: FVB/N

tag: genotype

value: spontaneous mammary tumor


title: H3K27ac_DCA_Input_rep1

description:
H3K27ac_DCAI1
H3K27ac_DCAI1_TTAGGC

value: TTAGGC


title: H3K27ac_Lam_Input_rep2

description:
H3K27ac_LamI2
H3K27ac_LamI2_ATCACG

value: ATCACG


title: Diffuse Large B-cell Lymphoma patient DLBCL_078


title: APS_T

source_name: Ab+Pal treated sensitive/residual tumor CD45- cells


title: H3K27ac_DCA_Input_rep2

description:
H3K27ac_DCAI2
H3K27ac_DCAI2_ATGTCA

value: ATGTCA


title: H3K27ac_Sham_Input_rep1

description:
H3K27ac_ShamI1
H3K27ac_ShamI1_CGATGT

value: CGATGT


title: H3K27ac_Lam_Input_rep1

description:
H3K27ac_LamI1
H3K27ac_LamI1_ACAGTG

value: ACAGTG


title: H3K27ac_Sham_Input_rep2

description:
H3K27ac_ShamI2
H3K27ac_ShamI2_AGTCAA

value: AGTCAA


title: H3K27ac_SNA_Input_rep2

description:
H3K27ac_SNAI2
H3K27ac_SNAI2_AGTTCC

value: AGTTCC


title: H3K27ac_SNA_Input_rep1

description:
H3K27ac_SNAI1
H3K27ac_SNAI1_TGACCA

value: 6-8 weeks old


title: Diffuse Large B-cell Lymphoma patient DLBCL_076

value: Diffuse Large B-cell Lymphoma

value: tumor specimen


title: Diffuse Large B-cell Lymphoma patient DLBCL_075


title: Diffuse Large B-cell Lymphoma patient DLBCL_077


title: WT1

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to GRCh38 with Bismark
Genome_build: GRCh38

source_name: liver

extract_protocol:
Mouse liver tissue lysate was enriched for mitochondria. RNA was treated with Ribo Zero Gold and DNase. Bisulfite treatment (Epigentek, three cycles of 90°C for 5 min and 60°C for 1h)
Illumina TruSeq small RNA

value: wild type

value: liver

tag: molecule subtype

value: mitochondrial enriched RNA


title: H3K9ac_DCA_ChIP_rep2

description:
H3K9ac_DCA2
H3K9ac_DCA2_GTGAAA

value: Dorsal Root Ganglia (DRG)

value: H3K9ac Abcam Ab10812

value: GTGAAA


title: H3K9ac_Lam_ChIP_rep2

description:
H3K9ac_Lam2
H3K9ac_Lam2_ACTTGA

value: ACTTGA


title: H3K9ac_DCA_ChIP_rep1

description:
H3K9ac_DCA1
H3K9ac_DCA1_GATCAG

value: GATCAG


title: Diffuse Large B-cell Lymphoma patient DLBCL_073


title: H3K9ac_SNA_ChIP_rep2

description:
H3K9ac_SNA2
H3K9ac_SNA2_GTCCGC

value: GTCCGC


title: H3K9ac_Lam_ChIP_rep1

description:
H3K9ac_Lam1
H3K9ac_Lam1_CTTGTA

value: CTTGTA


title: H3K9ac_SNA_ChIP_rep1

description:
H3K9ac_SNA1
H3K9ac_SNA1_CAGATC

value: CAGATC


title: Diffuse Large B-cell Lymphoma patient DLBCL_074


title: Diffuse Large B-cell Lymphoma patient DLBCL_072


title: H3K9ac_DCA_Input_rep1

description:
H3K9ac_DCAI1
H3K9ac_DCAI1_TTAGGC

value: TTAGGC


title: H3K9ac_DCA_Input_rep2

description:
H3K9ac_DCAI2
H3K9ac_DCAI2_ATGTCA

value: ATGTCA


title: H3K9ac_Sham_ChIP_rep1

description:
H3K9ac_Sham1
H3K9ac_Sham1_GCCAAT

value: GCCAAT


title: H3K9ac_Lam_Input_rep1

description:
H3K9ac_LamI1
H3K9ac_LamI1_ACAGTG

value: 6-8 weeks old

value: ACAGTG


title: TripleD3, biological rep3

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

hyb_protocol: 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Expression Console Software using the MAS5 algorithm to generate .CHP files.

data_processing: The resulting data were processed using OmicSoft Array Studio (Version 9.0) software. The CEL files were used to identify differentially expressed genes by the Genomics Suite Gene Expression workflow of Partek software package version 7.17 (Partek Inc., St. Louis, MO, USA). The Robust Multichip Analysis (RMA) algorithm with quantile for normalization and log2 transformation was applied to generate signal values of all samples. Differentially expressed genes were defined using the filters of ANOVA unadjusted p value less than 0.01 and absolute fold change greater than 2. All experiments were performed with triplicate with independent pools of RNA.

source_name: Lung

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented.

growth_protocol: normal feed condition

extract_protocol: TRIzol reagent puls QIAGEN RNeasy total RNA isolation kit to clean up.

tag: genotype/varation

value: 12-13 months


title: TripleD2, biological rep2


title: TripleD1, biological rep1


title: H3K9ac_Sham_ChIP_rep2

description:
H3K9ac_Sham2
H3K9ac_Sham2_CCGTCC

value: CCGTCC


title: H3K9ac_Lam_Input_rep2

description:
H3K9ac_LamI2
H3K9ac_LamI2_ATCACG

value: ATCACG


title: Diffuse Large B-cell Lymphoma patient DLBCL_071

value: Diffuse Large B-cell Lymphoma

value: tumor specimen


title: H3K9ac_SNA_Input_rep2

description:
H3K9ac_SNAI2
H3K9ac_SNAI2_AGTTCC

value: Dorsal Root Ganglia (DRG)

value: AGTTCC


title: H3K9ac_SNA_Input_rep1

description:
H3K9ac_SNAI1
H3K9ac_SNAI1_TGACCA

value: TGACCA


title: H3K9ac_Sham_Input_rep2

description:
H3K9ac_ShamI2
H3K9ac_ShamI2_AGTCAA

value: AGTCAA


title: Tumor3, biological rep3

source_name: Lung tumor


title: H3K9ac_Sham_Input_rep1

description:
H3K9ac_ShamI1
H3K9ac_ShamI1_CGATGT

value: CGATGT


title: Diffuse Large B-cell Lymphoma patient DLBCL_069


title: Diffuse Large B-cell Lymphoma patient DLBCL_068


title: WT2, biological rep1

value: wild type


title: WT3, biological rep3


title: Diffuse Large B-cell Lymphoma patient DLBCL_067


title: 8h Rep 3 total

city: New York

first: Florian

last: Uhlitz

state: NY

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Half-life estimates based on ActD-mediated transcriptional shut-down were derived from microarray gene expression time course data (Fig EV1 A in the accompanying publication).
Since quantile normalisation assumes constant total RNA levels across samples (Bar-Joseph et al, 2012, http://doi.org/10.1038/nrg3244), RMA was performed without quantile normalisation for ActD samples.
Samples were instead normalised to median expression of 61 long-lived mRNAs (t1/2 > 16 hours) consistently identified in two published data sets on human mRNA half-life (Friedel et al, 2009, http://doi.org/10.1093/nar/gkp542; Yang et al, 2003, http://doi.org/10.1101/gr.1272403). Both time series were than fitted to an exponential decay function to infer decay rates.
Half-life estimates based on metabolic labelling with 4SU followed by RNA sequencing were calculated using all three fractions of RNA, i.e. total RNA, labelled RNA (eluate) and unlabelled RNA (flow-through). Dynamic transcriptome analysis (DTA) was used for quantification (Miller et al, 2011, http://doi.org/10.1038/msb.2010.112).
Median, mean and standard deviation of half-lives for all expressed genes was calculated from the three different data sets (ActD ON, ActD OFF, 4SU) and are provided as supplementary data (processed data file Table_EV2.tsv).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing half-lives for alle expressed genes based on transcriptional shutdown (ActD) or metabolic labelling (4SU).

molecule: polyA RNA

source_name: HEK293∆RAF1:ER cells

growth_protocol: HEK293∆RAF1:ER cells were cultured in DMEM complete w/o phenol red.

extract_protocol:
Total RNA was extraced with Trizol.
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: For RNA labeling, 4SU at a concentration of 200µM was added as indicated. Induction of RAF was done by addition of 0.5µM 4OHT as indicated.

tag: 4su treatment

value: 1h before harvesting

tag: 4oht induction

value: 8h before harvesting

tag: rna isolation

value: total RNA


title: 4h Rep 3 total

value: 4h before harvesting


title: Diffuse Large B-cell Lymphoma patient DLBCL_070


title: Tumor2, biological rep2


title: 2h Rep 3 total

value: 2h before harvesting


title: WT1, biological rep1


title: Tumor1, biological rep1


title: Diffuse Large B-cell Lymphoma patient DLBCL_065


title: Diffuse Large B-cell Lymphoma patient DLBCL_064


title: 8h Rep 3 eluate

value: labeled RNA (eluate)


title: 1h Rep 3 total


title: 4h Rep 3 eluate


title: Diffuse Large B-cell Lymphoma patient DLBCL_063


title: Diffuse Large B-cell Lymphoma patient DLBCL_066


title: RNAseq_KO_Rep3_Cl13_d8

city: Philadelphia

first: Omar

last: Khan

state: PA

address: 421 Curie Blvd. BRB II/III

institute: University of Pennsylvania

data_processing:
FASTQ files were aligned using STAR 2.5.2a against the mm10 murine reference genome.
The aligned files were processed using PORT gene-based normalization (https://github.com/itmat/Normalization).
Differential gene expression was performed with Limma. Limma-voom was used to identify transcripts that were significantly differentially expressed between experimental groups using an adjusted p-value <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: RNA tag counts files

source_name: P14 CD8 T cells

extract_protocol:
To assess the transcriptional and epigenetic impact of TOX deletion in T cells, 250 WT and 250 TOX-/- naïve CD44LOWCD62LHI P14 cells sorted from peripheral blood of donors, mixed, and co-transferred into WT mice. Recipients were subsequently infected with LCMV Cl-13 and splenocytes were harvested 8 days following infection. Ten spleens were pooled for each of the 3 replicates prior to processing, CD8+ T cell enrichment (using EasySep CD8+ T cell negative selection kit, Stem Cell Technologies), and staining of single cell suspensions. 1x105 WT and TOX-/- P14 cells were sorted to a purity of >98% for each replicate.
To extract RNA, 50,000 cells were resuspended in buffer RLT supplemented with beta-mercaptoethanol and processed with a RNeasy Micro Kit (Qiagen) as per the manufacturer’s instructions. Total RNA libraries were prepared using a Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara).

value: Spleen

value: P14 CD8 T cell

value: TOX-/-


title: 2h Rep 3 eluate


title: 1h Rep 3 eluate


title: Diffuse Large B-cell Lymphoma patient DLBCL_060

value: Diffuse Large B-cell Lymphoma


title: Diffuse Large B-cell Lymphoma patient DLBCL_061

value: tumor specimen


title: Diffuse Large B-cell Lymphoma patient DLBCL_062


title: Diffuse Large B-cell Lymphoma patient DLBCL_059


title: RNAseq_WT_Rep2_Cl13_d8

value: WT


title: RNAseq_KO_Rep1_Cl13_d8


title: Diffuse Large B-cell Lymphoma patient DLBCL_058


title: RNAseq_WT_Rep1_Cl13_d8


title: ATACseq_KO_Rep3_Cl13_d8

data_processing:
Samples were aligned to mm10 reference genome with Bowtie2.
Unmapped, unpaired, and mitochrondrial reads were removed using samtools. ENCODE Blacklist regions were removed (https://sites.google.com/site/anshulkundaje/projects/blacklists). PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value = 0.01.
A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged using bedtools merge. The number of reads in each peak was determined with bedtools coverage.
Differentially expressed peaks were identified following DESeq2 normalization using a FDR cutoff of <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq peak counts files

extract_protocol:
To assess the transcriptional and epigenetic impact of TOX deletion in T cells, 250 WT and 250 TOX-/- naïve CD44LOWCD62LHI P14 cells sorted from peripheral blood of donors, mixed, and co-transferred into WT mice. Recipients were subsequently infected with LCMV Cl-13 and splenocytes were harvested 8 days following infection. Ten spleens were pooled for each of the 3 replicates prior to processing, CD8+ T cell enrichment (using EasySep CD8+ T cell negative selection kit, Stem Cell Technologies), and staining of single cell suspensions. 1x105 WT and TOX-/- P14 cells were sorted to a purity of >98% for each replicate.
ATAC libraries were generated as described previously with minor changes. Briefly, nuclei from 50,000 cells were isolated using a lysis solution composed of 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, and 0.1% IGEPAL CA-630. Immediately following cell lysis, nuclei were pelleted in low-bind 1.5ml tubes (Eppendorf) and resuspended in TD Buffer with Tn5 transposase (Illumina). Transposition reaction was performed at 37 degrees Celsius for 45 minutes. DNA fragments were purified from enzyme solution using MinElute Enzyme Reaction Cleanup Kit (Qiagen). Libraries were barcoded (Nextera Index Kit, Illumina) and amplified with NEBNext High Fidelity PCR Mix (New England Biolabs). Library quality was assessed using a TapeStation instrument.


title: RNAseq_KO_Rep2_Cl13_d8


title: ATACseq_KO_Rep1_Cl13_d8


title: ATACseq_KO_Rep2_Cl13_d8


title: ATACseq_WT_Rep3_Cl13_d8


title: ATACseq_WT_Rep2_Cl13_d8


title: RNAseq_WT_Rep3_Cl13_d8


title: ATACseq_WT_Rep1_Cl13_d8


title: Diffuse Large B-cell Lymphoma patient DLBCL_056


title: Diffuse Large B-cell Lymphoma patient DLBCL_055


title: RNAseq_TOX_Rep2_3T3

source_name: NIH3T3 fibroblasts

extract_protocol:
NIH3T3 cells were transduced with TOX+GFP or control GFP only RV viruses and cultured for 48 hours prior to cell sorting.
To extract RNA, 50,000 cells were resuspended in buffer RLT supplemented with beta-mercaptoethanol and processed with a RNeasy Micro Kit (Qiagen) as per the manufacturer’s instructions. Total RNA libraries were prepared using a Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara).

tag: cell line

value: embryo

value: fibroblast

tag: transduction

value: TOX-encoding retrovirus


title: Diffuse Large B-cell Lymphoma patient DLBCL_050


title: Diffuse Large B-cell Lymphoma patient DLBCL_046


title: Diffuse Large B-cell Lymphoma patient DLBCL_045


title: RNAseq_TOX_Rep3_3T3


title: RNAseq_CT_Rep3_3T3

value: control retrovirus


title: Diffuse Large B-cell Lymphoma patient DLBCL_051


title: Diffuse Large B-cell Lymphoma patient DLBCL_049


title: Diffuse Large B-cell Lymphoma patient DLBCL_052


title: Diffuse Large B-cell Lymphoma patient DLBCL_047


title: Diffuse Large B-cell Lymphoma patient DLBCL_048


title: Diffuse Large B-cell Lymphoma patient DLBCL_042


title: RNAseq_CT_Rep2_3T3


title: Diffuse Large B-cell Lymphoma patient DLBCL_043


title: Diffuse Large B-cell Lymphoma patient DLBCL_053


title: Diffuse Large B-cell Lymphoma patient DLBCL_054


title: Diffuse Large B-cell Lymphoma patient DLBCL_044


title: RNAseq_TOX_Rep3

source_name: CD8 T cells

extract_protocol:
In ectopic and enforced expression experiments, in vitro differentiated CD8+ T cells transduced with TOX+GFP or control GFP only (>2 biological replicates each) were sorted on GFP expression 6 days following initial activation to a purity of >98%.
To extract RNA, 50,000 cells were resuspended in buffer RLT supplemented with beta-mercaptoethanol and processed with a RNeasy Micro Kit (Qiagen) as per the manufacturer’s instructions. Total RNA libraries were prepared using a Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara).

value: CD8 T cells

value: Tox-encoding retrovirus


title: Diffuse Large B-cell Lymphoma patient DLBCL_041


title: Diffuse Large B-cell Lymphoma patient DLBCL_057


title: RNAseq_CT_Rep1_3T3


title: RNAseq_TOX_Rep1


title: Diffuse Large B-cell Lymphoma patient DLBCL_039


title: RNAseq_TOX_Rep1_3T3


title: Diffuse Large B-cell Lymphoma patient DLBCL_040


title: RNAseq_CT_Rep2


title: Diffuse Large B-cell Lymphoma patient DLBCL_038


title: ATACseq_TOX_Rep2

extract_protocol:
In ectopic and enforced expression experiments, in vitro differentiated CD8+ T cells transduced with TOX+GFP or control GFP only (>2 biological replicates each) were sorted on GFP expression 6 days following initial activation to a purity of >98%.
ATAC libraries were generated as described previously with minor changes. Briefly, nuclei from 50,000 cells were isolated using a lysis solution composed of 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, and 0.1% IGEPAL CA-630. Immediately following cell lysis, nuclei were pelleted in low-bind 1.5ml tubes (Eppendorf) and resuspended in TD Buffer with Tn5 transposase (Illumina). Transposition reaction was performed at 37 degrees Celsius for 45 minutes. DNA fragments were purified from enzyme solution using MinElute Enzyme Reaction Cleanup Kit (Qiagen). Libraries were barcoded (Nextera Index Kit, Illumina) and amplified with NEBNext High Fidelity PCR Mix (New England Biolabs). Library quality was assessed using a TapeStation instrument.


title: ATACseq_TOX_Rep3


title: ATACseq_CT_Rep3


title: Diffuse Large B-cell Lymphoma patient DLBCL_035


title: Diffuse Large B-cell Lymphoma patient DLBCL_036


title: ATACseq_TOX_Rep1


title: Diffuse Large B-cell Lymphoma patient DLBCL_037


title: ATACseq_CT_Rep2


title: ATACseq_CT_Rep1


title: Diffuse Large B-cell Lymphoma patient DLBCL_032


title: Diffuse Large B-cell Lymphoma patient DLBCL_031


title: Diffuse Large B-cell Lymphoma patient DLBCL_033


title: Diffuse Large B-cell Lymphoma patient DLBCL_030


title: articular cartilage, WT rep2

city: La Jolla

first: Tomas

last: Duffy

state: CA

address: 10550 N Torrey Pines Rd

institute: TSRI

data_processing:
Approximately, 30 million 75 bp single-end reads per sample were sequenced on a Nextseq500 (Illumina).
Briefly, adapters and low quality bases were removed using TrimGalore (https://github.com/FelixKrueger/TrimGalore) and mapped to the mouse mm9 genome using STAR. Raw counts were obtained using featureCounts.
Differential gene expression analysis was carried out with DESeq2. Genes with an adjusted p- value <0.05 were considered differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: CRY2KOvsWT.DEseq2.xls:  Excel file includes Normalized expression and adjusted p-values for differential expression for each gene.  The .txt file reports unnormalized count values.

source_name: articular cartilage

extract_protocol:
Cartilage was stored at -20oC in Allprotect Tissue Reagent (Qiagen, Valencia, CA) immediately after resection from the subchondral bone. For RNA isolation, cartilage was pulverized in a 6770 Freezer/Mill Cryogenic Grinder (SPEX SamplePrep, Metuchen, NJ), and homogenized in Qiazol Lysis Reagent (Qiagen) using 25mg tissue per 700ul Qiazol. RNA was isolated using the miRNeasy Mini kit (Qiagen) with on-column DNAse digestion, followed by removal of proteoglycans using RNAmate (BioChain Institute, Newark, CA). 5Mouse articular cartilage was collected from both sides of the femoral condyle and tibial plateau from 3-month-old mice. The cartilage was homogenized and incubated in TRIzol (Invitrogen) at room temperature. After addition of chloroform, samples were centrifuged, and the supernatant was collected for RNA isolation.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).

value: articular cartilage

value: 3 months old


title: articular cartilage, CRY2-KO rep3


title: articular cartilage, CRY2-KO rep1


title: articular cartilage, WT rep3


title: articular cartilage, WT rep1


title: APRTT_AIC_TIL_Rep1

source_name: Tumor  infiltrating leukocytes/CD45+ cells from Ab+Cabo+ICB treated Ab+Pal resistant transplanted tumor

value: FVB/N

value: transplanted mammary tumor


title: Diffuse Large B-cell Lymphoma patient DLBCL_027


title: Diffuse Large B-cell Lymphoma patient DLBCL_026


title: articular cartilage, CRY2-KO rep2


title: Diffuse Large B-cell Lymphoma patient DLBCL_023


title: Diffuse Large B-cell Lymphoma patient DLBCL_028


title: APRTT_AC_TIL_Rep2

source_name: Tumor  infiltrating leukocytes/CD45+ cells from Ab+Cabo treated Ab+Pal resistant transplanted tumor


title: Diffuse Large B-cell Lymphoma patient DLBCL_025


title: Diffuse Large B-cell Lymphoma patient DLBCL_024


title: Diffuse Large B-cell Lymphoma patient DLBCL_022


title: APRTT_AC_TIL_Rep1


title: Diffuse Large B-cell Lymphoma patient DLBCL_034


title: Diffuse Large B-cell Lymphoma patient DLBCL_029


title: Diffuse Large B-cell Lymphoma patient DLBCL_019


title: Diffuse Large B-cell Lymphoma patient DLBCL_021


title: Diffuse Large B-cell Lymphoma patient DLBCL_018


title: Diffuse Large B-cell Lymphoma patient DLBCL_020


title: APRTT_TIL_Rep2

source_name: Transplanted Ab+Pal resistant tumor infiltrating leukocytes/CD45+ cells


title: APRTT_AIC_TIL_Rep2


title: APRTT_MDSC2_Rep2

source_name: Transplanted Ab+Pal resistant tumor infiltrating MDSC/Gr dim-Ly6G- cells


title: APRTT_TIL_Rep1


title: APRTT_MDSC1_Rep2

source_name: Transplanted Ab+Pal resistant tumor infiltrating MDSC/Gr high-Ly6G+ cells


title: APRTT_MDSC1_Rep1


title: APR_TIL_Rep2

data_processing:
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat.  The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat. SRR8176997 (001), SRR8176998 (002).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene

source_name: Ab+Pal treated resistant/progressive tumor infiltrating leukocytes/CD45+ cells

value: spontaneous mammary tumor


title: APR_TIL_Rep1

data_processing:
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat.  The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat. SRR8176995 (001), SRR8176996 (002).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene


title: APRTT_MDSC2_Rep1


title: APS_TIL_Rep1

data_processing:
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat.  The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat. SRR8176991 (001), SRR8176992 (002).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene

source_name: Ab+Pal treated sensitive/residual tumor infiltrating leukocytes/CD45+ cells


title: KPS_2-11

city: Essen

first: Martin

last: Trippler

address: Hufelandstr. 55

department: Gastroenterology and Hepatology

institute: University Duisburg-Essen, Essen University Hospital

description: liver tissue of PML knockout mice

hyb_protocol: Samples were hybridized on a GeneChip HT MG-430 PM 16-Array Plate using the GeneTitan MC Instrument (Affymetrix) and the GeneTitan Hybridization, Wash, and Stain Kit (Affymetrix)according to the manufacturer's protocols

scan_protocol: Hybridization signals were detected with Affymetrix Gene Chip Scanner 3000

data_processing: CEL files were processed for further data analysis by the GeneChip Command Console Software (AGCC, version 3.2.4, Affymetrix). Robust multiarray average (RMA) normalization was carried out with the Expression Console Software (version 1.2.1, Affymetrix)

label: Biotin

source_name: PML-KO

label_protocol: RNA samples were preprocessed with the 3' IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions

growth_protocol: Transgenic mice (PML-/-, HCVtg, PML-/- HCVtg) as well as WT mice were left untreated under frequent observation. After one year ten male mice of each group were sacrificed and analyzed.

extract_protocol: For RNA isolation, 30 mg of murine or human liver or tumor tissue was lysed in QIAzol Lysis Reagent (Qiagen Inc., Valencia, CA, USA) by mechanic homogenization using TissueRuptor (Qiagen Inc., Valencia, CA, USA). Total RNA and miRNA was isolated by phenol-chloroform extraction followed by isopropanol precipitation. RNA purification was done using the miRNeasy kit (Qiagen Inc., Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Mice were not subjected to any treatment

value: whole liver

tag: gender

value: male

tag: genotype/variation

value: PML-/-


title: Diffuse Large B-cell Lymphoma patient DLBCL_017

source_name: biopsy

tag: diagnosis

value: Diffuse Large B-cell Lymphoma

tag: tissue


title: Ctrl_TIL_Rep2

data_processing:
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat.  The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat. SRR8176989 (001), SRR8176990 (002).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene

source_name: control treatment tumor infiltrating leukocytes/CD45+ cells


title: KPS_2-14

description: liver tissue of PML knockout, HCV transgenic mice

source_name: HCV+PML-KO

value: PML-/- HCV-transgenic


title: APS_TIL_Rep2

data_processing:
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat.  The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat. SRR8176993 (001), SRR8176994 (002).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene


title: KPS_2-10

description: liver tissue of HCV-transgenic mice

source_name: HCV

value: HCV-transgenic


title: Diffuse Large B-cell Lymphoma patient DLBCL_015

value: tumor specimen


title: KPS_2-09

description: liver tissue of HCV-transgenic mice


title: Diffuse Large B-cell Lymphoma patient DLBCL_009


title: Diffuse Large B-cell Lymphoma patient DLBCL_013


title: Diffuse Large B-cell Lymphoma patient DLBCL_016


title: Diffuse Large B-cell Lymphoma patient DLBCL_008


title: Diffuse Large B-cell Lymphoma patient DLBCL_010


title: Diffuse Large B-cell Lymphoma patient DLBCL_012


title: KPS_2-08

description: liver tissue of wildtype contol mice

source_name: WT-Ko

value: WT control


title: KPS_3-17

description: liver tissue of wildtype control mice


title: KPS_2-13


title: KPS_2-05


title: Diffuse Large B-cell Lymphoma patient DLBCL_011


title: Ctrl_TIL_Rep1

data_processing:
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat.  The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat. SRR8176987 (001), SRR8176988 (002).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene


title: KPS_3-20

description: liver tissue of PML knockout mice


title: Diffuse Large B-cell Lymphoma patient DLBCL_014

data_processing: Raw cel files were RMA normalized using the ExpressionFileCreator module of GenePattern31, and quality checked for batch effects by unsupervised clustering of the 3,000 most variably expressed genes across the dataset.


title: Ab_T

source_name: Anti-HER2/neu antibody treated tumor CD45- cells


title: Ctrl_T

source_name: control treatment tumor CD45- cells

value: mammary tumor


title: Pal_T

source_name: CDK4/6 inhibitor Palbociclib treated tumor CD45- cells


title: KPS_2-03


title: flash

city: Shanghai

first: shaoang

last: wen

state: Shanghai

address: NO.320 Yueyang Road Shanghai, China

institute: institute of neuroscience

data_processing:
Illumina bcl2fastq2 v2 software used for basecalling
Read 1 (21 bp long) contains both barcode and UMI. Bases 1-12 are cell barcode and bases 13-20 are UMI. Position 21 is usually a T and can be ignored.
sequenced reads were tagged with cell barcodes and molecular barcodes with Drop-seq tools v1.12, and aligned to GRCm38 whole genome with STAR, the final digital gene expression (DGE) matrix were generated by Drop-seq tools v1.12 as described by Macosko et al (2015).
The DGEs were filtered into STAMPs DGEs (single-cell transcriptomes attached to microparticles) by  dropbead (R package)
The STAMPs DGEs were normalized to their total reads counts
Genome_build: GRCm38
Supplementary_files_format_and_content: digital gene expression matrix

source_name: suprachiasmatic nucleus

growth_protocol: Mice were group-housed (<5 mice per cage) with ad libitum access to water and food.

extract_protocol:
Mice were sacrificed by acute cervical dislocation. Mice heads were chilled in the ice-cold dissection buffer for 10 seconds immediately. Brains were dissected out from the chilled head rapidly. The SCN region were microdissected in ice-cold dissection buffer by microsurgery forceps and knives according to the mice brain atlas . The SCN region tissues from 5 mice were pooled together. Tissues were digested by papain for 45 min and DNase I for 3min in digestion buffer with bubbling (95% O2, 5%CO2) under 37℃ incubation. Digestion was neutralized by adding 2ml digestion neutralizing buffer (KCl 5.33 mM, NaHCO3 26.19 mM, NaCl 117.24 mM, NaH2PO4 1.01mM, Dextrose 5.56mM, DL-AP5 50μM, DNQX 20μM, TTX 0.1μM, 5%(v/v) FBS, 5%(v/v) Trehalose). Tissue pieces were dissociated into single-cell suspension by gently pipetting using Pasteur pipettes with polished tips. Cell suspension was passed through 40μm filter and centrifuged (200g) for 7min at 4℃. The precipitate was re-suspended in 1ml Drop-seq buffer. Cell concentrations were determined with hemocytometer and diluted into 150 cell/μl with Drop-seq buffer.
cDNA libraries were prepared using drop-seq protocols described by Macosko et al (2015).

treatment_protocol: For the circadian time point sampling, after 12 hours light/dark cycle (LD) entrain for 2 weeks, mice were adapted in constant darkness (DD) for 2 days and sacrificed respectively at 12 circadian time (CT) points in dark. For the light pulse stimulate sampling, mice were entrained under 12 hours light/dark cycle (LD) for 2 weeks and adapted in constant darkness (DD) for 2 days; after stimulating with 250 Lux white light at CT18 for 1 hour, mice were sacrificed and sampled immediately.

tag: strain

value: suprachiasmatic nucleus

tag: age

value: 8 weeks

tag: sampling enviroment

value: constant dark followed 1hour light stimulate


title: CT58

value: constant dark


title: KPS_2-04


title: Diffuse Large B-cell Lymphoma patient DLBCL_007


title: KPS_2-01


title: SCN, YJ-3_S1

data_processing:
*I1_001.fastq.gz: contains the 8 nt sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98  nt RNA sequence.
basecalling and mapping were done with Cellranger V3.
sequenced reads were tagged with cell barcodes and molecular barcodes and aligned to GRCm38 whole genome with  with cellranger V3
The DGEs were filtered into STAMPs DGEs (single-cell transcriptomes attached to microparticles) by  dropbead (R package)
the digital gene expression matrix were generated with cellranger V3
Genome_build: GRCm38
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

extract_protocol:
Mice were sacrificed by acute cervical dislocation. Mice heads were chilled in the ice-cold dissection buffer for 10 seconds immediately. Brains were dissected out from the chilled head rapidly. The SCN region were microdissected in ice-cold dissection buffer by microsurgery forceps and knives according to the mice brain atlas .
cDNA libraries were prepared according to 10X geomics V2 chemistry
10X geomics single cell trascriptome V2 chemistry

treatment_protocol: WT mice sacrificed at subjective day, no special treatments.


title: Diffuse Large B-cell Lymphoma patient DLBCL_006


title: Diffuse Large B-cell Lymphoma patient DLBCL_004


title: KPS_1-06


title: Diffuse Large B-cell Lymphoma patient DLBCL_003


title: CT54


title: KPS_1-15


title: CT50


title: KPS_1-02


title: Diffuse Large B-cell Lymphoma patient DLBCL_005


title: 9A6

data_processing:
Illumina bcl2fastq2 v2 software used for basecalling
sequence alignment and digital gene expression matrix(DGE) generation were performed using STAR
The RPKM DGE was generated by normalizing the count DGE to their total reads counts and total exon length
The coordinate of each LCM sample was generated by registration to a standard SCN
Genome_build: GRCm38
Supplementary_files_format_and_content: both "counts.txt" and "rpkm.txt" contains genes(by row) and all the  samples (by colums)

extract_protocol:
RNA was extracted using the protocols described by Jun Chen et al (2017)
cDNA libraries were prepared using the  Smart-seq2 protocol
Tagmentation-based library construction,using the Tn5 transposase

treatment_protocol: For staining of SCN, place slide in 100%, 90%,70%, 50% ethanol each for 30 seconds. Mark the area to be stained with a Barrier Pen. Add 300 µl of Cresyl Violet solution to tissue section and stain for 1-2 minutes. Drain off stain and transfer slides into 50%, 70%,90%,100%,100% ethanol each for 30 seconds. Air-dry the slides at room temperature for 5 min before  subjected to laser capture microdissection on the Applied Biosystems Arcturus LCM System .

tag: medial lateral

tag: dorsal ventral

tag: anterior posterior


title: KPS_1-16

description: liver tissue of Wildtype contol mice


title: Diffuse Large B-cell Lymphoma patient DLBCL_002

extract_protocol: Trizol or Qiagen RNA extraction kit


title: CT46


title: Mantle Cell Lymphoma patient MCL_042

value: Mantle Cell Lymphoma


title: 8B7


title: Diffuse Large B-cell Lymphoma patient DLBCL_001


title: 8B3


title: RNAseq_CT_Rep1

source_name: CD8 T cells

value: Spleen

tag: cell type

value: CD8 T cells

value: control retrovirus


title: CT42


title: 8A8


title: CT38


title: 8A6


title: CT34


title: 8A4


title: 8A2


title: CT30


title: Mantle Cell Lymphoma patient MCL_041


title: Mantle Cell Lymphoma patient MCL_043


title: 7C6


title: CT18


title: CT22


title: 7C4


title: CT26


title: 7C2


title: Mantle Cell Lymphoma patient MCL_039


title: 7B7


title: 7B9


title: CT14


title: Mantle Cell Lymphoma patient MCL_038


title: Mantle Cell Lymphoma patient MCL_036


title: Mantle Cell Lymphoma patient MCL_034


title: 7B5


title: 7B1


title: Mantle Cell Lymphoma patient MCL_035


title: 7A10


title: Patient_7_Tumor

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background and batch corrected using the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) implemented in the Transcriptome Analysis Console software version 4.0 (TAC 4.0).

source_name: Bladder: tumoral tissue, stage T1, grade 3

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 30 ngs total RNA (GeneChip Whole Transcript WT Expression Arrays, Affymetrix).

growth_protocol: All bladder cancer patients underwent transurethral resection (TUR).

extract_protocol: Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: tissue type

value: Bladder:tumoral tissue


title: Patient_10_Tumor

source_name: Bladder: tumoral tissue, stage T2. grade 3


title: 7A6


title: 7B3


title: 7A8


title: 7A4


title: Mantle Cell Lymphoma patient MCL_033


title: Mantle Cell Lymphoma patient MCL_030


title: Mantle Cell Lymphoma patient MCL_040


title: 7A2


title: RNAseq_TOX_Rep2

value: Tox-encoding retrovirus


title: Mantle Cell Lymphoma patient MCL_031


title: Patient_5_Tumor

source_name: Bladder: tumoral tissue, stage T2, grade 3


title: Mantle Cell Lymphoma patient MCL_029


title: Mantle Cell Lymphoma patient MCL_028


title: Patient_9_Tumor


title: Patient_4_Tumor


title: 6D5


title: Patient_3_Tumor

source_name: Bladder: tumoral tissue, stage Ta, grade 1


title: Patient_8_Non-Tumor

source_name: Bladder: non-tumoral tissue

value: Bladder:non-tumoral tissue


title: Mantle Cell Lymphoma patient MCL_026


title: Mantle Cell Lymphoma patient MCL_027


title: Mantle Cell Lymphoma patient MCL_025


title: Mantle Cell Lymphoma patient MCL_037


title: Mantle Cell Lymphoma patient MCL_032


title: Patient_7_Non-Tumor


title: 6C6


title: 6C4


title: Patient_2_Tumor

source_name: Bladder: tumoral tissue, stage Ta, grade 2


title: Mantle Cell Lymphoma patient MCL_024


title: 6C2


title: 6B9


title: 6D3


title: 6B7


title: Mantle Cell Lymphoma patient MCL_021


title: Mantle Cell Lymphoma patient MCL_020


title: Mantle Cell Lymphoma patient MCL_023


title: Patient_9_Non-Tumor


title: Mantle Cell Lymphoma patient MCL_019


title: Patient_5_Non-Tumor


title: Patient_6_Non-Tumor


title: Mantle Cell Lymphoma patient MCL_022


title: Mantle Cell Lymphoma patient MCL_018


title: 6B5


title: Patient_4_Non-Tumor


title: Mantle Cell Lymphoma patient MCL_016


title: 6B1


title: 6A8


title: 6A6


title: immortal.pod.post-thermoswitch.r2

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description:
TT1805RNA08
RNASeq.pod_pre-shock.vs.pod_post-shock.xlsx
RNASeq.pod_post-shock.vs.D28GFP+.xlsx
RNASeq.pod_post-shock.vs.RC.xlsx

data_processing:
Base call by bcl2fastq v. 2.17
Fastq files were aligned using TopHat2.
TPM values were calculated with Partek E/M distributed on Partekflow (http://www.partek.com/partek-flow/)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with TPM values
RNASeq.pod_pre-shock.vs.D28GFP+.xlsx: D28GFP+ samples refer to the D28GFP+ samples refers to those appears in GSE124392 (GSM3531625 -GSM3531628)
RNASeq.pod_post-shock.vs.D28GFP+.xlsx: D28GFP+ samples refer to the D28GFP+ samples refers to those appears in GSE124392 (GSM3531625 -GSM3531628)
RNASeq.pod_pre-shock.vs.RC.xlsx: RC samples refers to those appears in GSE127344 (GSM3634121- GSM3634124).
RNASeq.pod_post-shock.vs.RC.xlsx: RC samples refers to those appears in GSE127344 (GSM3634121- GSM3634124).
RNASeq.pod_pre-shock.vs.pod_post-shock.xlsx

source_name: immortalized podocyte culture

growth_protocol: Saleem et al., 2002; Ni et al., 2012

extract_protocol:
RNA was exracted with Qiagen Rneasy micro kit (cat #: 74004)
Kapa stranded mRNA-Seq library (#KK8420)

treatment_protocol: cultured at 37C, which stops proliferation and induces maturation. Protocols from PMID: 11856766 and 22591222.

value: immortalized podocyte culture

tag: heat shock activation

value: Cultured at 37C


title: immortal.pod.pre-thermoswitch.r2

description:
TT1805RNA16
RNASeq.pod_pre-shock.vs.pod_post-shock.xlsx
RNASeq.pod_pre-shock.vs.D28GFP+.xlsx
RNASeq.pod_pre-shock.vs.RC.xlsx

treatment_protocol: cultured at 33C, which keeps the podocyte cell line proliferating. Protocols from PMID: 11856766 and 22591222.

value: Cultured at 33C


title: immortal.pod.pre-thermoswitch.r1

description:
TT1805RNA10
RNASeq.pod_pre-shock.vs.pod_post-shock.xlsx
RNASeq.pod_pre-shock.vs.D28GFP+.xlsx
RNASeq.pod_pre-shock.vs.RC.xlsx


title: immortal.pod.post-thermoswitch.r1

description:
TT1805RNA09
RNASeq.pod_pre-shock.vs.pod_post-shock.xlsx
RNASeq.pod_post-shock.vs.D28GFP+.xlsx
RNASeq.pod_post-shock.vs.RC.xlsx


title: Mantle Cell Lymphoma patient MCL_015

source_name: biopsy

value: tumor specimen


title: 6B3


title: Mantle Cell Lymphoma patient MCL_014


title: 6A2


title: Mantle Cell Lymphoma patient MCL_013


title: 6A4


title: Patient_2_Non-Tumor


title: Patient_3_Non-Tumor


title: Patient_1_Non-Tumor


title: V_1UM_3

city: Vancouver

first: Liam

last: Brunham

state: British Columbia

address: 1081 Burrard Street

department: Department of Medicine

country: Canada

institute: University of British Columbia

description:
RNAseq_Ibrutinib_rawcounts.txt
RNAseq_Ibrutinib_significant_genes.xls

data_processing:
Basecalls were performed using illumina BaseSpace workflow version 1.1.0.
STAR aligner version STAR-2.5.0b was used for alignment to hg38 genome assembly.
Rawcounts were generated by featureCounts in Subread package version 1.6.3.
Genes with rawcounts more that 5 in at least 2 samples were used for differential expression analysis by DEseq package in R.
Adjusted p-value less that 0.05 was considered significant in differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file includes rawcounts for each sample. Matrix table excel file shows significant differential expressed gened in atrial- and venticular- like CMs samples comparing drug treatment in 1uM and 0uM doses.

source_name: hESC-derived cardiomyocytes

growth_protocol: hESC HES2 cells were differentiated into CMs using an embryoid body (EB) protocol that employed Activin A and BMP4 signaling for mesoderm induction followed by Wnt inhibition for cardiac specification. To generate atrial CMs, retinoic acid (RA) was added at the cardiac mesoderm stage (Devalla et al., 2015; Lee et al., 2017; Zhang et al., 2011). The timing and concentrations of cytokines utilized were optimized using previously described analyses (Dubois et al., 2011; Evseenko et al., 2010; Kataoka et al., 1997; Kattman et al., 2011; Prall et al., 2007).

extract_protocol:
Total RNA of hESC-CMs were isolated by illustra™ RNAspin Mini Isolation Kit (GE Healthcare). RNA quality was assessed by measuring the RNA integrity number (RIN) using Bioanalyzer (Agilent Technologies). All 12 samples for library preparation have RIN within 8 to 10.
250ng of total RNA was prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). RNA sequencing was performed on Illumina NextSeq 500 with 2x43 paired_end sequence reads in the depth of 20 millions.

treatment_protocol: hESC-derived atrial- and ventricular-like cardiomyocytes were treated with 1uM ibrutinib in experiment group and vehicle (DMSO) in control group for 24 hours with 3 replicates in each condition.

value: Ventricular-like cardiomyocytes

tag: treatment

value: 1uM ibrutinib

tag: hesc strain


title: 5D3

value: suprachiasmatic nucleus


title: V_1UM_2


title: Patient_10_Non-Tumor


title: 5C6

value: 8 weeks


title: Mantle Cell Lymphoma patient MCL_011


title: Mantle Cell Lymphoma patient MCL_012


title: V_1UM_1


title: 5C4


title: V_NT_3

value: vehicle (DMSO)


title: Mantle Cell Lymphoma patient MCL_010


title: Mantle Cell Lymphoma patient MCL_009


title: Mantle Cell Lymphoma patient MCL_008


title: V_NT_1


title: 5C2


title: Mantle Cell Lymphoma patient MCL_007


title: Mantle Cell Lymphoma patient MCL_006


title: 5B7


title: 5B5


title: A_1UM_3

value: Atrial-like cardiomyocytes


title: A_NT_2


title: A_NT_1


title: A_NT_3


title: Mantle Cell Lymphoma patient MCL_005

value: Mantle Cell Lymphoma


title: A_1UM_1


title: A_1UM_2


title: 5A6


title: 5A8


title: 5B1


title: 5B3


title: V_NT_2


title: 37.kidney_2

data_processing:
Fastq files were aligned to hg38 with TopHat2
Gene-level quantification was performed with Partek E/M through Partek Genomic Suite
Gene-level read couns was normalized to TPM through Partek Genomic Suite
Genome_build: hg38

source_name: embryonic kidneys depleted of renal corpuscles

extract_protocol:
Ambion Recoverall Total Nucleic Acid Isolation Kit and QIAGEN Rneasy Micro Kit; Qiagen Rneasy micro kit
Kapa stranded mRNA-Seq library (#KK8420)
polyA selected RNA-Seq

tag: gestational week

value: week 21


title: Mantle Cell Lymphoma patient MCL_003


title: 5A4


title: 5A2


title: 36.kidney_1

value: week 18

value: embryonic kidneys depleted of renal corpuscles


title: Mantle Cell Lymphoma patient MCL_002


title: 4D5


title: 35.RC_4

source_name: renal corpuscles from embryonic kidneys

value: embryonic renal corpuscles


title: Mantle Cell Lymphoma patient MCL_001


title: Mantle Cell Lymphoma patient MCL_004


title: Patient_1_Tumor

value: Bladder:tumoral tissue


title: Follicular Lymphoma patient FL_065

value: Follicular Lymphoma


title: Follicular Lymphoma patient FL_063


title: 4D3


title: 34.RC_3

value: week 16.5


title: Mantle Cell Lymphoma patient MCL_017


title: 33.RC_2

value: week 16


title: MEL270.SF3B1_WT.input

city: Seattle

first: Guo-Liang

last: Chew

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences and Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

data_processing:
Merge gene annotations from UCSC knownGene, Ensembl 71, MISO v2.0
RNA-seq: RSEM v1.2.4 used to call Bowtie with option '-v 2' to align to merged annotation, remaining reads mapped to genome with TopHat v2.1.1, Isoform ratios were quantified with MISO V2
ChIP-Seq: Bowtie v1.0.045 with the arguments '-v 2 -k 1 -m 1 --best --strata' to align to merged annotation. Peaks were called using MACS2 v2.1.1.2016030949 against input control libraries with p < 10-5 and subsequently filtered to remove peaks contained within ENCODE blacklisted regions50 and the mitochondrial genome.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression estimates (TPM); .narrowPeak: output from MACS2 peak calling against input; ChIP-seq bigwig coverage

growth_protocol: K562 and MEL270 cell lines were cultured in RPMI/10% FCS, with penicillin (100 U/ml) and streptomycin (100 μg/ml).

extract_protocol:
Cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody.
ChIP-seq libraries were prepared with the Rubicon Thruplex DNAseq prep kit using standard protocols

treatment_protocol: Dox, DMSO, 6 days

tag: cell line

tag: lentiviral vector

tag: chip antibody


title: 4C4


title: 4C6


title: Follicular Lymphoma patient FL_062

tag: diagnosis


title: Follicular Lymphoma patient FL_064

tag: tissue


title: 4C2

tag: strain


title: 32.RC_1

value: week 17


title: MEL270.SF3B1_WT.GLTSCR1

value: GLTSCR1 (Santa Cruz SC-240516)


title: 4B9

tag: age


title: MEL270.SF3B1_WT.BRG1

value: BRG1 / SMARCA4 (Abcam EPNCIR111A)


title: 4B7


title: 4B5


title: MEL270.SF3B1_WT.BRD9

value: BRD9 (Abcam ab137245)


title: 4B3

value: suprachiasmatic nucleus


title: MEL270.SF3B1_K700E.input


title: Follicular Lymphoma patient FL_056

value: tumor specimen


title: Follicular Lymphoma patient FL_057


title: MEL270.SF3B1_K700E.BRG1


title: MEL270.SF3B1_K700E.GLTSCR1


title: Follicular Lymphoma patient FL_055


title: MEL270.DMSO.input

value: pINDUCER eGFP empty


title: Follicular Lymphoma patient FL_059


title: 4A8

value: 8 weeks


title: 4A6


title: Follicular Lymphoma patient FL_053


title: Follicular Lymphoma patient FL_054


title: 4C8


title: Follicular Lymphoma patient FL_060


title: MEL270.DMSO.GLTSCR1


title: Follicular Lymphoma patient FL_052


title: Follicular Lymphoma patient FL_058


title: 4A4


title: 3C6


title: MEL270.DMSO.BRG1


title: 3C4


title: MEL270.DMSO.BRD9


title: 4A10


title: Follicular Lymphoma patient FL_061


title: Follicular Lymphoma patient FL_050


title: Follicular Lymphoma patient FL_051


title: Follicular Lymphoma patient FL_048


title: MEL270.dBRD9.GLTSCR1

treatment_protocol: Dox, 500nM dBRD9, 6 days


title: Follicular Lymphoma patient FL_047


title: Follicular Lymphoma patient FL_046


title: Follicular Lymphoma patient FL_049


title: MEL270.dBRD9.BRG1


title: HuOrg_D28_1: human kidney organoid, differentiation day 28, sample 1

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Reads were mapped using STAR 2.5.1b and the NCBI GTF annotation accession NCBI:GCA_000001405.14
Count tables were generated from the FASTQ files using the Cell Ranger software version 1.3.1 with default parameters.
Read 1 is the Cell Barcode + UMI and read 2 is the actual RNA sequence
bam file contains cell barcode for each read at CR:Z tag
Genome_build: GRCh37.p13

source_name: human kidney organoid, differentiation day 28, organoid 1

extract_protocol:
10X Genomics: Chromium Single Cell 3’ v2
single cell RNA-Seq of poly A selected mRNA;

value: human kidney organoid

tag: developing stage

value: Differentiation day28


title: 3B5

tag: medial lateral


title: 3B3

tag: dorsal ventral


title: HuOrg_D16_2: human kidney organoid, differentiation day 16, sample 2

source_name: human kidney organoid, differentiation day 16, organoid 2

value: Differentiation day16


title: 3B7

tag: anterior posterior


title: 3A8


title: HuOrg_D28_2: human kidney organoid, differentiation day 28, sample 2

source_name: human kidney organoid, differentiation day 28, organoid 2


title: 3D5


title: MEL270.dBRD9.input


title: H15w_Z2: human week 15 kidney, Zone2 single cell RNA-Seq

source_name: human kidney, manually dissected inner cortex

value: Week 15


title: HuOrg_D16_1: human kidney organoid, differentiation day 16, sample 1

source_name: human kidney organoid, differentiation day 16, organoid 1


title: Follicular Lymphoma patient FL_045


title: 3B9

source_name: suprachiasmatic nucleus


title: Follicular Lymphoma patient FL_044


title: Follicular Lymphoma patient FL_042


title: Follicular Lymphoma patient FL_041


title: 3D3


title: H15w_Z1: human week 15 kidney, Zone1 single cell RNA-Seq

source_name: human kidney, manually dissected outer cortex


title: 3C8


title: H17w_Z2: human week 17 kidney, Zone2 single cell RNA-Seq

value: human kidney, manually dissected inner cortex

value: Week 17


title: 31_Day16eGFP_pos_4

description:
processed data file:
D16MAFBeGFP+_vs_D28MAFBeGFP+.txt

data_processing:
Fastq files were aligned to hg38 with TopHat2
Gene-level quantification was performed with Partek E/M through Partek Genomic Suite
Gene-level read couns was normalized to TPM through Partek Genomic Suite
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 16, batch 4

growth_protocol: Kidney differentiation followed protocol described in Morizane et al., 2016

extract_protocol:
Ambion Recoverall Total Nucleic Acid Isolation Kit and QIAGEN Rneasy Micro Kit; Qiagen Rneasy micro kit
Kapa stranded mRNA-Seq library (#KK8420)

tag: cell line source

tag: source cell type

value: human embryonic stem cells

tag: differentiation day

value: Day 16

tag: cell line of origin

value: H9 human embryonic stem cell

tag: genotype/variation


title: 30_Day16eGFP_pos_3

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 16, batch 3


title: 29_Day16eGFP_pos_2

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 16, batch 2


title: Follicular Lymphoma patient FL_038

value: Follicular Lymphoma


title: Follicular Lymphoma patient FL_039


title: H17w_Z1: human week 17 kidney, Zone1 single cell RNA-Seq

value: human kidney, manually dissected outer cortex


title: 2A6


title: 1C4


title: 2B5


title: Follicular Lymphoma patient FL_036


title: Follicular Lymphoma patient FL_037


title: Follicular Lymphoma patient FL_040


title: 28_Day16eGFP_pos_1

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 16, batch 1


title: 26_Day28eGFP_neg_3

description:
processed data file:
D28MAFBeGFP+_vs_D28MAFBeGFP-.txt

source_name: FACS-sorted eGFP- cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 3

value: Day 28


title: 2B7


title: 2A4


title: Follicular Lymphoma patient FL_034


title: 1B3


title: 27_Day28eGFP_neg_4

source_name: FACS-sorted eGFP- cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 4


title: Follicular Lymphoma patient FL_032

source_name: biopsy


title: 3C2


title: Follicular Lymphoma patient FL_030


title: 1B5


title: Follicular Lymphoma patient FL_035


title: 2C6


title: Follicular Lymphoma patient FL_031


title: Follicular Lymphoma patient FL_029


title: 23_Day28eGFP_pos_4

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 4


title: 24_Day28eGFP_neg_1

source_name: FACS-sorted eGFP- cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 1


title: 1A4


title: 22_Day28eGFP_pos_3

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 3


title: 21_Day28eGFP_pos_2

source_name: FACS-sorted eGFP+ cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 2


title: 25_Day28eGFP_neg_2

source_name: FACS-sorted eGFP- cells from Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 2


title: 3A6


title: 2C4


title: 19_Day28_4

description:
processed data file:
TPM-table_progression_org_differentiation_all-reps.txt

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 4


title: Follicular Lymphoma patient FL_043


title: 18_Day28_3

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 3


title: 17_Day28_2

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 2


title: Follicular Lymphoma patient FL_028


title: 16_Day28_1

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 28, batch 1


title: Follicular Lymphoma patient FL_025


title: Follicular Lymphoma patient FL_026


title: Follicular Lymphoma patient FL_027


title: Follicular Lymphoma patient FL_024


title: Follicular Lymphoma patient FL_023


title: 15_Day22_3

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 22, batch 3

value: Day 22


title: 14_Day22_2

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 22, batch 2


title: Follicular Lymphoma patient FL_033


title: 13_Day22_1

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 22, batch 1


title: CT38

city: MILL VALLEY

first: Brian

middle: A

last: Hodge

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

hyb_protocol: cDNA libraries were hybridized to Affymetrix Mouse Gene 1.0 ST microarrays (1 sample/timepoint).

scan_protocol: not provided

data_processing: RMA was used for both gene-level and transcript level analysis. Transcript level anlaysis files are included as supplementary files, both in .chp and .txt formats. Sample data tables include gene-level analysis.

source_name: Gastrocnemius Muscle Tissue, Vehicle Treated, collected at CT38

label_protocol: not provided

growth_protocol: iMS-Bmal1(flox/flox) mice were housed in individual cages in light controlled boxes and were entrained to 12-h LD cycles for 14 days.

extract_protocol: Total RNA was extracted with the TRIzol reagent (Invitrogen) according to manufacturer's directions. Total RNA was isolated from four biological replicates and pooled together at each time-point. RNA samples were treated with TURBO Dnase (Ambion) to remove genomic DNA contamination.

treatment_protocol: Following entrainment mice were either injected with tamoxifen or vehicle (15% ethanol in sunflower seed oil) for five consecutive days to generate iMS-Bmal1-/- (Tamoxifen treated) or (Vehicle treated) mice. Following the injections mice were reared for five weeks on a 12h LD cycle and Ad libitum access to food. Mice were then released into constant darkness for 30 h and sacrificed in darkness (dim red light) every 4 hours for 24 hours starting at CT18.

tag: gender

value: male

value: Gastrocnemius Muscle

tag: genotype

value: wildtype

tag: timepoint


title: CT34

source_name: Gastrocnemius Muscle Tissue, Vehicle Treated, collected at CT34


title: Follicular Lymphoma patient FL_021

value: tumor specimen


title: 12_Day16_3

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 16, batch 3


title: Follicular Lymphoma patient FL_019


title: CT30

source_name: Gastrocnemius Muscle Tissue, Vehicle Treated, collected at CT30


title: CT18

source_name: Gastrocnemius Muscle Tissue, Vehicle Treated, collected at CT18


title: CT26

source_name: Gastrocnemius Muscle Tissue, Vehicle Treated, collected at CT26


title: RSBS9 CD133 +ve

city: Chandigarh

first: Shifa

last: Javed

state: Outside US

address: Sector 12, Chandigarh, India

department: Cytology and GynecPathology

country: India

institute: Postgraduate Institute of Medical Education and Research

description: Gene expression after sorting cells

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent's human GXP_8X60k Array . (AMADID: 039494). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

source_name: Primary cultured cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Cells Cultured in DMEM-F12 media (Invitrogen, USA) and 10%FBS (USA origin), at 37C in 5%CO2 till 70%confluency

extract_protocol: The RNA extraction from the samples was performed by Qiagen RNeasy Mini Kit with DNAse treatment (Cat.No. 74004) as per manufacturer’s protocol.

treatment_protocol: Sorted the cells with Flow cytometry with ALDH and CD133 antibody

tag: disease state

value: Cervical cancer

value: Female


title: Follicular Lymphoma patient FL_020

first: Michael

last: Green

address: 1515 Holcombe Blvd, Unit 903

source_name: biopsy

tag: diagnosis


title: Follicular Lymphoma patient FL_016

tag: tissue


title: Follicular Lymphoma patient FL_018


title: Follicular Lymphoma patient FL_022


title: RSBS9 CD133 -ve

description: Gene expression after sorting cells


title: CT22

source_name: Gastrocnemius Muscle Tissue, Vehicle Treated, collected at CT22


title: iMS-Bmal1-/- CT34

source_name: Gastrocnemius Muscle Tissue, Tamoxifen Treated, collected at CT34

value: Bmal1 knockout


title: iMS-Bmal1-/- CT38

source_name: Gastrocnemius Muscle Tissue, Tamoxifen Treated, collected at CT38


title: RSBS14 Tissue

description: Gene expression of tissue complete

source_name: Cervical cancer tissue


title: Follicular Lymphoma patient FL_017


title: RSBS14 ALDH +ve

description: Gene expression after sorting cells


title: 09_Day10_3

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 10, batch 3

value: Day 10


title: 11_Day16_2

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 16, batch 2


title: Follicular Lymphoma patient FL_014


title: 10_Day16_1

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 16, batch 1


title: iMS-Bmal1-/- CT30

source_name: Gastrocnemius Muscle Tissue, Tamoxifen Treated, collected at CT30


title: RSBS14 CD133 -ve

description: Gene expression after sorting cells


title: iMS-Bmal1-/- CT26

source_name: Gastrocnemius Muscle Tissue, Tamoxifen Treated, collected at CT26


title: Follicular Lymphoma patient FL_015


title: RSBS14 ALDH -ve

description: Gene expression after sorting cells


title: Follicular Lymphoma patient FL_013


title: RSBS14 CD133 +ve

description: Gene expression after sorting cells


title: 08_Day10_2

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 10, batch 2


title: 06_Day8_3

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 8, batch 3

value: Day 8


title: Follicular Lymphoma patient FL_012


title: Bonobo_Hi-C

city: Pittsburgh

first: Yang

last: Yang

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

data_processing:
Hi-C contacts based on the corresponding genome assembly of each species were calculated from the Hi-C sequencing reads of the corresponding species using the processing pipeline of the software Juicer Tools, with the command: bash juicer.sh -g genomeID -s HindIII -D Juicer scripts directory -z reference genome file -p chromosome sizes path -y restriction site file -x. For each species, we merged the paired-end Hi-C sequencing reads from different lanes.
The genomic loci of Hi-C contacts in each species were mapped to the reference genome (human genome assembly hg38) using the tool liftOver with reciprocal mapping, with command: liftOver oldFile map.chain newFile unMapped -minMatch=0.5.
The .hic file of each species which stores the Hi-C contact matrix information of the species was obtained from the Hi-C contacts that were mapped to the human genome, using the software Juicer Tools, with the command: java -Xmx16g -jar path of juicer_tools.jar pre Hi-C contact file output_file genomeID.
Hi-C contact maps of each species were generated at the resolution of 50Kb using Juicer Tools with the normalization by Knight-Ruiz matrix balancing applied. The command is: java -jar path of juicer_tools.jar dump observed KR .hic file chromID1 chromID2 BP 50000 output_file.
Median filtering was performed to interpolate the missing values in the Hi-C contact map of each species in each synteny block. For each node without signal value in the Hi-C contact map, the median of Hi-C contact frequencies of the 8-connected neighbors was used as the value assigned to the node.
Anisotropic diffusion filtering was applied to the Hi-C contact map of each species in each synteny block to smooth the signals, using the function in the MedPy package.
The Hi-C contact frequencies of each species were normalized to the same scale over all the autosomes for all the species.
Genome_build: panTro5
Genome_build: panPan2
Genome_build: gorGor4
Supplementary_files_format_and_content: The .hic file of each species is compressed binary file that stores Hi-C contact matrices from multiple resolutions. The .hic files of non-human species are based on the human genome coordinates (human genome assembly hg38), as the Hi-C contacts in each species have been mapped to human genome. The files named by *_contact50K_norm.txt are the smoothed and normalized Hi-C contact frequencies of each species on all the autosomes based on the human genome coordinates, which include intra-chromosome contacts only. The first column is the chromosome ID. The second column is the starting position of the first locus in a Hi-C contact. The third column is the starting position of the second locus in a Hi-C contact. The paired genomic loci in a Hi-C contact are both 50Kb in length. The third column is the smoothed and normalized Hi-C contact frequency between the paired genomic loci.

organism: Pan paniscus

source_name: Bonobo lymphocyte

growth_protocol: The cell lines were a gift from the laboratory of Dr. Ajit Varki. Cells were grown as suspension cultures RPMI-1640 media supplemented with 15% Fetal bovine serum and Penicillin/Streptomycin. Cells were fixed in suspension culture at density of 1 million cells/mL with %1 formaldehyde for 10 minutes at room temperature. Fixation was quenched with glycine, and cells were harvested by centrifugation, washed with 1X DPBS, and frozen in aliquots of 5 million cells until ready for further processing.

extract_protocol:
Hi-C libraries were prepared using the original dilution Hi-C protocol and using the HindIII restriction enzyme. In brief, nuclei were isolated by performing gentle cell lysis on ice followed by 10 strokes with a Dounce homogenizer. Nuclei were washed in lysis buffer and resuspended in NEB Buffer 2, and digested with 400U of HindIII restriction enzyme and digested overnight. The following day the restriction enzyme was heat inactivated and ends were filled in with nucleotides including a biotin-14-dCTP and blunt end ligated for 4 hours. The samples were then subject to overnight proteinase K treatment and reverse cross linking. DNA was purified using phenol:chloroform extraction and ethanol precipitation. Libraries were prepared using Illumina TruSeq adaptors, and biotin containing fragments were isolated using streptavidin coated beads. Libraries were amplified using on-bead PCR amplification and purified using SPRI beads.
Illumina TruSeq paired end

tag: cell type

value: lymphocyte


title: Gorilla_Hi-C

organism: Gorilla gorilla

source_name: Gorilla lymphocyte


title: Single-cell Hi-C data of shoot cell 4

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
Library strategy: Single cell Hi-C
The Nuc_processing software was used to take paired sequenced fastq files to create processed single-cell Hi-C contact files (ncc). The Nuc_dymanic software (parameter: -s 8 2 1 0.5 0.2 0.1 0.05 0.02 0.01 0.005) was used to calculated single cell genome structure, the output files (pdb) were for viewing the 3D genome structures in pymol.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: For ncc and pdb file were all blank-delimited text files of output of Nuc_processing and Nuc_dynamic softwares, respectively.

organism: Oryza sativa Japonica Group

source_name: Single shoot cell of rice

growth_protocol: Rice seeds were germinated and grown in a greenhouse or in paddy field.

extract_protocol:
After isolation, cells were immediately aspirated with a glass micropipette and blown out to 0.53 M mannitol (pH 5.7, adjusted with 0.1 M MES) containing 2% (v/v) formaldehyde by using a glass micropipette system. After 15 minutes, the cells were aspirated and blown out to fresh 0.53 M mannitol without formaldehyde for washing, Finally, the fixed clean cells were aspirated one by one, and blown into a 200 μl PCR well containing 7.7 μl Dpn II buffer (1X), at 4°C and kept on ice for next steps.
For the precise protocol for library construction, please see the paper of this data linked to. Briefly,7.7 μl 1×Dpn II buffer containing single cell was heated in 62 °C for 7 min to directly lyse cell and to loosen the nuclear membrane.For each well, 0.3 μl (3 U) Dpn II (R0543, NEB) was added after cooling, and incubate at 37 °C for 14 hours.Denature Dpn II at 62 °C for 10 min. Add 2 μl ligation mixture (1 μl 10×T4 ligase buffer, 1 μl (400 U) T4 DNA ligase, M0202, NEB),hold at 16 °C for 4.5 hours, then at room temperature for 30 min.Denature ligase and de-crosslink at 65 °C for 6 hours. DNA amplification was applied with REPLI-g Single Cell Kit (150345, QIAGEN).Shear DNA to 150-500 bp range by sonication.Finally,contruct the library for illumina sequencing by following the classic steps including end repairing, adaptor ligation, and DNA amplification.

value: Shoot cell isolated from 12-day-after-germination seedling

tag: cultivar

value: Dongjin


title: 07_Day10_1

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 10, batch 1

value: human embryonic stem cells

value: H9 human embryonic stem cell


title: Single-cell Hi-C data of shoot cell 3


title: 05_Day8_2

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 8, batch 2


title: 04_Day8_1

source_name: Kidney organoid derived from MAFB-P2A-eGFP H9 hESC, collected on differentiation day 8, batch 1


title: SIHA ALDH +ve

description: Gene expression after sorting cells

source_name: Cell line


title: iMS-Bmal1-/- CT22

source_name: Gastrocnemius Muscle Tissue, Tamoxifen Treated, collected at CT22


title: 03_hESC_3

source_name: MAFB-P2A-eGFP H9 human embryonic stem cells_before differentiation_batch3

value: Day 0


title: iMS-Bmal1-/- CT18

source_name: Gastrocnemius Muscle Tissue, Tamoxifen Treated, collected at CT18


title: SIHA ALDH -ve

description: Gene expression after sorting cells


title: 02_hESC_2

source_name: MAFB-P2A-eGFP H9 human embryonic stem cells_before differentiation_batch2


title: Follicular Lymphoma patient FL_011

city: Houston

institute: MD Anderson Cancer Center

source_name: biopsy

value: Follicular Lymphoma


title: BMNC_Subj5

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

country: Denmark

institute: Bispebjerg Hospital

data_processing:
Reads were filtered using SOAPnuke v1.5.2 and parameters: -l 15 -q 0.2 -n 0.05
Clean reads were mapped to the human genome (hg19) using HISAT2 v2.0.4 and parameters: -p 8 --phred64 --sensitive -I 1 -X 1000
Clean reads were mapped to reference RNA using Bowtie2 v2.2.5 and parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16  -k 200
Expression levels were assessed using RSEM v1.2.12 and default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Blood

extract_protocol:
Cells were isolated and RNA purified with TriReagent followed by oligo dT selection.
RNA was submitted to BGI Europa and analyzed according to their standard procedure: mRNA enriched by oligo dT selection was fragmented and reverse transcribed by N6 random priming. The synthesized cDNA was subjected to end-repair and 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments and the ligation products purified and subjected to PCR amplification. The PCR products were denatured by heat and the single strand DNA cyclized by splint oligo and DNA ligase. Finally, they were sequenced on the BGISEQ-500 platform

value: Male

tag: age

tag: injured muscle

value: Medial gastrocnemius

tag: days since injury


title: Follicular Lymphoma patient FL_010


title: Exudate_Subj5

source_name: Muscle injury exudate


title: Exudate_Subj6


title: PPC-GOOD-12

city: Bath

first: Alberto

last: D'Angelo

address: Claverton Down

department: Biology and Biochemistry

institute: University of Bath

description: Tumor RNA samples were analyzed using nCounter PanCancer immune profile panel consisting of 770 human immune-related genes

hyb_protocol: An overnight hybridization reaction was used to incorporate the resulting material, carried out by combining 20 ml of nCounter Reporter probes in hybridization buffer, 5 ml of nCounter Capture probes and 5 ml of the total RNA sample for a total reaction volume of 30 ml. The hybridizations were incubated at 65 °C for 16–20 h.

scan_protocol: Target abundance values can then be determined through the nCounter Digital Analyzer by counting the individual fluorescent barcodes. A high-density scan was performed for each assay (encompassing 600 fields of view).

data_processing:
After hybridization, the cartridges were analyzed in the Digital Analyzer that counts (representing the number of molecules) and arranges the barcodes.
For the mRNA content normalization, housekeeping genes were then used. To facilitate downstream statistical analysis, values < 0 were blanketed and considered equal to 1. After initial normalization steps, data were imported to GraphPad Prism to be processed for statistical analysis.

label: multiple fluorophores

source_name: primary pancreatic cancer

label_protocol: Color-coded barcodes are used to represent single-target transcripts in the reaction.

growth_protocol: The tissues were formalin-fixed and paraffin embedded (FFPE)

extract_protocol: Total RNA from fresh frozen tumor tissues was extracted using Qiagen Rneasy (Qiagen Inc., Toronto, ON, Canada) as per the manufactur's instructions.

treatment_protocol: Based on the stage of the disease, patients received chemotherapy

tag: individual

value: Patient 6

value: pancreatic cancer

value: F

tag: histology

value: adenocarcinoma

tag: outcome

value: good prognosis


title: PPC-GOOD-11

value: Patient 5

value: M


title: PPC-GOOD-07

value: Patient 4


title: 01_hESC_1

source_name: MAFB-P2A-eGFP H9 human embryonic stem cells_before differentiation_batch1

tag: cell line source

tag: source cell type

tag: differentiation day


title: BMNC_Subj4

tag: gender


title: BMNC_Subj6


title: Exudate_Subj4


title: Follicular Lymphoma patient FL_006

data_processing: Raw cel files were RMA normalized using the ExpressionFileCreator module of GenePattern31, and quality checked for batch effects by unsupervised clustering of the 3,000 most variably expressed genes across the dataset.

value: tumor specimen


title: PPC-WORSE-06

value: Patient 3

value: worse prognosis


title: PPC-WORSE-04

value: Patient 2


title: Brain Slices after 14 Day cultivation

city: Freiburg

first: Dieter

middle: Henrik

last: Heiland

address: Breisacherstr. 64

department: Department of Neurosurgery

institute: Medical Center Freiburg

data_processing:
Basecalling by Albacore 2.0.1, Quality Control, Identification of Barcoded Samples by PoreChop
Alignment by MiniMap2
Nanopore Pipeline (www.github.com/heilandd/)
Postprocessing by DESeq2 and AutoPipe (Cran)
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files of counts per barcode

source_name: Slices

extract_protocol:
RNA-extraction
Library was constructed by Nanopore cDNA sequencing Kit, SQK-PCS109
cDNA Sequencing

value: neocortex

tag: sample type

tag: batch


title: BMNC_Subj2

value: Biceps femoris caput longum


title: Brain Slices after 7 Day cultivation


title: Follicular Lymphoma patient FL_009

value: Follicular Lymphoma


title: Follicular Lymphoma patient FL_008


title: Follicular Lymphoma patient FL_005


title: PPC-WORSE-01

value: Patient 1

tag: disease state


title: Follicular Lymphoma patient FL_004

tag: diagnosis


title: Follicular Lymphoma patient FL_003

tag: tissue


title: Follicular Lymphoma patient FL_007


title: Acute Brain slice

description: Acute

value: Acute


title: Follicular Lymphoma patient FL_002


title: Exudate_Subj2

value: Male


title: Wild Type RNA Seq

city: Kansas City

first: Indranil

last: Biswas

state: KS

address: 3901 Rainbow Blvd

department: Microbiology

institute: University of Kansas Medical Center

data_processing:
Resulting reads were subjected to quality control (Sickle v1.200) (https://github.com/najoshi/sickle) and adapter contamination removal (Scythe v0.991) (https://github.com/vsbuffalo/scythe).
High-quality, adapter-free reads were mapped onto the S. mutans chromosome (GenBank accession number NC_004350) using TopHat v2.0.10 (https://github.com/infphilo/tophat).
Differentially expressed genes (DEGs) were identified using Cufflinks v2.2.1 (https://github.com/cole-trapnell-lab/cufflinks).
A fold change threshold of 2 and a significance threshold q of _0.05 were applied, after which DEGs were manually classified into functional groups based on the KEGG database.

organism: Streptococcus mutans UA159

source_name: Bacterial total RNA wiout rRNA

growth_protocol: Grown at 37C in THY broth

extract_protocol:
Total RNAs from exponential-growth-phase cultures of S. mutans UA159 and its isogenic sprV deletion mutant were prepared using the RNeasy kit (Qiagen) following the manufacturer’s recommendations. Cell pellets were pretreated with the RNAprotect bacterial reagent to stabilize RNA. Prepared RNA was quantified spectrophotometrically and subjected to RNase-free DNase (Qiagen) treatment for 45 min. After removal of DNA, mRNA was enriched from the total RNA using the Ribo-Zero rRNA removal kit (llumina) according to the manufacturer’s recommendations.
Resulting mRNA was quantified fluorometrically and subjected to the Illumina paired-end 100-bp library preparation protocols as per the manufacturer’s recommendations.

treatment_protocol: None.

tag: strain

tag: genotype/variation

value: Wild Type


title: Input-DNA_LNCaP

status: Public on Jun 18 2019

city: MARSEILLE

first: Chaima

last: cherif

address: 27 Bd lei Roure CS 30059

country: France

institute: crcm 1068 inserm

data_processing:
ChIPseq :
basecalling was performed using Illumina CASAVA
Reads with Phred quality score less than 30 were filtered out
Replicate concurrency was verified by PCA plots
Sequences were mapped to the human genome using Bowtie2 alignment tool (ref: PMID 22388286) with default parameters
bigWig files were generated using Deeptools 2.0 suite (bamCompare) and normalized by the total number of mapped tags such that each file corresponds to the same amount of reads.
Peak callings were performed using MACS2 (broad mode, pval=0.01, broad cut-off = 0.01) using inputs as controls
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Prostate cancer cells

growth_protocol: The androgen-independent (AI) prostate cancer cell line PC-3 were purchased from the American Type Culture Collection (Rockville, MD) and maintained in Dulbecco’s Modified Eagle’s Medium (Invitrogen, Cergy Pontoise, France), supplemented with 10% fetal bovine serum (FBS). The human sensitive prostate cancer cell line LNCaP was kindly provided by the University of Virginia (Charlottesville, VA) and the human Normal prostate PNT1A cell line was maintained in RPMI 1640 (Roswell Park Memorial Institute) (Invitrogen, Cergy Pontoise, France), supplemented with 10% FBS. Cells were maintained at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer's instructions.

tag: cell line

value: LNCaP

tag: cell type

value: Derived from metastatic site:Left supraclavicular lymph node.

tag: passages

tag: source tissue

value: androgen sensitive prostate cancer

tag: chip antibody

value: none (input)


title: Menin_ChIPSeq_PNT1a

source_name: Prostate cells

value: Human post pubertal prostate normal, immortalised with SV40

value: Normal prostate

value: rabbit anti-Menin polyclonal antibody (Bethyl, INC)


title: Menin_ChIPSeq_LNCaP


title: Input-DNA_PC-3

value: Derived from metastatic site:Bone

value: androgen resistant prostate cancer


title: KO_H4_ChIP

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University

data_processing:
Basecalls were performed in BaseSpace using the FASTQ generation application, version 1.0.0.
Reads were aligned to the human genome build hg19 using Bowtie2 version 2.3.0. The following command was used: bowtie2 -t -p 4 -D 15 -R 2 -L 32 -i S,1,0.75 -x hg19 -U <reads>.fastq -S <output>.sam.
Peaks were identified using MACS2 version macs2 2.1.1.20160309 using options to detect broad peak distributions for histone marks. For H4 ChIP-Seq, the corresponding input replicates were used as the control and for γH2AX ChIP-Seq, the first input replicate was used as the control. The following command was used: macs2 callpeak -t <ChIP>.bam -c <input>.bam -n <output> --outdir ./macs2/ -g hs --broad --broad-cutoff 0.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks_broadpeak.bed: Bed files contain peaks that were found in each sample using the MACS2 data processing step.

source_name: U2OS osteosarcoma cells

growth_protocol: U2OS cells and the resulting CRISPR clones were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 50 U/mL penicillin and 50 µg/mL streptomycin. Cells were grown at 37°C in humidified air containing 5% CO2.

extract_protocol:
ChIP was conducted according to protocols adapted from Cecchini et al., 2014. Briefly, asynchronously cycling cells were fixed in 2mM ethylene glycol bis(succinimidyl succinate) (EGS) in 1X PBS followed by 1% formaldehyde. Fixing reactions were neutralized with 0.125M glycine. Cross-linked chromatin was sonicated so most chromatin was ≤400 bp. Sheared chromatin was then normalized between experimental groups and pre-cleared with protein G Dynabeads and IgG. Pre-cleared chromatin was then incubated with protein G Dynabeads and ChIP antibodies to immunoprecipitate proteins. DNA was isolated for library preparation, and 20 replicates per genotype for γH2AX ChIP-Seq were pooled to achieve DNA yield required for library preparation.
Libraries were constructed according to the NEBNext Ultra II DNA library prep kit.

value: Osteosarcoma cells

value: H4 (clone 62-141-13, EMD Millipore)


title: SprV Mutant RNA Seq

value: SprV Mutant


title: KO_gH2AX

value: gammaH2AX (clone JBW301, EMD Millipore)


title: KO_input_2


title: Input-DNA_PNT1a


title: Het_gH2AX


title: KO_H4_ChIP_2


title: Het_input_2


title: Menin_ChIPSeq_PC-3


title: Het_H4_ChIP


title: Het_H4_ChIP_2


title: WT_gH2AX


title: Follicular Lymphoma patient FL_001

department: Lymphoma/Myeloma

extract_protocol: Trizol or Qiagen RNA extraction kit

value: Follicular Lymphoma

value: tumor specimen


title: Het_input


title: WT_H4_ChIP


title: WT_H4_ChIP_2


title: WT_input_2


title: ChIPseq_MCF10A_H3K27ac_minusDOX

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

institute: University of Wuerzburg

data_processing:
For ChIP-seq analysis, reads were aligned to the human (hg19) or murine (mm10) genome with BOWTIE v1.1.2 (Langmead, 2010) using default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Genome-wide read density files ("bedgraph") were generated with the genomeCoverageBed function from the bedtools suite v2.26.0 (Quinlan et al., 2010).
For RNA-seq analysis, reads were aligned to the murine genome (mm10) with TopHat v2.1.0 (Kim et al., 2013) using BOWTIE2 (Langmead, 2010) and default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Reads per gene (Ensembl database GRCm38.p6) were counted with the "summarizeOverlaps" function in the R package {GenomicFeatures}.
Non- or weakly expressed genes were removed (threshold: mean read count per gene over all samples >1).
Differential gene expression was called using EdgeR and adjusting the calculated p-value with the Benjamini-Höchberg procedure.
Genome_build: mm10 (GRCm38) or hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Supplementary_files_format_and_content: RNA-seq: RNAseq_KPL_countmatrix.txt containing raw read counts for all samples and all genes.
Supplementary_files_format_and_content: RNA-seq: RNAseq_KPL_plusOHT_vs_minusOHT.txt containing gene names, gene description, log2FC, log2CPM, p-value, Benjamini-Höchberg-adjusted p-value (FDR).

growth_protocol: KPL cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/ streptomycin. MCF10A-YAP5SA cells were cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.

extract_protocol: For ChIP-Seq, chromatin from 2 x 10e7 KPL cells or 3.5 x 10e7 MCF10A-YAP5SA was isolated and immunoprecipitated as described above. Libraries for ChIP-Seq were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) according to the manufacturer’s instructions. Size-selection was performed using Agencourt AMPure XP beads (Beckman Coulter) (150 bp). DNA fragments were amplified by 10-15 cycles of PCR and library quality was analyzed with the Biorad Experion system and the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using pico green.

treatment_protocol: To delete Lin9, KPL cells were treated with 10 nm 4-OHT (Sigma) for 72 hours. The expression of YAP5SA was induced in MCF10A-YAP5SA cells by the addition of 0.5 µg/ml doxycycline for 12 hours.

tag: treatment

value: ctrl


title: WT_input


title: ChIPseq_MCF10A_H3K4me3_plusDOX

value: doxycycline

value: H3K4me3 (Abcam ab8580)


title: ChIPseq_MCF10A_H3K4me1_plusDOX

value: H3K4me1 (Abcam ab8895)


title: ChIPseq_MCF10A_H3K4me3_minusDOX


title: ChIPseq_MCF10A_H3K27ac_plusDOX


title: KO_input