title: genomic DNA from malignant melanoma clinical sample 1103P

description:
SAMPLE 2
Malignant melanoma clinical sample.

value: Male


title: genomic DNA from malignant melanoma clinical sample 1205M

status: Public on Oct 22 2020

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description:
SAMPLE 8
Malignant melanoma clinical sample.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from primary cell culture or clinical samples using QIAamp DNA FFPE Tissue Kit according to standard instructions.

tag: gender

tag: age

tag: disease state

value: malignant melanoma

tag: tissue

value: lymph node

tag: tumor thickness

tag: stage (ajcc 7th)


title: C103_D100

type: SRA

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

molecule: total RNA

source_name: Intestine

growth_protocol: Enteroids were grown in conditions indicated in the manuscript

extract_protocol:
RNA was isolated and enteroids according to E.Z.N.A.® Total RNA Kit I protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Enteroids were treated with either 1,25D3 (100nM) or an eqaul volume of Ethanol (Control)

tag: treatment

tag: status

value: Differentiated

tag: segment

tag: patient line


title: genomic DNA from malignant melanoma clinical sample 1109P

description:
SAMPLE 4
Malignant melanoma clinical sample.

value: skin


title: Cut_and_run_H3K27me2_SDHC_KO_1

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3
Mapped reads were used to generate genomic coverage bedGraph files using bedtools v2.27.0.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

organism: Mus musculus

source_name: immortalized mouse embryonic fibroblast cell line

growth_protocol: Cells grown in DMEM (low glucose) containing 10% FBS at 37 degrees Celsius in 5% CO2.

extract_protocol:
Cells harvested by trypsinization, and CUT&RUN performed using standard procedure.
Rubicon Genomics ThruPLEX DNA-seq 48 S kit.

treatment_protocol: Gene rearrangement induced by adding doxycycline to media at 1 microgram/mL final concentration.

tag: genotype

tag: condition

value: SDHC KO

tag: antibody

tag: antibody manufacturer and catalog number

value: Abcam cat# 24684


title: Cut_and_run_H3K27me2_SDHC_KO_3


title: genomic DNA from malignant melanoma clinical sample 1101P

description:
SAMPLE 1
Malignant melanoma clinical sample.


title: SZ15 CTR

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
The sequenced reads were mapped onto the GrCh38 homo sapiens reference genome, version GrCh38.v81 using CLC Genomics Workbench 12.0 (Qiagen) and gene expression values TPM (Transcripts per million) were calculated using CLC Genomics Workbench 12.0.
Paired-end raw read FASTq files were quality checked using the CLC Genomics Workbench 12.0 per default parameters. Failed reads were removed at this time.
Heatmaps were generated in TreeView3 using values normalized for each donor as follows: library size normalization is automatically performed using the TMM (trimmed mean of M values) method. For each desired comparison, gene differential expression was calculated from regularized log-fold-changes and multiple-testing-corrected P-values. Genes were considered to be differentially expressed when P < 0.05 and log2FC was >0.585 in either direction (which corresponds to FC > 1.5 in either direction). Volcano plots, PCA plots, and Venn diagrams were generated from genes that were initially filtered to exclude those with low overall expression in all samples.
Default parameters can be found at: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/1200/index.php?manual=Introduction_CLC_Genomics_Workbench.html
Genome_build: GrCh38
Supplementary_files_format_and_content: Excel files with gene expression data

source_name: CD4+ cells from SZ patient blood

growth_protocol: All cultures were performed in complete RPMI-1640 medium (ThermoFisher) containing rhIL-2 (10ng/ml, PeproTech) and IL-7 (5ng/ml, PeproTech).16 Cells were activated by the Dynabeads CD3/CD28 T cell Expander (ThermoFisher, bead-to-cell ratio: 1:1).

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Blood samples were purified for CD4+ cells using EasySep enrichment kit (StemCell Technologies). RNA was isolated from samples obtained from SS (n=4), MF (n=3), and HC (n=3) independent donors on 48 hours of culture with/without STAT-6 inhibitor. Total RNA was isolated using the RNeasy purification Kit (Qiagen), and cDNA was obtained employing the High Capacity Reverse Transcription cDNA synthesis kit (Applied Biosystems). RNA was quantified by a Qubit Fluorometer (Invitrogen) and RNA integrity was checked using an Agilent Bioanalyzer and RNA 6000 Nano Kit (Agilent Technologies).
Libraries were prepared using ultra DNA library prep kits. RNA sequencing analysis was performed on Illumina NextSeq500 using 500-bp paired-end reads by Health Science Sequencing core facility at University of Pittsburgh. Between 10 and 30 million read pairs were generated per sample.

treatment_protocol: STAT-6 was inhibited by the STAT-6-specific inhibitor AS151749930 (100nM, Axon Medchem)

tag: tumor type

value: Sezary syndrome


title: SZ14 + STAT6i

value: STAT6 inhibitor


title: Cut_and_run_H3K27me2_Control_2

value: Control


title: SZ14 CTR


title: SZ8 + STAT6i


title: Cut_and_run_H3K27me2_Control_1


title: C104_D100


title: C104_H0

value: Control (0nM)

value: Undifferentiated


title: C104_D0


title: PF42 + STAT6i

source_name: CD4+ cells from normal blood


title: C109_H100


title: Cut_and_run_H3K4me3_SDHC_KO_1

value: Abcam cat# ab8580


title: SZ8 CTR


title: C109_D100


title: Cut_and_run_H3K4me3_SDHC_KO_3


title: C109_H0


title: SZ7 CTR


title: C109_D0


title: SZ7 + STAT6i


title: Cut_and_run_H3K4me3_Control_1


title: eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.X1A.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.X1A.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.X1A.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.X1A.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.X1A.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 10  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps reads to the HB27 (GCF_000008125.1) genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 10  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.X1AUnmappedAligned.out.bam
Takes output from STAR genome alignments. Run samtools sort. Command: samtools sort -o /full/path/to/files/file_R1.X1AUnmappedAligned.out.sorted.bam /full/path/to/files/file_R1.X1AUnmappedAligned.out.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.X1AUnmappedAligned.out.sorted.bam
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  HERA.HER1_CLIP.X1AUnmappedAligned.out.bam.sorted.merged.bam /full/path/to/files/file_R1.X1AUnmappedAligned.out.sorted.bam /full/path/to/files/file_R1.X1BUnmappedAligned.out.sorted.bam
Takes output from samtools sort, makes bam index for use downstream.  Command: samtools index HERA.HER1_CLIP.X1AUnmappedAligned.out.bam.sorted.merged.bam
Takes output from samtools sort.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128 -o HERA.HER1_CLIP.X1AUnmappedAligned.out.bam.sorted.merged.r2.bam HERA.HER1_CLIP.X1AUnmappedAligned.out.bam.sorted.merged.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  --bam HERA.HER1_CLIP.X1AUnmappedAligned.out.bam.sorted.merged.r2.bam  --species hb27  --outfile /full/path/to/files/CombinedID.merged.r2.peaks.bed --maxgenes 1000000 --save-pickle
Genome_build: hb27
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

organism: Thermus thermophilus HB27

growth_protocol: Thermus thermophilus HB27 (DSM 7039, DSMZ; ATCC BAA-163) was grown in liquid media (8 g l-1 peptone, 4 g l-1 yeast extract, 2 g l-1 NaCl, pH 7.5) at 75°C. At an OD600 of 0.8 (Hera2, Hera3) or 1.0 (Hera1, Hera4), cells from cultures Hera1 and Hera2 were spread in a thin layer in a heated Petri dish, and RNA-protein complexes were cross-linked by illumination with UV light (254 nm, 400 J cm-2).

extract_protocol:
The isolation of RNA-protein complexes, trimming of the RNA, and preparation of the cDNA library was performed as described (Van Nostrand et al. 2016). Briefly, cells were thawed in lysis buffer (50 mM Tris/HCl, pH 7.4, 100 mM NaCl, 1% (w/v) NP-40, 0.1% (w/v) SDS, 0.5% (w/v) sodium desoxycholate, and Protein Inhibitor Cocktail III (1:200, EMD Millipore) and disrupted by sonification. The crude extract was treated with DNase and RNase to remove DNA and to trim the protein-bound RNA. Hera-RNA complexes were immunoprecipitated using an anti-Hera antibody from rabbit (Eurogentec), and isolated using sheep anti-rabbit Dynabeads.
Subsequent steps were performed with RNA bound to the beads. After dephosphorylation with FastAP (ThermoFisher) and T4 PNK (NEB), a barcoded RNA adapter was ligated to the 3′ end (T4 RNA Ligase, NEB). RNA-protein complexes were separated by SDS-PAGE and transferred to nitrocellulose membranes. The region from 55-130 kDa (75 kDa above the molecular mass of Hera) was excised, the membrane was suspended in buffer and treated with proteinase K (NEB). RNA was isolated by phenyl/chloroform extraction, purified on spin columns (Zymo Research), and reverse-transcribed with AffinityScript (Agilent). Excess oligonucleotides were removed by treatment with ExoSAP-IT (Affymetrix). The second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5′ end) was ligated to the 3’-end of the cDNA (T4 RNA Ligase, NEB). After cleanup on Dynabeads MyOne Silane (ThermoFisher), the required number of PCR cycles was determined from qPCR experiments, the DNA was amplified by PCR, purified with the PippinPrep system (Sage Science), and sequenced on the Illumina HiSeq.

treatment_protocol: Cultures Hera3 and Hera 4 were subjected to a cold shock by rapidly reducing the growth temperature to 60°C for 10 min, followed by cross-linking. UV-irradiated cells were pelleted by centrifugation (4000 rcf, 10 min), the pellets were shock-frozen in liquid nitrogen and stored at -80°C until library preparation was performed.

value: anti-Hera (rabbit)

tag: antibody manufacturer

value: Eurogentec

tag: antibody catalog #

tag: antibody lot

tag: cell line


title: genomic DNA from malignant melanoma clinical sample 1104P

description:
SAMPLE 3
Malignant melanoma clinical sample.

tag: gender

value: Female

tag: age

tag: disease state


title: C111_H100


title: Cut_and_run_CTCF_SDHC_KO_3

value: CTCF

value: Abcam cat# ab70303


title: C111_H0


title: eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 1


title: Cut_and_run_CTCF_SDHC_KO_1


title: C111_D100


title: Cut_and_run_CTCF_Control_2


title: eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 2


title: eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 1


title: Cut_and_run_CTCF_Control_1


title: C111_D0


title: eCLIP Thermus thermophilus, cold-shock conditions, replicate 2

tag: inline barcode1

tag: inline barcode2


title: ATAC-seq_SDHC_KO_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3
Mapped reads were used to generate genomic coverage bedGraph files using bedtools v2.27.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed bedGraph files show genomic coverage.

extract_protocol:
OMNI ATAC-seq performed on 50,000 cells.  Amplified libraries were purified, and the sizes of library DNA were determined by the Fragment Analyzer (Advanced Analytical Technologies, IA) using the High Sensitivity NGS Fragment Analysis Kit (cat# DNF-486). The enrichment of accessible regions was determined by the quantification of the fold difference between positive and negative genomic loci using real-time PCR.
OMNI ATAC-seq library construction


title: eCLIP Thermus thermophilus, cold-shock conditions, replicate 1


title: C112_H100

tag: treatment

tag: status


title: C112_H0

tag: segment

tag: patient line


title: ATAC-seq_SDHC_KO_1

tag: genotype

tag: condition


title: C112_D100


title: eCLIP Thermus thermophilus, normal-growth conditions, replicate 2

tag: antibody


title: eCLIP Thermus thermophilus, normal-growth conditions, replicate 1


title: ATAC-seq_Control_2


title: ATAC-seq_Control_1


title: C112_D0


title: NIC_FLOAT1_S15

city: Pavia

first: Stella

last: Gagliardi

state: Pavia

address: Via Mondino, 2

department: GPG center

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA was performed using R package DESeq2
Genome_build: M24
Supplementary_files_format_and_content: RSEM output: transcript_id, gene_id, length, effective_length, expected_count, TPM, FPKM, IsoPct

source_name: NPCs grown inside the Nichoid and replated in standard floating condition for 7 more days.

growth_protocol: NSCs were maintained in culture in Neurobasal Medium (GIBCOTM, Life Technologies) containing 2% B-27 supplement (Life Technologies), 2% L-Glutamine (Euroclone), 1% penicillin and streptomycin (Euroclone), b-FGF (human recombinant, 20 ng/mL) and hEGF (human recombinant, 20 ng/mL).

extract_protocol:
Neural Precursors Cells (NPCs) expressing green fluorescent protein (GFP) were isolated 6 h post-mortem from adult C57BL/6-Tg(UBC-GFP)30Scha/J mice weighing 25–30 g (Charles River)
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 200-ng total RNA (Illumina). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

treatment_protocol: NIC samples were harvested, collected by centrifugation (123xg for 10 minutes), mechanically dissociated and counted with trypan blue reagent (Sigma Aldrich). 10 000 cells were seeded at the centre of the Nichoid in a single drop of 35 μL NSCs medium. The multi-well was kept in the incubator for 1 hour to allow cells to enter the 3D niches and then 465μL of NSCs medium were added. The multi-wells were kept in the incubator until the end of each specific biological experiment. After 7 days NPCs grown in NIC samples were harvested, collected by centrifugation and replated in standard floating condition for 7 more days

tag: tissue

value: Sub Ventricular Zone

tag: cell type

value: Neural Precursors Cells (NPCs)

tag: strain


title: C131_H100


title: NIC_FLOAT1_S12


title: 100 DBP R2

city: Santa Barbara

first: Kellie

last: Heom

state: California

address: UC Santa Barbara

department: Chemical Engineering

institute: University of California Santa Barbara

data_processing:
library strategy: EMBR-seq (Method is detailed in Wangsanuwat, Heom et al.)
In the sequencing libraries, the left mate contains information about the sample barcode (nucleotides 7-12 in read1). The right mate is mapped to the bacterial transcriptome. Prior to mapping, only reads containing valid sample barcodes were retained. Subsequently, the reads were mapped to the reference transcriptome using Burrows-Wheeler Aligner (BWA) with default parameters
Genome_build: ASM584v2
Supplementary_files_format_and_content: Text file with rows for each gene detected and 96 columns for different barcodes.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 - empty plasmid

extract_protocol:
Trizol total RNA extraction from E. coli was performed according to the manufacturer's protocol.
(1) Poly adenylation. 100 ng of total RNA in 2 µL was combined with 3 µL poly(A) mix, comprised of 1 µL ThermoFisher 5x first strand buffer [250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2], 1 µL blocking primer mix (50 µM), 0.8 µL nuclease-free water, 0.1 µL 10 mM ATP, and 0.1 µL E. coli poly(A) polymerase. The mixture was incubated at 37°C for 10 min. In the control group, no blocking primers were added and 1.8 µL of nuclease-free water was added instead. The blocking primer mix was prepared by mixing equal volumes of 50 µM blocking primers specific to 5S, 16S, and 23S rRNA. (2) Reverse transcription. The polyadenylation product was mixed with 0.5 µL 10 mM dNTPs, 1 µL RT primers (25 ng/µL), and 1.3 µL blocking primer mix (50 µM), and heated to 65°C for 5 min, 58°C for 1 min, and then quenched on ice. In the control samples, the blocking primers were again replaced with nuclease-free water. Next, 3.2 µL RT mix, consisting of 1.2 µL 5x first strand buffer, 1 µL 0.1 M DTT, 0.5 µL RNaseOUT, and 0.5 µL Superscript II reverse transcriptase was added to the solution, followed by 1 h incubation at 42°C. The temperature was then raised to 70°C for 10 min to heat inactivate Superscript II. (3) Second strand synthesis. 49 µL of the second strand mix, containing 33.5 µL water, 12 µL 5x second strand buffer [100 mM Tris-HCl (pH 6.9), 23 mM MgCl2, 450 mM KCl , 0.75 mM β-NAD, 50 mM (NH4)2 SO4], 1.2 µL 10 mM dNTPs, 0.4 µL E. coli ligase, 1.5 µL DNA polymerase I, and 0.4 µL RNase H, was added to the product from the previous step. The mixture was incubated at 16°C for 2 h. cDNA was purified with 1x AMPure XP DNA beads and eluted in 24µL nuclease-free water that was subsequently concentrated to 6.4 µL. (4) In vitro transcription. The concentrated solution was mixed with 9.6 µL of Ambion in vitro transcription mix (1.6 µL of each ribonucleotide, 1.6 µL 10x T7 reaction buffer, 1.6 µL T7 enzyme mix) and incubated at 37°C for 13 h. Next, the aRNA was treated with 6 µL EXO-SAP at 37°C for 15 min followed by fragmentation with 5.5 µL fragmentation buffer (200 mM Tris-acetate (pH 8.1), 500 mM KOAc, 150 mM MgOAc) at 94°C for 3 min. The reaction was then quenched with 2.75 µL stop buffer (0.5 M EDTA) on ice. The fragmented aRNA was size selected with 0.8x AMPure RNA beads and eluted in 15 µL nuclease-free water. Thereafter, Illumina libraries were prepared as described previously in Hashimshony et al. 2016 Genome Biology.

tag: starting total rna

tag: method

value: blocking primer (EMBR-seq)

tag: tex treatment

value: yes


title: 100 DBPP R1

value: blocking primer w 3' phosphate


title: C131_H0


title: C131_D100

value: Differentiated


title: 100 DBN R2

value: no blocking primer (control)


title: CASTAT5 tumor CD4+ T cells ATAC-seq

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
The ATACseq analysis was performed on Galaxy server. Adaptor and quality trimming were performed using Trim Glore! Modules (Galaxy v0.4.3.1). Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings. Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ATAC-seq peak calling was performed on Galaxy server using MACS2 v2.1.2 with following command “-q 0.05 --nomodel --shift --100 --extsize 200 -B --SPMR --keep-dup all --call -summits”.
The Bed file contains common peaks among three biological replicates were generated using bedTools Multiple Intersect function for CASTAT5 and control samples, respectively. The two bed files were combined using bedtools MergeBED function (Galaxy v1.2.0) to generate a single bed file that contains all peaks identified in both CASTA5 and control samples. Finally, the number of paired fragments overlaps with the intervals identified in the merged peak file was counted using bedtools MultiCovBed function (Galaxy v2.27.1) for each of six ATAC-seq samples, respectively.
DEseq2 package v1.24.0  was used to call differential peaks and ChIPseeker v1.20.0. was used annotate the differential peaks.
DiffBind (Galaxy v. 2.6.6.4)  was used to identify differential peaks with fixed window length of 400bp (summit ± 200bp), which were used for motif analysis by MEME-ChIP v5.05 and HOMER v4.9.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by deepTools bamCoverage function (Galaxy v3.1.2.0.0) and visualized in Integrated genome viewer (IGV) v2.5.2. Normalization/scaling methods: RPGC (1x sequencing depth ) : number of reads per bin /(total number of mapped reads * fragment length / effective genome size). Bin size was set to 10bp.

source_name: FACS_sorted CD4 T cells

growth_protocol: CD4 T cells were purified from 6.5-TCR Tg mouse splenocytes and stimulated with mouse CD3/CD28 activation Dynabeads in the presence of rhIL2 overnight. Cells were harvested and transduced twice in two consecutive days with retroviral supernatant. Cells were harvested 24 hours after the second transduction.

extract_protocol: The ATACseq libraries were prepared based on the Omni-ATACseq protocols with some minor modification (Corces MR, Nature Methods volume 14, pages959–962(2017)). Briefly, 60,000 FACS-sorted CD4+ T cells were suspended in 60 ml ATAC- Resuspension Buffer  (RSB, 10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin), incubated on ice for 3 minutes, and then washed with 1ml RSB buffer without NP40 and Digitonin. The resulted nuclei were pelleted at 500 RCF for 10 minutes at 4°C in a fixed angle centrifuge and resuspended in 30ml of Tagmentation DNA (TD) buffer. 5ml of the nuclei was removed, mixed with Trypan Blue solution at (1:1) ratio and examined under microscope to confirm a successful nuclei preparation. The remaining 25ml of nuclei was incubated with 2.5ul of Nextera Tn5 transposase (Illumina) in a total volume of 50ml 1× TD buffer containing 0.01% Digitonin and 0.1% Tween-20. The transposition reaction was performed at 37 °C for 50 minutes in a PCR machine. The transposition mixture was purified using a Zymo DNA Clean and Concentrator kit. The ATAC libraries were amplified for 11-13 cycles using NEBNext 2X MasterMix and Nextera Index primers. The amplified libraries were size-selected using AMPure breads (0.5x) to remove the large fragment of DNA and then purified using Zymo DNA Clean and Concentrator kit. Six ATAC libraries were pooled and sequenced on a NextSeq500 instrument in a pair-end 75 cycle run. 60-100 million read pairs were obtained for each sample.

treatment_protocol: A20HA Tumor cells were subcutaneously injected to the right flank of mice. When tumor sizes reached the desired sizes, mice were randomly assigned into groups to receive the specified treatments. Cyclophosphamide (CTX) was i.p. injected to mice at 150 mg/kg one day before T cell transfer. For adoptive CD4 T-cell transfer, in vitro cultured T cells were harvested and injected into each recipient via tail vein.

tag: cell surface marker

tag: genotype/variation

value: Stat5a (H229R & S711F) mutant

value: Balb/c


title: 100 CNP R3

value: no


title: C131_D0

value: Control (0nM)


title: D102_H100

value: Undifferentiated

value: Duodenum


title: Control tumor CD4+ T cells ATAC-seq

value: Empty Vector


title: CASTAT5 spleen CD4+ T cells ATAC-seq


title: D102_H0


title: 100 CNPP R2


title: Control spleen CD4+ T cells ATAC-seq


title: D102_D100


title: 100 DBP R1


title: CASTAT5 in vitor CD4+ T cells ATAC-seq

source_name: in vitro CASTAT5-transduced CD4 T cells


title: D102_D0


title: Control in vitro CD4+ T cells ATAC-seq

source_name: in vitro activated CD4 T cells


title: 100 DBN R1


title: CASTAT5 spleen CD4+ T cells ATAC-seq 3


title: D103_H100


title: 100 CNP R2


title: NIC_FLOAT1_S11


title: 100 CNPP R1


title: D103_H0


title: CASTAT5 spleen CD4+ T cells ATAC-seq 2


title: D103_D100


title: 100 CNN R2


title: D103_D0


title: 20 CNP R4

value: 20 ng


title: Control spleen CD4+ T cells ATAC-seq 3


title: D104_H100


title: 100 CNN R3


title: Control spleen CD4+ T cells ATAC-seq 2


title: 20 CNN R3


title: 2 CNP R3

value: 2 ng


title: D104_H0


title: Control spleen CD4+ T cells ATAC-seq 1


title: 2 CNN R1


title: CASTAT5 spleen CD4+ T cells scRNAseq

data_processing:
The raw reads in fastq format was processed using 10X genomics cellranger analysis package. CASTAT5 and control samples will be pooled using cellranger aggr pipeline.
The cellranger pipeline outputs containing gene-by-cell expression data from the aggregated libraries were imported into R package Seurat 3.1.4 to create a Seurat object(85). Quality control measures were implemented in Seurat to filter out cells expressing > 6000 genes. Cells with a higher percentage of mitochondrial genes (percent of mt >0.3) were also excluded from the subsequent analysis. Normalization and scaling were performed within Seurat before subsequent analysis such as PCA, umap, tSNE, and clustering analyses. Visualization of the scRNA data was performed using Seurat tSNEplot, Vinplot, Featureplot, Dotplot, and DoHeatmap functions. Cell cycle analysis was performed using the Seurat cell cycle scoring function. A cell cycle gene signature containing 97 cell cycle-related genes(86) were used to derive the G1/S and G2/M scores.
Genome_build: mm10

growth_protocol: CD4 T cells were purified from 6.5-TCR Tg mouse splenocytes and stimulated with mouse CD3/CD28 activation Dynabeads in the presence of rhIL2 overnight. Cells were harvested and transduced twice in two consecutive days with retroviral supernatant u. Cells were harvested 24 hours after the second transduction.

extract_protocol:
FACS-sorted donor CD4+ T cells were processed for scRNAseq libraries using the Chromium Controller (10X Genomics).
scRNAseq libraries were generated for approximately 2,000 cells per sample using 10X 3’ single cell mRNAseq V3 reagents.  The scRNAseq libraries were sequenced using Illumina NextSeq500 sequencer to collect approximately 80k reads per cell.  Each cell was tagged with a Unique Molecular Identifier (UMI) sequence, which represents the identity of each single cell throughput the analysis pipeline.
Single cell RNA-Seq

treatment_protocol: A20HA Tumor cells were subcutaneously injected to the right flank of mice. When tumor sizes reached the desired sizes, mice were randomly assigned into groups to receive the specified treatments. Cyclophosphamide (CTX) was dissolved in PBS and i.p. injected to mice one day before T cell transfer. For adoptive CD4 T-cell transfer, in vitro cultured T cells were harvested and injected into each recipient via tail vein.


title: 0.2 CNP R2


title: D104_D0


title: D104_D100


title: Control spleen CD4+ T cells scRNAseq


title: 0.2 CNN R1


title: D109_H100


title: D109_H0


title: NIC4_S9: NPCs grown inside the Nichoid

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA was performed using R package DESeq2
Genome_build: M24
Supplementary_files_format_and_content: RSEM output: transcript_id, gene_id, length, effective_length, expected_count, TPM, FPKM

source_name: Sub Ventricular Zone

treatment_protocol: NIC samples were harvested, collected by centrifugation (123xg for 10 minutes), mechanically dissociated and counted with trypan blue reagent (Sigma Aldrich). 10 000 cells were seeded at the centre of the Nichoid in a single drop of 35 μL NSCs medium. The multi-well was kept in the incubator for 1 hour to allow cells to enter the 3D niches and then 465μL of NSCs medium were added.

value: Neural Precursor Stem Cells (NPCs)

value: nichioid


title: CASTAT5 spleen CD4+ T cells ATAC-seq 1


title: D109_D100


title: NIC1_S6: NPCs grown inside the Nichoid


title: 20 CNP R3


title: Cut_and_run_H3K4me3_Control_2

value: Control

tag: antibody manufacturer and catalog number

value: Abcam cat# ab8580


title: 20 CNN R2


title: D144_H100


title: D109_D0


title: CRT4_S4: NPCs grown in floating conditions

value: control


title: CRT2_S2: NPCs grown in floating conditions


title: NIC2_S7: NPCs grown inside the Nichoid


title: 2 CNP R2

value: blocking primer (EMBR-seq)


title: D144_H0


title: D144_D100

value: Differentiated


title: CRT1_S1: NPCs grown in floating conditions


title: 20 CNP R2


title: 0.2 CNP R1


title: 2 CNP R1


title: MF6 + STAT6i

source_name: Skin Tumor

tag: tumor type

value: mycosis fungoides

value: STAT6 inhibitor


title: D2_H100

tag: treatment


title: H3K27me3_ChIPseq_WT_2

city: Singapore

first: Qi-Ling

last: Zhou

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Sigapore

data_processing:
The paired-end ChIP-seq reads are mapped by bowtie2 to the mouse reference genome GRCm38 (mm10).
PCR duplicates are filtered out from the resulting BAM files using samtools rmdup.
Alignments with mapping quality below 20 are also filtered out.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. The ChIP-seq signal will be shrunk to fit the size of its control if the control is smaller in size.

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
For ChIPseq, cells were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 200 to 500 base pair and protein-DNA complexes were pulled down by antibodies.
For ChIPseq samples, libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing.

value: WT

value: bone marrow

value: Hematopoietic stem and progenitor cells

tag: developmental stage

value: adult

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys27) (C36B11), Cat# 9733BC, Cell Signaling Technology, Lot. 8


title: Cut_and_run_Acetyllysine_Control_2

value: Acetyllysine

value: PTM Biolabs cat# PTM-105


title: D2_H0

value: Control (0nM)

tag: status

value: Undifferentiated

tag: segment

value: Duodenum

tag: patient line


title: H3K27ac_ChIPseq_KO_2

tag: genotype

value: CTCF KO

value: Rabbit polyclonal to Histone H3 (acetyl K27) - ChIP Grade, Cat# ab4729, Abcam, Lot. GR261979-1


title: H3K27ac_ChIPseq_WT_2

tag: tissue


title: 20 CNP R1

value: 20 ng

value: no


title: D2_D100

value: Differentiated


title: 100 CNP R1

value: blocking primer (EMBR-seq)


title: ZNF143_ChIPseq_WT_2

tag: cell type

value: Anti-ZNF143 rabbit serum, generated in our lab


title: 100 CNN R1

value: no blocking primer (control)


title: D2_D0


title: CTCF_ChIPseq_WT_2

tag: strain

value: WT

value: bone marrow

value: Anti-CTCF antibody, Cat# 07-729 Millipore, Lot. 2757161


title: H2AK119_ChIP_SF8628_PTC028

city: Aurora

first: Etienne

last: Danis

state: CO

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
The quality of fastq files was accessed using FastQC
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads
The ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 (v. 2.3.2).
Samtools (v. 1.5) was used to convert the sam files into bam files, to filter out unmapped reads and to sort the bam files.
When the total number of reads per sample was inferior to 40M, the libraries were re-sequenced and the additional bam files generated from the second sequencing were merged with the bam files from the first sequencing.
The total number of reads used for peak calling was normalized using samtools view -hs (random extraction of a specified percentage of reads). The same number of reads was used for the RNA polymerase II ChIP-seq and for the inputs.
Samtools sort was used to sort the bam files after read extraction.
Bam files were indexed using samtools index.
Bedtools genomecov was used to create bedgraph files from the bam files.
Igvtools toTDF was used to create tdf files from the bedgraph files.
Peaks were called using macs2 (v. 2.1.1.20160309) with default parameters using python (v. 2.7.14).
Peak locations were further annotated using the clusterProfiler, ChIPseeker and ngs.plot.r R packages.
Genome_build: hg38
Supplementary_files_format_and_content: The bam files were generated with samtools.
Supplementary_files_format_and_content: The tdf files were generated with igvtools toTDF.

source_name: diffuse intrinsic pontine glioma

growth_protocol: See SAMPLES section

extract_protocol:
The growth medium was aspirated from cells (70% confluence) and replaced with a 1% formaldehyde in 1X DPBS for 10 min at room temperature. The cross-linking was terminated by addition of glycine to a final concentration of 0.125 M and incubation for 5 min. The cells were washed twice with cold PBS and scraped in ChIP lysis buffer (1% SDS, 10 mM EDTA and 50 mM Tris-HCl pH 8.1) containing COmplete EDTA free protease inhibitors (Sigma). The cell lysates were sonicated with a Bioruptor Plus (Diagenode) for 25 cycles (30 seconds ON and 30 seconds OFF). The size of the sonicated DNA fragments was checked on an 1X TAE1 % agarose gel electrophoresis and ranged between 250 to 500 bp. After removing the debris via centrifugation, chromatin extracts were collected and protein concentration was determined by BCA protein assay reagents (Pierce).  For immunoprecipitation, chromatin extracts with 1 mg of total protein for each sample were incubated with primary antibodies (dilution 1:50) overnight at 4ºC. Primary antibodies used are included in table under “Western blotting” below. After incubation with the primary antibody, 20 uL of pre-washed magnetic beads (Magna ChIP Protein A+G Magnetic Beads, Millipore Sigma) were added to each sample for 2 hours at 4ºC. Using a magnetic rack, the immunoprecipitates were washed successively with 1 ml of low salt buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), high salt buffer (20 mM Tris-HCl [pH 8.0], 500 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), LiCl washing buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, , 1.0% NP40, 1.0% deoxycholate, 1 mM EDTA) and twice with TE buffer. The DNA-protein complexes were eluted with 300 μl of IP elution buffer (1% SDS, 0.1 M NaHCO3). The eluents were pooled together and the cross-links were reversed by adding NaCl (a final concentration 0.2 M) into the eluents and incubating them at 65 ºC overnight. The DNAs were recovered by proteinase K and RNase A digestion, followed by phenol/chloroform extraction and ethanol precipitation. Pellets were resuspended in 50 μl of 10 mM Tris-HCl [pH 8.0]. ChIP-DNA was quantified using the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific).
Libraries were prepared according to Nugen's instructions accompanying their Ovation Ultralow System V2 kit.

treatment_protocol: The small-molecule inhibitor used in this study is PTC-028 (orb181369, Biorbyt). This drugs was all dissolved in DMSO to make stock concentrations to use in in vitro experiments.

tag: cell line

tag: passage

value: H2AK119ub1 - clone E6C5 - #05-678 - from Millipore

tag: growth protocol

value: DMEM-High glucose (Invitrogen), 10% fetal bovine serum (Atlanta Biologicals), 1% Non-Essential Amino Acids, 1% Antibiotic-Antimycotic


title: CD8 TILs, PD1–Biotin– Replicate 3

city: San Diego

first: Peng

last: Wu

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: Scripps Research

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
09id03btNEGpdNEGrp03-0NN

data_processing:
Read quality was checked using MultiQC
The reads were trimmed for the adapter sequences using cutadapt 1.18 with Python 3.6.3.
The trimmed reads were mapped to the reference genome using the STAR aligner 2.5.2a.
Gene abundance was estimated with python 2.7.11, and HTSeq 0.11.0
he differential gene expression analyses was performed using R 3.5.1, and DESeq2 1.20.0
Distribution of mapped reads over genome features was obtained for each sample using RSeQC 2.6.4.
Genome_build: Ensembl GRCm38 release 91
Supplementary_files_format_and_content: cvs file containing gene abundances of each condition

source_name: CD8 tumor infiltrating lymphocytes

extract_protocol:
Total RNA were extracted from 10000 cells per sample using PicopureTM RNA isolation kit (Qiagen RNase-Free DNase set were used to digest trace DNA).
Library was prepared using SMARTseq HT kit

treatment_protocol: PD1+Biotin+, PD1+Biotin- and PD1- CD8 TILs from murine MC38 tumor were collected by FACS. Then TILs were cultured in T cell medium containing 100 IU/mL IL2 for 24 hours.

value: CD8 TILs from MC38

tag: replicate

tag: pd1 status

tag: biotin status

value: Biotin–


title: H3K27me3_ChIPseq_KO_2

value: Hematopoietic stem and progenitor cells

value: adult

value: Tri-Methyl-Histone H3 (Lys27) (C36B11), Cat# 9733BC, Cell Signaling Technology, Lot. 8


title: BMI1_ChIP_SF8628_PTC028

value: Bmi1 - clone D42B3 - Rabbit mAb #5856 -from Cell Signaling Technologies


title: CKIT micorbead enriched and UPEC exposed cells

city: Indianapolis

first: Andrew

last: Schwaderer

state: IN

address: 1044 West Walnut Street

department: Pediatric Nephrology

institute: Indiana University School of Medicine

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated
CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files
The FASTQ files were then aligned to the reference genome with RNA-seq aligner STAR.
The aligned reads were traced back to the individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell. The filtered gene-cell barcode matrices generated with CellRanger were used for further analysis with the R package Seurat development version 3.0.0.9000
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file containing count matrix for each gene and cell

source_name: Normal Kidney Margin Biopsy

extract_protocol:
Enriched cells were exposed to saline and UPEC for 1 hr, washed and then processed with 10x genomics chromium single cells platform. cDNA was prepared using chromium single cell 3` reagent kit v2 (ver B) (User guide: CG0052 ver B). Quality of cDNA library was analyzed by Bioanalyzer. Libraries were sequenced using Illumina Novaseq6000 instrument.
cDNA was prepared using chromium single cell 3` reagent kit v2 (ver B) (User guide: CG0052 ver B)

treatment_protocol: Enriched intercalated cells were equally divided into 2 wells. Cells in one well were treated with saline and in other well with UPEC

value: Enriched Intercalated cells

value: Normal margins from mass resection

value: UPEC


title: CKIT micorbead enriched and Saline exposed cells

value: Saline


title: D144_D0

value: Control (0nM)

value: Differentiated

value: Duodenum


title: SF8628_PTC028_2

data_processing:
The reads were trimmed and clipped for quality control in Trimmomatic (v0.36).
Read quality was checked for each sample using FastQC v0.10.1.
High quality reads were then imported into STAR (v2.4.0.1) for alignment into BAM files.
The function summarizeOverlaps from the GenomicAlignments package (v1.16.0) was used to count the reads from BAM files.
DESeq (v1.32.0) was then used to get differential expression genes on the raw counts.
Alignment was done using the transcriptome hg38 (from UCSC)
Genome_build: hg38
Supplementary_files_format_and_content: txt file includes raw read counts.

growth_protocol: DMEM-High glucose (Invitrogen), 10% fetal bovine serum (Atlanta Biologicals), 1% Non-Essential Amino Acids, 1% Antibiotic-Antimycotic

extract_protocol:
RNA from cell lines were extracted with a RNeasy Plus RNA kit (Qiagen) and the purity of the RNA isolated was examined using an Agilent 2100 bioanalyzer.
mRNA libraries were made from the isolated pure RNA and RNA sequencing was performed using Nova-Seq.

treatment_protocol: The small-molecule inhibitor used in this study is PTC-028 (orb181369, Biorbyt). This drug was dissolved in DMSO to make stock concentrations to use in in vitro experiments.Stable knockdown of genes was carried out using shRNAs targeting different genes. Briefly, the cells (~100,000/well) were seeded onto a 6-well plate and the cells were transduced with the lentiviral shRNA using polybrene (polybrene final concentration of 8 ng/ml). Transduced cells were selected using puromycin (2µg/ml) and the cells were routinely maintained in the cell culture medium containing 1µg/ml of puromycin. ShRNAs targeting BMI1 was obtained from transOMIC technologies and from the Functional Genomic Core Facility at the University of Colorado, Denver.

tag: agent


title: 0.02 CNP R1

tag: starting total rna

tag: method

value: blocking primer (EMBR-seq)

tag: tex treatment

value: no


title: CD8 TILs, PD1+Biotin+ Replicate 3

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
07id03btPOSpdPOSrp03-2PP

value: Biotin+


title: input_SF8628_PTC028

tag: chip antibody

value: DMEM-High glucose (Invitrogen), 10% fetal bovine serum (Atlanta Biologicals), 1% Non-Essential Amino Acids, 1% Antibiotic-Antimycotic


title: H2AK119_ChIP_SF8628_DMSO

value: H2AK119ub1 - clone E6C5 - #05-678 - from Millipore


title: SF8628_PTC028_3


title: 20 CNN R1

value: 20 ng

value: no blocking primer (control)


title: SF8628_PTC028_1


title: CD8 TILs, PD1–Biotin– Replicate 2

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
06id02btNEGpdNEGrp02-0NN

value: CD8 TILs from MC38

value: Biotin–


title: SF8628_DMSO_3

value: DMSO


title: CD8 TILs, PD1+Biotin– Replicate 2

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
05id02btNEGpdPOSrp02-1NP


title: SF8628_DMSO_2


title: BMI1_ChIP_SF8628_DMSO

value: Bmi1 - clone D42B3 - Rabbit mAb #5856 -from Cell Signaling Technologies


title: input_SF8628_DMSO


title: CD8 TILs, PD1+Biotin+ Replicate 2

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
04id02btPOSpdPOSrp02-2PP


title: CTCF_ChIPseq_KO_2

value: CTCF KO

value: bone marrow

value: Hematopoietic stem and progenitor cells

tag: developmental stage

value: adult

value: Anti-CTCF antibody, Cat# 07-729 Millipore, Lot. 2757161


title: H2AK119_ChIP_SU-DIPG04_PTC028

value: SU-DIPG04 cells were cultured in tumor stem media (TSM) consisting of all the following components from Invitrogen:Neurobasal-A medium (1:1), D-MEM/F-12 (1:1),  HEPES Buffer Solution (10 mM), MEM Sodium Pyruvate Solution (1 mM), MEM Non-Essential Amino Acids (0.1 mM), GlutaMAX-I Supplement (1:100), Antibiotic-Antimycotic (1X), B-27 Supplement Minus Vitamin A (1X), except all the growth factors, human-basic FGF (20 ng/mL), human-EGF (20 ng/mL), human PDGF-AA (10 ng/mL), human PDGF-BB (10 ng/mL) from Shenandoah Biotech and the heparin (2 ug/mL) from StemCell Technologies.


title: SF8628_DMSO_1


title: CD8 TILs, PD1–Biotin– Replicate 1

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
03id01btNEGpdNEGrp01-0NN


title: BMI1_ChIP_SU-DIPG04_PTC028


title: DIPG4_PTC028_3

growth_protocol: SU-DIPG04 cells were cultured in tumor stem media (TSM) consisting of all the following components from Invitrogen: Neurobasal-A medium (1:1), D-MEM/F-12 (1:1),  HEPES Buffer Solution (10 mM), MEM Sodium Pyruvate Solution (1 mM), MEM Non-Essential Amino Acids (0.1 mM), GlutaMAX-I Supplement (1:100), Antibiotic-Antimycotic (1X), B-27 Supplement Minus Vitamin A (1X), except all the growth factors, human-basic FGF (20 ng/mL), human-EGF (20 ng/mL), human PDGF-AA (10 ng/mL), human PDGF-BB (10 ng/mL) from Shenandoah Biotech and the heparin (2 ug/mL) from StemCell Technologies.


title: CD8 TILs, PD1+Biotin– Replicate 3

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
08id03btNEGpdPOSrp03-1NP


title: CD8 TILs, PD1+Biotin– Replicate 1

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
02id01btNEGpdPOSrp01-1NP


title: input_SU-DIPG04_PTC028


title: BMI1_ChIP_SU-DIPG04_DMSO


title: H2AK119_ChIP_SU-DIPG04_DMSO


title: RNAseq3_KO

data_processing:
The paired-end RNA-seq reads are mapped by STAR to the mouse reference genome GRCm38 (mm10).
Alignments with mapping quality below 20 are filtered out. Normalization between the samples was based on the proportionality of the numbers of the mapped reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. Normalization between the samples was based on the proportionality of the numbers of the mapped reads.

molecule: polyA RNA

source_name: Hematopoietic stem cells

extract_protocol:
For ChIPseq, cells were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 200 to 500 base pair and protein-DNA complexes were pulled down by antibodies.For RNAseq, cells were lysed with Trizol, RNAs were isolated using phenol-chloroform extraction. For HiC cells were fixed with 2% formaldehyde and then insoluble chromatin fraction were isolated following Arima HiC kit protocol.
For ChIPseq samples, libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. For RNAseq samples,  libraries were prepared using SMART Seq v4 Ultra Low Input RNA kit from Takara and Nextera XT DNA library prep kit from Illumina according to the manufacturer’s instructions. For HiC samples, libraries were prepared using Arima HiC kit and Swift biosciences® Accel NGS® 2S plus DNA library kit following the low input procedure instructions.

value: Hematopoietic stem cells


title: DIPG4_PTC028_1


title: CD8 TILs, PD1+Biotin+ Replicate 1

description:
RawGeneCounts.csv
NormalizedGeneCounts.csv
TPMcounts.csv
01id01btPOSpdPOSrp01-2PP


title: DIPG4_DMSO_3


title: input_SU-DIPG04_DMSO


title: RNAseq1_KO


title: RNAseq2_KO


title: DIPG4_PTC028_2


title: DIPG4_DMSO_2


title: T-ALL 39 (IonCode_0132)

city: Milano

first: Alessandro

last: Beghini

address: Via A.Di Rudinì

department: Dept. of Health Sciences

institute: University of Milan

data_processing:
Ion Torrent Suite 5.12.1 software
The BaseCaller module of the Ion Torrent Suite v. 5.12.1-27 software was used to perform the reads filtering, adapter trimming and quality trimming of the reads with default parameters.
The TMAP module of the Ion Torrent Suite v. 5.12.1-27 software (algorithm "map4")  was employed to align the reads to the reference genome hg19 with default  parameters.
The ampliSeqRNA plugin v. 5.12.0.1 was used to generate the "Absolute Reads Matrix" containing the absolute read count for each gene. For further information about the Ion Torrent Pipeline refer to Torrent Suite Software 5.12 User Guide (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017972_031419_TorrentSuite_5_12_UG_.pdf ).
Genome_build: hg19
Supplementary_files_format_and_content: Differential expression analysis among conditions (WNT10B IVS1 pos -vs- WNT10B  IVS1 neg) was performed using the R package edgeR (v3.28.1) starting from the file  "Absolute Reads Matrix". From the initial 178 genes, 21 were filtered out using the  edgeR function filterByExpr with default parameters, which removes lowly expressed  genes. Then, the data were library normalized (TMM) and the dispersion was  estimated by quantile-adjusted conditional maximum likelihood (qCML). The  statistical analysis for differential expression was carried out using the exactTest .  Only genes with a Benjamini-Hochberg corrected p-value < 0.05 and with an  absolute log2Fold-change >= 2 were considered statistically significant.

source_name: leukemic blasts

extract_protocol:
RNA was isolated from cells using Quick-RNATM MiniPrep Plus kit (Zymo Research, Italy); concentration was verified on Quibit Fluoromiter (ThermoFischer Scientific)
RNA libraries were prepared using 10ng of total RNA  according to the Ion AmpliSeq™ Kit for Chef DL8 protocol (ThermoFischer Scientific # A29024) for automated preparation of libraries for Ion Chef™ instrument.

value: MO-derived mononuclear cells


title: T-ALL 257 (IonCode_0131)


title: RNAseq1_WT

value: WT


title: RNAseq3_WT


title: DIPG_DMSO_1


title: T-ALL 326 (IonCode_0130)


title: H3K27me3_ChIPseq_WT

value: Tri-Methyl-Histone H3 (Lys27) (C36B11), Cat# 9733BC, Cell Signaling Technology, Lot. 8


title: H3K27me3_ChIPseq_KO


title: H3K27ac_ChIPseq_KO

value: Rabbit polyclonal to Histone H3 (acetyl K27) - ChIP Grade, Cat# ab4729, Abcam, Lot. GR261979-1


title: RNAseq2_WT


title: H3K27ac_ChIPseq_WT


title: Cranial Osteoblasts, D28_f3

city: 济南市

first: Hui

last: Gao

state: 山东省

address: 济南药谷（经十东路邢村立交桥东）A座2504室

country: China

institute: 山东大学

description: total RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rattus_norvegicus.Rnor_6.0（release 93） whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Rattus_norvegicus.Rnor_6.0（release 93）
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: Cranial bone cells

growth_protocol: 36 cell samples cultured in osteogenic inductive medium (OIM, medium supplemented with 10% FBS, 50 mg/L ascorbic acid and 10 mmol/L β-glycerophosphate (Sigma-Aldrich)) at day 1 (cultured in α-MEM), 3, 7, 14, 21, 28 from 3 individuals

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: each individual involved 12 samples with or without F. nucleatum infected (MOI=0, 50)) were analyzed

value: Wistar

value: Cranial Osteoblasts

tag: age

value: post natal 24-48h

value: wild type

tag: individual

tag: infection

value: F. nucleatum

tag: time


title: Cranial Osteoblasts, D28_f2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA

tag: strain

tag: cell type

tag: genotype


title: DD05001D (IonCode_0126)

source_name: mononuclear cells

value: PB-derived mononuclear cells


title: ZNF143_ChIPseq_KO

value: CTCF KO

tag: tissue

value: Anti-ZNF143 rabbit serum, generated in our lab


title: Cranial Osteoblasts, D28_c3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA

value: control


title: Cranial Osteoblasts, D28_f1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: ZNF143_ChIPseq_WT

value: bone marrow

value: Hematopoietic stem and progenitor cells

value: adult


title: CTCF_ChIPseq_KO

value: Anti-CTCF antibody, Cat# 07-729 Millipore, Lot. 2757161


title: T-ALL 281 (IonCode_0129)

value: MO-derived mononuclear cells


title: Cranial Osteoblasts, D28_c2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: T-ALL 327 (IonCode_0127)


title: CTCF_ChIPseq_WT

value: WT


title: Cranial Osteoblasts, D28_c1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: transhet-6

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

data_processing:
Illumina BaseSpace was used for base-calling.
Reads were trimmed using AdapterRemoval v2.2.1 setting a minimum quality of 30 and a minimum length of 35.
A pseudo-alignment to the zebrafish transcriptome (according to the Ensembl GRCz11 (release 96), with the sequences for unspliced transcripts additionally included) using kallisto v0.43.1
Transcript abundances were summarised using the catchkallisto() function of edgeR
Genome_build: GRCz11

organism: Danio rerio

source_name: Whole brain

growth_protocol: Fish were allowed to develop over 3 tanks, side-by-side in the same system until 6 months of age.

extract_protocol:
Total RNA was extracted from individual brains using the mirVana miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA).  DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA-free Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). PolyA amplification was performed for the construction of sequencing libraries.
Demultiplexed libraries were provided by the sequencing centre at the South Australian Health and Medical Research Institute (SAHMRI) as 75bp single-end reads.

tag: gender

value: Male

tag: tank


title: transhet-5


title: Cranial Osteoblasts, D21_f1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D21_c3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: FC05006D (IonCode_0125)


title: Cranial Osteoblasts, D21_f3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: T10

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
Quality control and base calling was completed using Illumina CASAVA.
Raw fastq reads were adapter trimmed and quality assessed using the Trimgalore wrapper for FastQC and Cutadapt. Reads with phred scores >30 were retained.
Reads were aligned to the canFam3.1 reference genome using Tophat and genes quantified and differential expression assessed using Cuffdiff.
Genome_build: canFam3.1
Supplementary_files_format_and_content: BAM alignment file

organism: Canis lupus familiaris

source_name: OSA tumor

extract_protocol:
OSA tumor and non-tumor tissue was obtained from a total four non-malignant bone and three osteosarcoma specimens via veterinary surgeons following amputation treatment or immediately following euthanasia. Confirmation of OSA was confirmed by pathologists via histopathological examination. A 1cm3 piece of tumor was extracted along with a 1cm3 piece of adjacent non-tumor affected bone tissue. These samples were placed directly into RNAlater® and shipped at room temperature and stored at -20°C. OSA tumor and matched adjacent non-tumor bone tissue samples were homogenized. and RNA extracted using Qiagen RNeasy Mini Kit (Qiagen, Germany) according to manufacturer’s instructions. The extracted RNA was stored at -80°C. RNA was quantified using both a NanoDrop 8000 (Thermo Fisher Scientific, USA), and an Agilent 2100 Bioanalyzer (Agilent, USA). RNAseq was completed at Edinburgh Genomics using an Illumina HiSeq platform. In all cases >20 million reads were obtained from all samples analysed.
Illumina TruSeq stranded library prepartion for paired end sequencing.

value: Osteosarcoma


title: Cranial Osteoblasts, D21_f2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA

value: Wistar


title: T3


title: N9

source_name: non-tumor

value: Grossly non malignant bone


title: N8


title: transhet-2

value: Female


title: V1482Afs-2


title: V1482Afs-6


title: V1482Afs-4


title: R122Pfs-6


title: R122Pfs-1


title: R122Pfs-2


title: transhet-1


title: R122Pfs-4


title: transhet-3


title: transhet-4


title: V1482Afs-5


title: T1


title: V1482Afs-3


title: N3


title: V1482Afs-1


title: Cranial Osteoblasts, D7_f1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA

value: Cranial Osteoblasts

value: post natal 24-48h

value: wild type


title: Cranial Osteoblasts, D14_f2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA

value: F. nucleatum


title: Cranial Osteoblasts, D14_f1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D14_c2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D21_c2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D7_f3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D14_c3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D21_c1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D14_c1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D7_f2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D14_f3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: N1


title: R122Pfs-5

description: Note this sample was incorrectly genotyped post sequencing so the name of the fastq file does not match the genotype

value: wild-type


title: Cranial Osteoblasts, D7_c3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA

value: control


title: Cranial Osteoblasts, D7_c2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: WT-5


title: WT-9


title: Cranial Osteoblasts, D7_c1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D3_f3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: peritoneal macrophages, Arrb2_3

city: Shanghai

first: Yihua

last: Zhang

state: Shanghai

address: Fudan University

institute: Fudan University

data_processing:
RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with cutadapt, then aligned to Mus musculus GRCm38 genome with Ensembl.
The numbers of counts were summarized at the gene level using HTseq. Gene expression values were computed from fragments per kilo bases per million fragments (FPKM) values produced by addition of a pseudocount of 1 and log2 transformation of the results. These FPKM values were used for drawing the heatmap with the pheatmap R package. Paired differential gene expression analyses were performed with DEseq R package by addition of fold change > 2 and p-value < 0.05. Volcano plots of these differential genes were drawing with ggplots2 R package. GO or KEGG enrichment analyses of differential genes were performed using topGO or KAAS, respectively. The terms or pathways involved in host antiviral immune response with fold change > 2 and p-value < 0.05 were used to drawing GO term enrichment or KEGG pathway enrichment. The PPI analysis of differential genes was performed with STRING database and PPI network model was drawn with Cytoscape.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression.xlsx

source_name: peritoneal macrophages

growth_protocol: For preparing mouse peritoneal macrophages, 6-week-old homozygous Arrb2-/- mice and their WT littermates were injected with 1.5 ml Brucella broth (4%) intraperitoneally. After 3 days, the peritoneal lavage fluid was collected from the mice and washed three times with PBS. Peritoneal macrophages were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Wild-type and Arrb2-/- PMs treated for 16 h with HSV-1 before they were lysed with RNAiso Plus according to the manufacturers’ instructions. The lysates were sent to Personalbio for cDNA library construction and sequencing by Illumina NovaSeq 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild-type and Arrb2-/- peritoneal macrophages treated for 16 h with HSV-1 before lysed.

value: peritoneal macrophages

value: Arrb2 -/-

value: HSV-1 for 16 h


title: peritoneal macrophages, Arrb2_1


title: WT-6


title: peritoneal macrophages, WT_2


title: peritoneal macrophages, Arrb2_2


title: WT-4


title: Cranial Osteoblasts, D3_f2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D3_f1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D3_c2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D3_c1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: R122Pfs-3


title: peritoneal macrophages, WT_3


title: peritoneal macrophages, WT_1


title: Cranial Osteoblasts, D1_f2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D1_f1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D1_c3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D3_c3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D1_f3

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: Cranial Osteoblasts, D1_c2

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: CLBL-1 8.0

city: Taipei

first: Chen-Si

last: Lin

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Veterinary Medicine

country: Taiwan

institute: Nationwide Taiwan University

data_processing:
The sequencing quality processing tool (FASTX-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/) was used to filter out low quality sequencing reads. The command was “fastq_quality_filter –Q33 –q 20 –p 70”. “-q 20” indicated that the minimum phred score was 20 (20 means the sequencing error rate is 0.1% to a base) and “-p 70” indicated that the minimum percent of bases must have “-q” quality ≥70%.
HISAT2 (http://daehwankimlab.github.io/hisat2/) was used to align sequencing reads with Dog genome sequences (CanFam3.1) which were got from NCBI.
StringTie (https://ccb.jhu.edu/software/stringtie/) was employed to evaluate the expression level of transcripts.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: gene expression profile

source_name: diffuse large B-cell lymphoma cells

growth_protocol: CLBL-1 was grown in RPMI medium containing 10% fetal bovine serum (FBS) and supplemented with 1% penicillin G/streptomycin, incubating in a 37℃ incubator. CLBL-1 8.0, a doxorubicin-resistant CLBL-1, was maintained in RPMI medium containing with 10% FBS and 8 μM of doxorubicin hydrochloride and supplemented with 1% penicillin G/streptomycin, incubating in a 37℃ incubator.

extract_protocol:
RNA was extracted from three separate dishes containing no more than 5 x 106 cells per dish using TriRNA Pure Kit following the instruction manuals.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system. Then 3 μl USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: lymph node

tag: tumor stage

value: IV

tag: chemoresistance

value: resistance to doxorubicin


title: CLBL-1 8.0 (medium to high-methylated level)

description:
Methyl-Cap seq was performed to analyze the methylation profiles of CLBL-1 8.0. L: genes with low methylation status; M-H: genes with medium and high methylation status
CLBL8_DMR.xlsx

data_processing:
The sequencing quality processing tool (FASTX-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/) was used to filter out low quality sequencing reads. The command was “fastq_quality_filter –Q33 –q 20 –p 70”. “-q 20” indicated that the minimum phred score was 20 (20 means the sequencing error rate is 0.1% to a base) and “-p 70” indicated that the minimum percent of bases must have “-q” quality ≥70%
BWA (http://bio-bwa.sourceforge.net/) was used to align sequencing reads with Dog genome sequences (CanFam3.1) which were got from NCBI.
MACS2 (https://github.com/taoliu/MACS) was employed to identify hypermethylated peaks according to the results of sequencing alignment.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: hypermethylated peaks (excel format)

extract_protocol:
Total genomic DNA was extracted from no more than 5 x 10e6 cells using Genomic DNA isolation Kit.
We obtained the methylated sequences among the whole genome by the methylbinding domain protein provided by the MethylCap kit (Diagenode, NJ, USA)
A total amount of 800 pg captured DNA (meDNA captured sample) was taken for library preparation using QIAseq Ultralow Input Library Kit according to the manufacturer’s protocol. Briefly, the double-stranded DNA was end-repaired and 3’end adenylated followed by adapter ligation and PCR amplification. The length of library fragments ranging from 200 bp and 1 kb were further selected using AMPure XP beads. The fragment size of the resulting library was validated using Agilent 2200 TapeStation-D1000 Screentape system. The library was quantitatively measured by Kapa Library Quantification Kit for Illumina platform and Qubit dsDNA HS Assay kit. The library was sequenced using a 150 bp paired-end protocol on an Illumina Novaseq.

tag: cell line

tag: phentotype

tag: elution buffer

value: high salt concentration


title: Cranial Osteoblasts, D1_c1

address: 济南药谷（经十东路邢村立交桥东）A座2504室

description: total RNA


title: WT_ZnCl2_R2

status: Public on Oct 21 2020

first: Bernhard

middle: O.

last: Palsson

address: 9500 Gilman Dr.

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
RNA-seq sequence reads were mapped onto the reference genome (E. coli MG1655 NC_000913.3) using bowtie 1.1.2with the following options “-X 1000 -n 2 −3 3”.
Read count was performed using summarizeOverlaps from the R GenomicAlignments package, using options “mode=“IntersectionStrict”, singleEnd=FALSE, ignore.strand=FALSE, preprocess.reads=invertStrand”
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: Comma-separated text file includes TPM (Transcripts per million) for each sample

source_name: bacterial cells

growth_protocol: For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2.

extract_protocol:
For RNA-seq, 3 mL of culture were mixed with 6 mL of RNAprotect bacteria reagent (Qiagen) and processed according to the manufacturer’s instructions. Cell pellets were frozen and stored at -80 °C until processed. RNA was extracted using the Zymo Research Quick RNA fungal/bacterial microprep kit, according to the manufacturer's instructions. Ribosomal RNA was removed from total RNA preparations using RNase H. First, traces of genomic DNA were removed with a DNase I treatment. Then, secondary structures in the ribosomal RNA were removed by heating to 90 °C for one second. A set of 32-mer DNA oligonucleotide probes complementary to 5S, 16S, and 23S rRNA subunits and spaced nine bases apart were then annealed at 65 °C followed by digestion with Hybridase (Lucigen), a thermostable RNase H.  Hybridase was added at 65 °C, the reaction was incubated for 20 minutes at that temperature, then heated again to 90 °C for one second to remove remaining secondary structures, and finally returned to 65 °C for 10 minutes. The reaction was quickly quenched by the addition of guanidine thiocyanate while still at 65 °C before purifying the mRNA with a Zymo Research RNA Clean and Concentrator kit using their 200 nt cutoff protocol. Carryover oligos were removed with a DNase I digestion which was started at room temperature and gradually increased to 42 °C over a half hour. This was followed up with another column purification as stated above.
Paired-end library preparation was done using the KAPA RNA HyperPrep kit following the manufacturer’s instructions.

tag: media

value: LB medium + 1 mM ZnCl2

value: WT


title: WT-1


title: WT-3


title: CLBL-1

value: no chemoresistance


title: MCF-7_shMEN1_2

city: San Antonio

first: Tim

middle: Hui-Ming

last: Huang

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health at San Antonio

data_processing:
Illumina Real-Time Analysis software used for basecalling.
Sequenced reads were mapped to GRCh38 human genome using STAR-2.5.3a
Fragments Per Kilobase of transcript per Million mapped reads were calculated for each sample using RSEM software
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include expected counts, TPM and FPKM values for each Sample ...

source_name: MCF-7 breast cancer cell line

growth_protocol: T47D and MCF-7 breast cancer cell line were cultured in DMEM medium with 10%FBS and 1% penicillin/streptomycin aired with 5%CO2 at 37℃.

extract_protocol:
Total RNA was extracted by using the PureLink RNA Mini Kit, and each treatment had  2 biological replicates.
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit with Nextera XT Index Kit v2 Set A and B index primers.

treatment_protocol: T47D and MCF-7 cells were infected of either vehicle virus or shMEN1 virus to knockdown MEN1 gene expression.

value: MCF-7 breast cancer cell line


title: MCF-7_shMEN1_1


title: WT_ZnCl2_R1


title: T47D_veh_1

source_name: T47D breast cancer cell line

value: T47D breast cancer cell line


title: T47D_veh_2


title: T47D_shMEN1_1


title: T47D_shMEN1_2


title: ZraR_KO_LB_R1

value: LB medium

value: {delta}zraR


title: MCF-7_veh_1


title: MCF-7_veh_2


title: ZraR_KO_LB_R2


title: ZraR_KO_ZnCl2_R2


title: ZraR_KO_ZnCl2_R1


title: WT_M9-P_R1

value: M9 minimal medium without phosphate


title: WT_M9-P_R2


title: PhoB_KO_M9_R2

value: M9 minimal medium

value: {delta}phoB


title: WT_115-KCl_R2

value: TMA + 115 mM KCl


title: PhoB_KO_M9-P_R2


title: PhoB_KO_M9-P_R1


title: PhoB_KO_M9_R1


title: WT_115-KCl_R1


title: Transcriptome of IL-17A-treated Tregs 3

city: Xi'an

first: Yanghe

last: Liu

state: China

address: Xijing  Hospital, Fourth Military Medical University, 127 Changle West Road, Xi’an

institute: Fourth Military Medical University

description: IL-17A treated 3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample

source_name: PBMC

growth_protocol: Tregs were cultured in the presence or absence of 50 ng/ml IL-17 for 48 h with CD3/CD28 microbeads in 24-well plates.

extract_protocol:
Total RNA was extracted from Tregs using TRIzol reagent (Invitrogen, CA, USA).
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)   beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic   Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short   fragments using fragmentation buffer and reverse transcripted into cDNA with random   primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and   buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen,   Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing   adapters. The ligation products were size selected by agarose gel electrophoresis, PCR   amplified, and sequenced using Illumina Novaseq by Gene Denovo Biotechnology Co.   (Guangzhou, China).

treatment_protocol: Tregs were cultured with or without IL-17A(50ng/ml) for 2 days

value: PBMC

value: Treg

tag: treatment

value: IL-17A treated 3


title: Transcriptome of IL-17A-treated Tregs 1

description: IL-17A treated 1

value: IL-17A treated 1


title: Transcriptome of normal control Tregs 3

description: normal control 3

value: normal control 3


title: Transcriptome of IL-17A-treated Tregs 2

description: IL-17A treated 2

value: IL-17A treated 2


title: Transcriptome of normal control Tregs 2

description: normal control 2

value: normal control 2


title: Transcriptome of normal control Tregs 1

description: normal control 1

value: normal control 1


title: WT_01-KCl_R2

value: TMA + 0.1 mM KCl

value: WT


title: CLBL-1 (low-methylated level)

description:
Methyl-Cap seq was performed to analyze the methylation profiles of CLBL-1. L: genes with low methylation status; M-H: genes with medium and high methylation status
CLBL1_DMR.xlsx

value: lymph node

value: IV

value: no chemoresistance

value: low salt concentration


title: WT_01-KCl_R1


title: KdpE_KO_115-KCl_R2

value: {delta}kdpE


title: CLBL-1 (medium to high-methylated level)

value: high salt concentration


title: WT_EtOH_R2

value: LB medium + 5% ethanol


title: WT_EtOH_R1


title: ZraR2_Chipexo

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
The ChIP-exo sequence reads were mapped onto the reference genome (E. coli MG1655 NC_000913.3) using bowtie with default options. This generated SAM output files.
Peak calling for each experimental condition was done using the MACE program
Two level filtering of ChIP-exo data was done: first, we removed any peaks with S/N ratio of less than 1.5 to reduce false positive peaks. Top 5% of the signals at genomic positions was set as noise level
To further reduce the false positive peaks, a cut-off analysis was done for each regulator on the signal-to-noise (S/N) ratio
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

growth_protocol: For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. At an OD600=0.5.

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
cells were crosslinked in 1% Formaldehyde and DNA bound to each response regulator was isolated by chromatin immunoprecipitation (ChIP) with the specific antibodies that recognize myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen). This was followed by stringent washing. To perform on-bead enzymatic reactions of the ChIP-exo experiments, ChIP materials (chromatin-beads) were used.

value: ZraR myc tagged cells

tag: chip antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: ZraR1_Chipexo


title: BaeR_KO_EtOH_R1

value: {delta}baeR


title: BaeR_KO_ LB_R2

value: LB medium


title: BaeR_KO_LB_R1


title: CLBL-1 8.0 (low-methylated level)

value: resistance to doxorubicin


title: BaeR_KO_EtOH_R2


title: KdpE_KO_01-KCl_R2


title: KdpE_KO_115-KCl_R1

value: TMA + 115 mM KCl


title: CpxR_KO_LB_R1

value: {delta}cpxR


title: CpxR_KO_LB_R2


title: CpxR_KO_EtOH_R2


title: WT_LB_R2


title: KdpE_KO_01-KCl_R1


title: CpxR_KO_EtOH_R1


title: PhoB1_Chipexo

value: PhoB myc tagged cells


title: CpxR1_Chipexo

value: CpxR myc tagged cells


title: KdpE2_Chipexo

value: KdpE myc tagged cells


title: PhoB2_Chipexo


title: BaeR1_Chipexo

value: BaeR myc tagged cells


title: BaeR2_Chipexo


title: WT_LB_R1

value: WT


title: Fat Body Control 1

city: Bloomington

first: Lesley

last: Weaver

address: 1001 E 3rd Street

institute: Indiana University

data_processing:
Reads obtained from sequencing were aligned to the D. melanogaster reference genome using the TopHat read alignment tool
TopHat alignments were used to generate read counts for each gene using HTSeq
Read counts were subsequently used to generate the differential expression results using the DESeq2 R package
Genome_build: Drosophila_melanogaster_release_81
Supplementary_files_format_and_content: Excel xls files

organism: Drosophila melanogaster

extract_protocol:
Abdominal carcasses from 100 females of each genotype were dissected in Grace’s medium supplemented with 10% fetal bovine serum (FBS; Sigma). Fat body cells were dissociated from abdominal carcasses with 500 µl dissociation buffer [0.5% Trypsin (Sigma) plus 1 mg/ml collagenase (Sigma) in 1x PBS] per 50 carcasses for 30 minutes at room temperature. Samples were gently agitated every 5 minutes to facilitate separation of cells from the cuticle. 500 µl of Grace’s media plus 10% FBS was added to stop the enzymatic reaction and supernatants were placed in new tubes. Carcasses were rinsed with Grace’s medium plus 10% FBS and the two supernatants per genotype were combined. Dissociated cells were centrifuged at 3.3 rpm for 5 min at room temperature. Supernatants were removed and cells were immediately lysed in 250 µl lysis buffer from the RNAqueous-4PCR DNA-free RNA isolation for RT-PCR kit (Ambion). RNA was extracted from all samples following the manufacturer’s instructions
cDNA library construction, Illumina sequencing, and differential expression analysis was performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). The cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. The cDNA library for each sample was quality assessed using an Agilent Bioanalyzer 2100, and library preparations were sequenced on a NovaSeq6000 platform with PE150 read lengths.

treatment_protocol: Transgenes were induced in 0-2 day old females (grown at 18 degrees Celsius) for 5 days at 29 degrees Celsius. Each condition was performed in triplicate.

value: Fat body

value: 5 days of transgene induction

value: Wild-type


title: Fat Body svp RNAi 1-1

value: Svp RNAi


title: Fat Body Control 3-1


title: Fat Body Control 2-1


title: D4_2

city: Guangzhou

first: cuihua

last: wang

address: 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38_enst_v81) transcriptome using STAR (version 2.7)
The gene expression level was calculated by using  STAR
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the human genome, hg38 and Ensembl gene annotation track v81
Genome_build: hg38

source_name: in vitro hematopoietic cells

growth_protocol: H1 hESCs were subjected to EB-primed planar differentiatiation in defined cell culture conditions and in the absence of exogenous hematopoietic cytokines

extract_protocol:
total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMP4 and VEGF were used to initiate mesodermal differentiation of hESCs, then, starting from Day 3 of differentiation, the only growth factor in the culture medium was VEGF

value: H1 human embryonic stem cells

value: hVEGF

value: total differentiated hESC

tag: cell subtype


title: D2_3


title: D16_H1CD43CD45_negative3

value: hESC-derived cells


title: D2_1


title: D2_2


title: D4_1


title: D4_3


title: D16_H1CD43CD45_positive1


title: D16_H1CD43CD45_positive2


title: D0_3

value: EBs


title: D16_H1CD43CD45_positive3


title: D16_H1CD43CD45_negative2


title: D0_2


title: D0_1


title: CpxR2_Chipexo

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: KdpE1_Chipexo


title: PGC1a Rep3

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

data_processing:
trimmed high quality eeads were aligned to genome  using HISAT2
Transcripts per Million (TPMs) calculated using Subread
Differentially expressed genes (DEG) determined using DEseq2 with cutoffs of 2 fold and p value<0.05
Genome_build: mm10 ensembl

source_name: CD8 T cell

growth_protocol: CD8+ CD44hi T cells were stimulated with anti-CD3/CD28 coated beads for 24hr in the presence of IL-2 and IL-12, then washed and either expanded normally (labeled as ‘acute’ activation) or continuously cocultured with beads (labeled as ‘continuous’ activation) in the presence of IL2 for 5 addtional days. This expansion occurred either under normoxic (atmospheric, 20% O2) or hypoxic (1.5% O2) conditions.

extract_protocol:
Smart-seq v4 Ultra-low RNAsequencing kit (Clontech)
Nextera DNA XT. Dual-indexed libraries were sequenced via paired-end 75bp on Illumina Nextseq500,

treatment_protocol:
Ndufs4 deficient B16: C57BL/6 mice were given 250K Ndufs4-deficient B16-F10 (generated using transient transfection of Cas9-GFP and Ndufs4 targeted gRNA) or control B16-F10 cells intradermally. On day 14 (when tumors were 8-10mm), mice were sacrificed, tumors were processed with collagenase, dispase, and DNase, and live CD8+ PD1hi Tim3+ TIL were sorted.
PGC1a OE TIL: Thy1.1+ Pmel TCR Tg CD8+ T cells were isolated and activated with anti-CD3/CD28 + IL2, then after 24 hr, retrovirally transduced with either MSCV-driven retroviral expression vector encoding an IRES cassette (EV) or with PGC1a cloned into this vector (PGC1a). 4 days post-activation, Pmel T cells were sorted based on fluorescence expression and adoptively transferred into d7 B16-bearing C57BL/6 mice. On day 14 (when tumors were 8-10mm), mice were sacrificed, tumors were processed with collagenase, dispase, and DNase, and live CD8+ Thy1.1+ TIL were sorted.

value: RV expression CD8 TIL


title: Fat Body svp RNAi 2-1


title: D16_H1CD43CD45_negative1


title: Fat Body svp RNAi 3-1


title: PGC1a Rep2


title: Effect of Sdc1 knockout in mouse bcCML cells_WT3

city: La Jolla

first: Michael

last: Hamilton

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

data_processing:
kallisto pseudoaligner v0.44.0
sleuth v0.30.0 for differential expression analysis and gene count quantification
Genome_build: mm10
Supplementary_files_format_and_content: tpm and sleuth output

source_name: bcCML cells_WT

growth_protocol: KLS cells from WT or Sdc1-/- mice were sorted, infected with BCR-ABL and NUP98-HOXA9. Cells were sorted and only those positive for both oncogenes were transplanted into NSG mice. Chimerism was monitored by peripheral blood draws and all mice in both cohorts were sacrificed at the same time. Spleens were removed and cell sorting was used to extract the Lin- bcCML population.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Plus kit (QIAGEN).
RNA libraries were generated from 150ng of RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). Libraries were pooled and single end sequenced (1x75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina).

tag: condition

tag: donor strain background

tag: recipient strain

value: NSG

value: blast crisis chronic myeloid leukemia (bcCML) cells


title: Effect of Sdc1 knockout in mouse bcCML cells_Sdc1 KO2

source_name: bcCML cells_Sdc1 KO

value: SDC1 KO

tag: cell type


title: Effect of Sdc1 knockout in mouse bcCML cells_Sdc1 KO3


title: Effect of Sdc1 knockout in mouse bcCML cells_WT2


title: PGC1a Rep1

tag: strain


title: Empty Vector Rep3

tag: tissue


title: Empty Vector Rep2


title: Effect of Sdc1 knockout in mouse bcCML cells_Sdc1 KO1


title: Effect of Sdc1 knockout in mouse bcCML cells_WT1


title: Empty Vector Rep1


title: PD1+Tim3+ CD8 TIL_Ndufs4-def_B16_1

value: Ndufs4-deficient  B16 tumor tissue


title: Continuous Stim_Normoxia_1

value: in vitro generated


title: PD1+Tim3+ CD8 TIL_Ndufs4-def_B16_3


title: PD1+Tim3+ CD8 TIL_Ndufs4-def_B16_2


title: Continuous Stim_Hypoxia_3


title: Continuous Stim_Hypoxia_1


title: Acute Stim_Hypoxia_2


title: Continuous Stim_Hypoxia_2


title: PD1+Tim3+ CD8 TIL_B16_1

value: B16 tumor tissue


title: Continuous Stim_Normoxia_2


title: PD1+Tim3+ CD8 TIL_B16_2


title: Chronic Stim_Normoxia_3


title: PD1+Tim3+ CD8 TIL_B16_3


title: Acute Stim_Hypoxia_3


title: Acute Stim_Hypoxia_1


title: Acute Stim_Normoxia_1


title: Acute Stim_Normoxia_3


title: Acute Stim_Normoxia_2


title: KL2_AF10

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: fragmented DNA

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: embryonic stem cell

growth_protocol: ESCs were grown in N2B27 media supplemented with MEK inhibitor, GSK3 inhibitor, and LIF (2i/LIF).

extract_protocol:
RNA was extracted using Trizol reagent (Life technologies). RNAse free DNaseI (Sigma) was used to eliminate DNA contamination and the treated RNA was purified with RNeasy mini kit (Qiagen).
For ChIP, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). 100 µg sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, reverse-crosslinking, and submitted for library preparation.
PRO-seq was performed following a published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 μM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5’ RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit.

treatment_protocol: EB differentiation was performed using the hanging drop method. For NPC differentiation, cells were seeded on gelatinized dish in 2i/LIF media for a day. The two inhibitors and LIF were then withdrawn from the media and cells were kept in plain N2B27 media for 7 days. Cells were then dissociated and seeded in ultra-low attachment plates (Sigma) in N2B27 media containing 10ng/ml EGF (Peprotech) and 10ng/ml FGF2 (Peprotech) for 3 days to form neurospheres. Floating aggregates (neurospheres) were then seeded on gelatinized plates in N2B27 containing 10ng/ml EGF and 10ng/ml FGF2 for 2-4 days. Attached cells were dissociated and seeded again on gelatinized plates in N2B27 containing 10ng/ml EGF and 10ng/ml FGF2. Cells were passaged one more time and harvested for different assays.

value: embryonic stem cell

tag: genotype/variation

value: Wildtype/WT

value: AF10 (Santa Cruz 53156)