title: U-S2

first: Lu

last: Xiao

state: California

address: 369 N-S Axis, Stauffer I, 109

library_source: other

data_processing:
Sequencing reads were processed by previouly established  icSHAPE pipine (https://github.com/qczhang/icSHAPE).
Data was first demultiplexed, removed PCR dplicates and trimmed by using the scripts of icSHAPE pipeline.
Read quality was checked for each sample using FastQ v0.11.9
High-quality reads were then imported into bowtie2 v2.4.5 for alignment into BAM files.
BAM files were imported into the icSHAPE pipelineto calucate the RPKM and RT-stops frequency.
Assembly: Alignment was to the designed A/U RNA library sequences built from solid-phase synthesis.
Supplementary files format and content: excel (.xlsx); containingR-score of each samples calculated by RT-stop frequency per nucleotide.

molecule: other

organism: synthetic construct

source_name: Synthesized U RNA library

extract_protocol:
RNAs were purified by washing with Rnase-free water using centrifuge filters after probing
RNAs were all folded independently before mixing to build a library; and the mixing was done immediately before probing

treatment_protocol: A-case/U-case RNA libraries were probed with 50mM (S,R) 1/ 100uM (S,R) 2/ DMSO at 0℃ for 2h

value: Synthesized U RNA library

value: 100uM S2 for 2h at 0 degree


title: U-S1

status: Public on Nov 14 2023

type: SRA

city: Stanford

country: USA

institute: Stanford University

tag: tissue

tag: treatment

value: 50mM S1 for 2h at 0 degree


title: U-R2

value: 100uM R2 for 2h at 0 degree


title: Sample_IMQ1-13_IGO_12061_303

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

description: single cell

library_source: transcriptomic single cell

data_processing:
Adapter trimming: Trimmomatic (version 0.39): TrimmomaticPE Sample_R1.fastq.gz Sample_R2.fastq.gz -baseout Sample.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment: STAR (version 2.7.3a): STAR --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir mm39_100_RNA --readFilesIn Sample_1P.fastq.gz Sample_2P.fastq.gz --outFileNamePrefix Sample --outSAMtype BAM Unsorted --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.35 --outFilterMatchNmin 30 --alignEndsType EndToEnd
Sort: samtools (version 1.12): samtools sort -@ 4 -n -o Sample.bam SampleAligned.out.bam
Mate coordinates: samtools (version 1.12): samtools fixmate -@ 4 -rm Sample.bam Sample.fixmate.bam
Sort: samtools (version 1.12): samtools sort -@ 4 -o Sample.resort.bam Sample.fixmate.bam
Remove duplicates: samtools (version 1.12): samtools markdup -@ 4 -l 1500 -r -d 100 -s Sample.resort.bam Sample.duprm.bam
Index: samtools (version 1.12): samtools index -@ 4 -b Sample.duprm.bam
Count reads: GenomicAlignments (R, version 1.26.0): summarizeOverlaps (default parameters)
Assembly: mm39 (modified)
Supplementary files format and content: mtx file with counts (aligned to gene) against all samples
Supplementary files format and content: genes.tsv: gene names corresponding to row names of mtx file
Supplementary files format and content: cells.tsv: cell (sample) corresponding to column names of mtx file

molecule: total RNA

organism: Mus musculus

source_name: Skin

extract_protocol:
Cells were sorted into Buffer RLT (Qiagen catalog # 79216) and RNA was purified using the Agencourt RNAClean XP beads (Beckman Coulter catalog # A63987) at a 2.2X ratio.
First-strand cDNA synthesis was achieved using Maxima H Minus Reverse Transcriptase (ThermoFisher catalog # EP0751) according to the manufacturer’s protocol using oligo dT primers, plus the addition of a custom template-switch oligo in a 1mM final concentration. cDNA was amplified for 24 cycles using KAPA HiFi HotStart ReadyMix (Kapa Biosystems KK2601). After PicoGreen quantification, 0.1-20 ng of cDNA was used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina catalog # FC-131-1024) in a total volume of 6.25 µL with 12 cycles of PCR. Indexed libraries were pooled by volume and cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 2X ratio.

treatment_protocol: Mice were treated topically on the ears with either imiquimod or vehicle control for 3 days. Cells were isolated from skin and Treg cells were sorted into single wells.

value: Skin

tag: cell type

value: regulatory T cell

value: Imiquimod


title: U-DMSO

value: DMSO


title: A-DMSO

source_name: Synthesized A RNA library

value: Synthesized A RNA library


title: Human oocyte spent media, participant 005, rep 1 [P-005-0-4]

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: UCSD

library_source: transcriptomic

data_processing:
Adapters and low-quality bases were trimmed by Trimmomatic (version 0.36).
The trimmed sequences were aligned to the human reference genome (GRCh38/hg38) by STAR (version 2.5.4b) and de-duplicated by UMI.
Read counts per gene were calculated by featureCounts (version 1.6.1) with the RefSeq gene annotation GTF file (GRCh38/p14).
Read counts were converted to normalized counts (NC) by DESeq2 in R (R package DESeq2).
Assembly: hg38
Supplementary files format and content: IVF_NC.tsv: normalized counts level for each gene and sample with genes in rows and samples in columns
Library strategy: SILVER-seq

organism: Homo sapiens

extract_protocol:
The spent media in their original culture dishes were obtained immediately after embryo transfer to fresh media. The fertility center follows a 7-day standard procedure. In this procedure, the collected oocytes are screened for maturity (the time of screening is designated as the 0th hour). The mature oocytes (MII oocytes) undergo intracytoplasmic sperm injection and are subsequently cultured in G-1™ PLUS media (G1). At the 18th hour, the embryos are washed and transferred to new G1 media. The spent G1 media are collected (18h spent media, 62 droplets). At the 68th hour, the embryos are transferred to new G-2™ PLUS media (G2), and the spent G1 media are collected (68h spent media, 70 droplets). At the 120th hour, the embryos are evaluated, and the spent media are (120h spent media, 69 droplets). Depending on the evaluation, the embryos are either frozen for transferring to the uterus or transferred to fresh G2 media for additional culturing. Those embryos subjected to additional culturing are collected at the 160th hour (160h spent media, 60 droplets).
The spent media were carefully aspirated out from the original culture dishes and centrifuged at 500 ×g for 3 min under 4°C. The supernatant was aspirated and centrifuged again. A 7 μL aliquot of the supernatant of the 2nd round of centrifugation was used as the input to SILVER-seq.

value: Human oocyte spent media

tag: participant id

tag: collection time

tag: arrest status

tag: uniquely mapped_ratio_>_25%

value: Y

tag: cultured w/_cumulus_cells

value: N


title: Human oocyte spent media, participant 021, rep 1 [P-021-0-2]


title: LELab_IHF_manuscript_sample_1

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

description: submitter provided name: Caulobacter crecentus CB15N

library_source: genomic

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) or NextSeq550 short reads (75bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC_011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Assembly: NC_011916.1
Supplementary files format and content: Files starting with LeLab_coverage_output_: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

molecule: genomic DNA

organism: Caulobacter vibrioides

source_name: mixed population, stationary phase

growth_protocol: C. crescentus cell cultures (50 mL) were grown in PYE to a stationary phase and fixed with formaldehyde to a final concentration of 1%. When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media for C. crescentus): kanamycin (5/25); spectinomycin (25/100); oxytetracycline (1/2). Fixed cells were incubated at room temperature for 30 min, then quenched with 0.125 M glycine for 15 min. Cells were washed three times with 1x PBS (pH 7.4) and resuspended in 1 mL of buffer 1 (20 mM K-HEPES pH 7.9, 50 mM KCl, 10% glycerol, and Roche EDTA-free protease inhibitors). Subsequently

extract_protocol:
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 or NextSeq550 sequencing platform

value: mixed population, stationary phase

tag: genotype

value: CB15N WT

value: anti-FLAG


title: U-R1

value: 50mM R1 for 2h at 0 degree


title: LELab_IHF_manuscript_sample_7

value: delta_rogA ihfB::ihfB-flag


title: A-R2


title: LELab_IHF_manuscript_sample_8


title: Sample_IMQ1-18_IGO_12061_309

description: single cell


title: Sample_IMQ1-12_IGO_12061_302

description: single cell


title: Sample_IMQ1-17_IGO_12061_308

description: single cell


title: LELab_IHF_manuscript_sample_5


title: Human oocyte spent media, participant 005, rep 1 [P-005-0-3]


title: A-S2


title: A-R1


title: Sample_IMQ1-11_IGO_12061_301

description: single cell


title: A-S1


title: Human oocyte spent media, participant 005, rep 1 [P-005-0-2]


title: Human oocyte spent media, participant 005, rep 1 [P-005-0-1]


title: Sample_IMQ1-10_IGO_12061_300

description: single cell


title: sCAFs rom 4T1 tumors in BABL/C mouse repetition3

city: Rehovot

first: Aviad

last: Ben-Shmuel

state: Other

address: Nella and Leon Benoziyo Building for Biological Sciences, Herzl

department: Biomolecular Sciences

country: Israel

institute: Wiezmann Institute

description:
scaf_3
3' RNA-seq for digital gene expression quantitation

data_processing:
Illumina bcl2fastq software used for base calling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
aligment: STAR v2.4.2a parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis was done for genes having minimum 10 reads in at least one sample
Assembly: mm10
Supplementary files format and content: tab delimited text files include mRNA molecule count values for each sample

molecule: polyA RNA

source_name: Breast Tumor

growth_protocol: 8 week-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase inDMEM 20 min at 37oC. Spleens: spleens were crushed and treated with red blood cell lysis buffer for 5 minutes on ice. NK cells were isolated using Miltenyi mouse NK isolation kit.  For both spleens and tumors, NK cells were further purified via FACS. sCAFs were isolated using magentic seperation (CD45-Epcam-) and further purified via FACS
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: 8 week old BALB/c females were injected under anaesthesia with 100,000 4T1-GFP cells suspended in PBS, directly into the lower left mammary fat pad. To obtain NK cells and sCAFs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem.To obtain NK cells from spleens, spleens were excised post mortem.

value: Breast Tumor

value: Primary CAF


title: sCAFs rom 4T1 tumors in BABL/C mouse repetition2

description:
scaf_2
3' RNA-seq for digital gene expression quantitation


title: UVA176

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

description: Explant

data_processing:
Raw reads were demultiplexed using bcl2fastq script
Read quality was assessed using FastQC v0.11.9
adapter sequences were trimmed using Trim Galore v0.6.5
Reads with Phred scores <20 were removed
Trimmed reads were mapped to the hg38 human reference genome using STAR v2.7.3a
PCR duplicates were marked using Picard and WASP was used to filter reads prone to mapping bias
Total read counts and RPKM were calculated with RNA-SeQC v1.1.8  with additional flags “-n 1000 -noDoC -strictMode” and GENCODE v32 reference annotation
Transcript and isoform expression levels were estimated using RSEM v1.3.3
we used verifyBamID97 to check whether the reads were contaminated or sample swaps occurred and cross-checked four swaps with NGSCheckMate
Assembly: hg38
Supplementary files format and content: tab-delimited files include TPM values for each individual (column) for each gene (row)

source_name: Explant coronary artery, RCA segment

extract_protocol:
Frozen tissue samples were pulverized using a mortar & pestle on dry ice, processed in Qiazol in a bullet blender using RINO tubes, then RNA was isolated using the Qiagen miRNeasy mini RNA extraction kit
RNA seq libraries were prepared using manufacturer's instructions for the  Illumina TruSeq Stranded Total RNA Gold kit and barcodes were added using Illumina - TruSeq RNA Unique Dual (UD) Indexes kit
Ribosomal RNA depletion

value: coronary artery


title: Sample_IMQ1-1_IGO_12061_290

description: single cell


title: NK cells from 4T1 tumors in BABL/C mouse repetition 4

description:
Tumor4
3' RNA-seq for digital gene expression quantitation

value: 4T1 tumor infiltrating (TI) NK cells


title: UVA175

description: Explant

source_name: Explant coronary artery, LAD segment


title: Sample_IMQ-87_IGO_12061_287

description: single cell

value: Skin


title: Sample_IMQ-9_IGO_12061_203

description: single cell

value: regulatory T cell


title: sCAFs rom 4T1 tumors in BABL/C mouse repetition1

description:
scaf_1
3' RNA-seq for digital gene expression quantitation


title: UVA174

description: Explant


title: NK cells from 4T1 tumors in BABL/C mouse repetition 3

description:
Tumor3
3' RNA-seq for digital gene expression quantitation


title: NK cells from 4T1 tumors in BABL/C mouse repetition 2

description:
Tumor2
3' RNA-seq for digital gene expression quantitation


title: Ad Lib Controls, rep6

city: FORT WAYNE

first: Amal

last: Khalifa

state: Indiana

address: 2101 E. Coliseum Blvd, ET-125

department: Computer Science

institute: Purdue University  Fort Wayne

data_processing:
Quality Control, Fastp, version 0.23.2.
Read mapping, Bowtie2, version 2.4.2.
FeatureCounts, version 2.0.1
Differential expression analysis, Matlab (R2022a)
Assembly: GCF_015227675.2
Supplementary files format and content: xls, Average row count

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
RNA was isolated from frozen hippocampal samples stored at -80°C using the Monarch® RNA Total Isolation kit (NEB T2010S)
Samples were homogenized frozen in 1X DNA/RNA Protection Reagent (NEB T2011L), then processed according to kit instructions including on-column DNase digestion. Samples were eluted in 50 µL of RNAse-free water and frozen at -80°C until submitted for sequencing

value: hippocampus

tag: cell line

value: Female

value: Left hippocampus


title: Ad Lib Controls, rep5

value: Male


title: Ad Lib Controls, rep4


title: NK cells from 4T1 tumors in BABL/C mouse repetition 1

description:
Tumor1
3' RNA-seq for digital gene expression quantitation


title: Sample_IMQ-86_IGO_12061_286

description: single cell

value: Imiquimod


title: UVA170

description: Explant


title: Sample_IMQ-85_IGO_12061_285

description: single cell


title: UVA168

description: Explant


title: Ad Lib Controls, rep3

value: Right hippocampus


title: NK cells from  spleen of 4T1-bearing BALB/C mouse of repetition 4

description:
4T1_Sp_4
3' RNA-seq for digital gene expression quantitation

source_name: Spleen

value: Spleen

value: Primary NK cell


title: Sample_IMQ-84_IGO_12061_284

description: single cell


title: Sample_IMQ-83_IGO_12061_283

description: single cell


title: Sample_IMQ-82_IGO_12061_282

description: single cell


title: iOVCAR-3 cells

type: RNA

city: Taipei

first: YuAn

last: Chen

state: Taipei

address: 5F, No.2, Xuzhou Rd., Zhongzheng Dist

department: College of Medicine

country: Taiwan

institute: Graduate Institute of Medical Genomics and Proteomics, College of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: iOVCAR-3 induced ovarian cancer initiating cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: iOVCAR-3 cells were cultured in DMEM/F12 medium supplemented with 20 % KnockOut serum replacement (KOSR, Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA), 10 ng/mL bFGF (Gibco, USA Thermo Fisher Scientific Inc., Waltham, MA, USA), 0.1 mM NEAA (Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA), 1 mM Glutamine (Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA), and 0.1 mM 2-mercaptoethanol (Invitrogen, Thermo Fisher Scientific Inc., Waltham, MA, USA). Cultures were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: A CytoTune™-iPS 2.0 Sendai Reprogramming Kit was used for generation of iOVCAR-3s via transduction of Yamanaka factors following the manufacturer's protocol

value: transfected with OCT3/4, SOX2, KLF4, and c-MYC genes


title: UVA163

description: Explant


title: NK cells from  spleen of 4T1-bearing BALB/C mouse of repetition 2

description:
4T1_Sp_2
3' RNA-seq for digital gene expression quantitation


title: Sample_IMQ-81_IGO_12061_281

description: single cell


title: NK cells from  spleen of 4T1-bearing BALB/C mouse of repetition 1

description:
4T1_Sp_1
3' RNA-seq for digital gene expression quantitation


title: UVA161

description: Explant

source_name: Explant coronary artery, NA segment


title: Pair Fed, rep5


title: Pair Fed, rep6


title: UVA158

description: Explant


title: Control OVCAR-3 cells

source_name: OVCAR-3 ovarian cancer cells

value: control


title: NK cells from healthy BALB/C mouse spleen repetition 3

description:
Healthy_Sp_3
3' RNA-seq for digital gene expression quantitation


title: Sample_IMQ-80_IGO_12061_279

description: single cell


title: Pair Fed, rep4


title: Sample_IMQ-8_IGO_12061_202

description: single cell


title: NK cells from healthy BALB/C mouse spleen repetition 2

description:
Healthy_Sp_2
3' RNA-seq for digital gene expression quantitation


title: UVA157

description: Explant


title: LELab_IHF_manuscript_sample_24

value: mixed population, stationary phase

value: delta_rogA gtaT IBE2-3-4-5 (TT to GG) ihfB::ihfB-flag

value: anti-FLAG


title: Pair Fed, rep3


title: UVA156

description: Explant

value: coronary artery


title: Ad Lib Controls, rep2


title: UVA165

description: Explant


title: UVA167

description: Explant


title: Pair Fed, rep2


title: Sample_IMQ-78_IGO_12061_277

description: single cell


title: NK cells from  spleen of 4T1-bearing BALB/C mouse of repetition 3

description:
4T1_Sp_3
3' RNA-seq for digital gene expression quantitation


title: Pair Fed, rep1


title: S2 cells, Micro-C, replicate 1

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
Micro-C data were analyzed using hicpro (Servant et al., 2015) without specifying a restriction enzyme site and filtering out interactions within 400bp. The mcool files generated using hicpro were then visualized in the resgen.io browser (Abdennur and Mirny, 2020; Kerpedjiev et al., 2018).
Assembly: dm6
Supplementary files format and content: mcool files generated using HiC-Pro
Library strategy: Micro-C

organism: Drosophila melanogaster

growth_protocol: All the cell lines were cultured using the recipes and sources recommended on the DGRC web site.

extract_protocol:
Micro-C experiments were performed following previous study (Slobodyanyuk et al., 2022) with a few modifications.
Following binding of Micro-C fragments to streptavidin beads libraries were prepared as described for Hi-C libraries in (Chakraborty et al., 2023).


title: S2 cells, Micro-C, replicate 2


title: UVA153

description: Explant


title: Ethanol Treatment, rep5


title: D17 cells, Micro-C, replicate 2


title: Ethanol Treatment, rep4


title: Sample_IMQ-75_IGO_12061_274

description: single cell


title: UVA152

description: Explant


title: Sample_IMQ-74_IGO_12061_273

description: single cell


title: D17 cells, Micro-C, replicate 1


title: Ethanol Treatment, rep3


title: UVA151

description: Explant


title: Sample_IMQ-76_IGO_12061_275

description: single cell


title: Ethanol Treatment, rep2


title: Sample_IMQ-73_IGO_12061_271

description: single cell


title: UVA150

description: Explant


title: S2 cells, RNA-seq, replicate 4

data_processing:
Raw reads were trimmed with Trim Galore v0.6.4. , and then aligned to the Drosophila reference genome (BDGP6) using STAR v2.7.3a (Dobin et al., 2013), and then obtained gene-level read counts using the featureCount function from subread v2.0.0 (Liao et al., 2013). Differentially expressed genes were identified using DESeq2 v1.30.1 (Love et al., 2014) with the cutoff: FDR < 0.05, |log2Foldchange| > 1.
Assembly: dm6
Supplementary files format and content: tab-delimited table, TPM/RPKM values calculated by using RSEM

extract_protocol:
For each cell line RNA was made from 4 separate tissue culture flasks to generate four independent replicates. For each RNA prep 1Î107 cells spun down (1000 g, 3 min), washed twice with ice-cold PBS, and resuspended in 1 mL of ice-cold PBS, transferred to a 1.5 mL Eppendorf tube and spun down at full speed in a microfuge for 2 min at 4 ℃. The pellet was resuspended in 100 µL PBS. Added 1 mL of Trizol to the cell suspension and vortexed for 1 min. Incubated the samples at RT for 15 min. Added 200 µL of chloroform and vortexed for 2 min. Centrifuged the samples at 13,200 rpm 15 min at 4 ℃. Carefully transferred the top aqueous layer containing the RNA to a fresh tube. Measured the RNA concentration using the broad range Qubit RNA kit and a Qubit 3.0 fluorimeter (Invitrogen). An aliquot of the total RNA was further purified using the Qiagen RNeasy Micro kit following the manufacturer’s directions.
Libraries were made using the Illumina TruSeq Stranded mRNA sample prep kit, and then run on a NovaSeq 6000 using a SP 200 kit by the NICHD Molecular Genomics Core.


title: S2 cells, RNA-seq, replicate 3


title: UVA148

description: Explant


title: UVA154

description: Explant

source_name: Explant coronary artery, LAD/RCA segment


title: Ethanol Treatment, rep1


title: Sample_IMQ-77_IGO_12061_276

description: single cell


title: Sample_IMQ-72_IGO_12061_270

description: single cell


title: S2 cells, RNA-seq, replicate 2


title: UVA147

description: Explant


title: cells untreated ,72h s2461

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Adapter sequences and bad quality reads were trimmed using Trimmomatic (v0.38) with the following parameters: HEADCROP:3 TRAILING:10 MINLEN:25
Reads were then aligned to the Human reference genome (hg19) and quantified using STAR (v2.5.2b).
Assembly: hg19
Supplementary files format and content: tab -delimited raw read count

source_name: JMML MNC, isolated from pdx

growth_protocol: isolated cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS), cytokines and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) according to the manufacturer’s protocol.
Library preparation was carried out as described in the Illumina TruSeq Stranded RNA Sample Preparation Guide.

treatment_protocol: Azacitidine was added to the above mentioned culture at the indicated concentrations for 72h

value: JMML MNC, isolated from pdx

value: untreated


title: Sample_IMQ-71_IGO_12061_269

description: single cell

value: Skin

value: regulatory T cell


title: UVA146

description: Explant


title: cells untreated ,72h s801D


title: Ad Lib Controls, rep1

value: hippocampus


title: UVA144

description: Explant


title: UVA141

description: Explant


title: cells treated with 3uM aza,72h s2461

value: 3uM aza


title: D17 cells, RNA-seq, replicate 4


title: cells treated with 3uM aza,72h s801D


title: D17 cells, RNA-seq, replicate 3


title: Sample_IMQ-7_IGO_12061_200

description: single cell


title: cells treated with 0.1uM aza,72h s2461

value: 0.1uM aza


title: Sample_IMQ-69_IGO_12061_267

description: single cell

value: Imiquimod


title: Sample_IMQ-68_IGO_12061_266

description: single cell


title: D17 cells, RNA-seq, replicate 1


title: cells treated with 0.1uM aza,72h s801D


title: UVA139

description: Explant


title: UVA140

description: Explant


title: Sample_IMQ-66_IGO_12061_263

description: single cell


title: UVA138

description: Explant


title: S2 cells, ChIP-seq, TrxN, replicate 2

data_processing:
The raw reads were first trimmed with TrimGalore v0.6.4, and then aligned to the Drosophila reference genome (BDGP6) using Bowtie v2.3.5.1 (Langmead and Salzberg, 2012) with settings: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000. PCR duplicates were removed using the rmdup function of samtools v1.13 (Li et al., 2009). After confirming the data reproducibility, the replicated data were pooled together for further analysis. Peak calling was performed with MACS v2.2.6 (Zhang et al., 2008) with settings: -f BAMPE --keep-dup all --fe-cutoff 1.5 -q 0.05 -g dm. The peaks were further filtered by removing those that overlap ENCODE Blacklist V2 regions (Amemiya et al., 2019) using BEDtools 2.29.2 (Quinlan and Hall, 2010).
Assembly: dm6
Supplementary files format and content: BED files for the peak calling results

extract_protocol:
For each cell type started with 30 mL of cells at 6106 cells/ml. Added 1.87 mL of 16% formaldehyde and incubated at RT for 10 min with gentle rocking. The formaldehyde was quenched by adding glycine to a final concentration of 0.125 M followed by a 5 min incubation at RT with gentle rocking. The cells were spun down at 2000 g, 3 min, and washed twice with ice cold PBS. The cells were resuspended in 600 µL PBS, divided into 100 µL aliquots, spun down and the pellets were flash frozen and stored at -80 ℃. Each aliquot of cells can be used for up to 5 ChIP reactions. Cells were fixed and frozen from different flasks to generate independent biological replicates. The frozen formaldehyde fixed cell pellets were resuspended in 0.8 ml ice-cold cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP40, supplemented with protease inhibitors (Roche Complete EDTA-free protease inhibitor), incubated on ice for 10 min, then pelleted by centrifugation at 2000 g for 5 min at 4 ℃. The supernatant was removed and the pellet resuspended in 1 mL nuclear lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 0.2% SDS, supplemented protease inhibitors) and incubated for 10 min at 4 ℃ on a rocking platform. 0.5 ml of 400 mM NaCl IP dilution buffer (16.7 mM Tris-HCl pH 8, 1.2 mM EDTA, 400 mM NaCl, 1.1% Triton X100, 0.01% SDS, supplemented with protease inhibitors) – to a final salt concentration of 125 mM. The lysate was sonicated in 300 µL aliquots using a Q Sonica (Model Q800R3), at 40% amplitude for 30 sec OFF and 30 sec ON for a total of 5 min ON time. The sonicated samples were spun for 10 min at full speed in an Eppendorf centrifuge at 4 ℃. The 300 µL aliquots of each cell type sample were pooled again. 4 µL was removed as input (2% of a single ChIP reaction). To the remainder 100 uL of TE washed Protein A SepharoseTM Fast Flow (Cytiva) was added, and the samples were incubated at 4 ℃ for 1 hour with gentle rocking. The samples were spun at full speed in an Eppendorf centrifuge for 1 min, and the supernatant transferred to a fresh tube. For each IP, 200 uL of sonicated the sample was used + 800 uL 67 mM NaCl ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 1.2 mM EDTA, 67 mM NaCl, 1.1% Triton X100, 0.01% SDS, supplemented with protease inhibitors. The appropriate amount of antibody (Supplemental Table 1), was added and incubated rocking overnight at 4 ℃. 60 µL protein A/agarose bead slurry (prewashed with TE buffer prior to use) for 1 hour at 4 ℃ with rotation. The agarose was pelleted by centrifugation at 800 rpm at 4 ℃ for 1 min, the supernatant was carefully removed and the agarose was washed 5 min on a rotating platform at 4 ℃ sequentially with 1ml of the following buffers: Low salt immune complex buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.0, 150 mM NaCl), High salt immune complex wash (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 200 mM NaCl), LiCl immune complex wash (0.25 M LiCl, 1% NP40, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris pH 8.0) followed by two 5 min room temperature washes with TE buffer. The agarose was pelleted again at 800 rpm for 1 min and the DNA was eluted with 500 µL freshly made elution buffer (1% SDS, 0.1 M NaHCO3) for 30 min with gentle rocking. The agarose was pelleted and the supernatant transferred to a fresh tube. The crosslinks were reversed by adding 20 µL of 5 M NaCl and incubating at 65 ℃ for 4 hours. The cross links were also reversed in the input sample. 10 uL of 0.5 M ETDA, 20 uL of 1 M Tris-HCl pH 6.5 and 2 uL of 10 mg/mL proteinase K were added and the samples incubated at 45 ℃ for 1 hour. The DNA was recovered by phenol/chloroform extraction followed by ethanol precipitation with 2 µL of pellet paint, 50 µL 5 M NaOAc, 1 mL Ethanol. Washed and dried pellets were resuspended in PCR grade water.
1.5 ng of ChIP sample DNA (as measured by a Qubit 3.0 fluorimeter) was used to prepare each library. Libraries were made using either the Thruplex DNA-seq and dual index kits (Takara), or the NEBNext UltraTM II DNA library preparation kit and dual index kits (New England Biolabs). Libraries were made according to the manufacturer’s directions. Samples were sequenced by 50 bp pair-end sequencing with a NovaSeq 6000 with an SP100 kit.by the NICHD Molecular Genomics Core.


title: UVA136

description: Explant


title: Sample_IMQ-67_IGO_12061_265

description: single cell


title: S2 cells, RNA-seq, replicate 1


title: RNAseq_Kupffer cells_Clec4fCreId3f/f_replicate #1

city: New York

first: Zihou

last: Deng

state: NY

address: 165 E 118th St, Apt 3N

department: Immunology program

institute: MSKCC

description: Clec4fCreId3ff_ Id3ff_counts.txt.gz

data_processing:
Sequenced reads from the RNAseq were aligned to the mouse reference genome  mm10 using STAR v2.7.10a . The aligned reads were quantified as gene counts using HTSeq  with GENCODE release M30. DESeq2  was applied to the gene counts table to identify differentially expressed genes (DEGs). DEGs were ranked based on their log2 fold change and associated p-values.
Assembly: mm10
Supplementary files format and content: files containg gene expression TPM data

source_name: Liver

extract_protocol:
Cells were directly sorted into 1.5ml Eppendorf tube with 800µl TRIzol™ LS Reagent. Phase separation in cells lysed in TRIzol Reagent was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2ng total RNA with RNA integrity numbers ranging from 9.4 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE100 run, using the HiSeq 3000/4000 SBS Kit (Illumina).

value: Liver

value: Sorted liver Kupffer cells

value: Untreated


title: RNAseq_Kupffer cells_Clec4fCreId3f/f_replicate #2

description: Clec4fCreId3ff_ Id3ff_counts.txt.gz


title: Sample_IMQ-65_IGO_12061_262

description: single cell


title: Sample_IMQ-70_IGO_12061_268

description: single cell


title: D17 cells, RNA-seq, replicate 2


title: D17 cells, ChIP-seq, TrxN, replicate 2


title: Sample_IMQ-64_IGO_12061_261

description: single cell


title: RNAseq_Kupffer cells_Id3f/f_replicate #3

description: Clec4fCreId3ff_ Id3ff_counts.txt.gz


title: UVA133

description: Explant


title: RNAseq_Kupffer cells_Id3f/f_replicate #2

description: Clec4fCreId3ff_ Id3ff_counts.txt.gz


title: D17 cells, ChIP-seq, TrxN, replicate 1


title: Sample_IMQ-63_IGO_12061_260

description: single cell


title: UVA135

description: Explant


title: S2 cells, ChIP-seq, TrxC, replicate 2


title: RNAseq_Kupffer cells_Id3f/f_replicate #1

description: Clec4fCreId3ff_ Id3ff_counts.txt.gz


title: UVA132

description: Explant


title: S2 cells, ChIP-seq, TrxC, replicate 1


title: Sample_IMQ-61_IGO_12061_258

description: single cell


title: UVA130

description: Explant


title: Kc167 cells, ChIP-seq, TrxC, replicate 2


title: Kc167 cells, ChIP-seq, TrxC, replicate 1


title: Sample_IMQ-60_IGO_12061_257

description: single cell


title: Sample_IMQ-6_IGO_12061_199

description: single cell


title: D17 cells, ChIP-seq, TrxC, replicate 2


title: S2 cells, ChIP-seq, TrxN, replicate 1


title: UVA127

description: Explant


title: RNAseq_Tim4+CD206hi Kupffer cells_Tumor_replicate #2

description: Tim4+CD206hi_TF_Tumor _counts.txt.gz

tag: cell population

value: Intraportal injected tumor for 2 weeks


title: Sample_IMQ-62_IGO_12061_259

description: single cell


title: UVA128

description: Explant


title: RNAseq_Tim4+CD206hi Kupffer cells_Tumor free_replicate #3

description: Tim4+CD206hi_TF_Tumor _counts.txt.gz


title: UVA129

description: Explant


title: RNAseq_Tim4+CD206hi Kupffer cells_Tumor_replicate #1

description: Tim4+CD206hi_TF_Tumor _counts.txt.gz


title: UVA126

description: Explant


title: Sample_IMQ-59_IGO_12061_255

description: single cell


title: RNAseq_Tim4+CD206hi Kupffer cells_Tumor free_replicate #2

description: Tim4+CD206hi_TF_Tumor _counts.txt.gz


title: Sample_IMQ-58_IGO_12061_254

description: single cell


title: D17 cells, ChIP-seq, TrxC, replicate 1


title: S2 cells, ChIP-seq, Spps, replicate 2


title: RNAseq_Tim4+CD206hi Kupffer cells_Tumor_replicate #3

description: Tim4+CD206hi_TF_Tumor _counts.txt.gz


title: RNAseq_Tim4+CD206hi Kupffer cells_Tumor free_replicate #1

description: Tim4+CD206hi_TF_Tumor _counts.txt.gz


title: S2 cells, ChIP-seq, Spps, replicate 1


title: UVA125

description: Explant


title: Sample_IMQ-57_IGO_12061_253

description: single cell


title: RNAseq_Tim4+CD206+ Kupffer cells_Tumor_replicate #3

description: Tim4+CD206+_TF_Tumor _counts.txt.gz


title: UVA124

description: Explant


title: Sample_IMQ-56_IGO_12061_252

description: single cell


title: RNAseq_Tim4+CD206+ Kupffer cells_Tumor_replicate #2

description: Tim4+CD206+_TF_Tumor _counts.txt.gz


title: UVA123

description: Explant


title: RNAseq_Tim4+CD206+ Kupffer cells_Tumor_replicate #1

description: Tim4+CD206+_TF_Tumor _counts.txt.gz


title: Kc167 cells, ChIP-seq, Spps, replicate 1


title: UVA122

description: Explant


title: D17 cells, ChIP-seq, Spps, replicate 2


title: Kc167 cells, ChIP-seq, Spps, replicate 2


title: Sample_IMQ-53_IGO_12061_249

description: single cell


title: UVA121

description: Explant


title: RNAseq_Tim4+CD206+ Kupffer cells_Tumor free_replicate #3

description: Tim4+CD206+_TF_Tumor _counts.txt.gz


title: Sample_IMQ-54_IGO_12061_250

description: single cell


title: D17 cells, ChIP-seq, Spps, replicate 1


title: RNAseq_Tim4+CD206+ Kupffer cells_Tumor free_replicate #2

description: Tim4+CD206+_TF_Tumor _counts.txt.gz


title: Sample_IMQ-52_IGO_12061_248

description: single cell


title: UVA119

description: Explant


title: Sample_IMQ-51_IGO_12061_247

description: single cell


title: S2 cells, ChIP-seq, Sfmbt, replicate 2


title: S2 cells, ChIP-seq, Sfmbt, replicate 1


title: RNAseq_Tim4+CD206+ Kupffer cells_Tumor free_replicate #1

description: Tim4+CD206+_TF_Tumor _counts.txt.gz


title: WCE-e1-rep1a-H3K9me3

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

description: Whole-cell extract - Input DNA

data_processing:
ChIP-seq data were analyzed as described in Engreitz et al. Nature 2016
Assembly: hg19
Supplementary files format and content: TDF: Coverage at 5bp resolution across genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/)

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e1

growth_protocol: K562 cells expressing catalytically-dead Cas9 fused to a KRAB repressive domain from a doxycycline-inducible promoter were grown in RPMI with 10% FBS.

extract_protocol: ChIP-Seq: We performed ChIP-Seq as described in Engreitz et al. Nature 2016

tag: grna target

tag: grna sequence

value: GGAGCCAGATAAGTCAACGG

tag: gender

value: female


title: UVA118

description: Explant


title: D17 cells, ChIP-seq, Sfmbt, replicate 2


title: Sample_IMQ-50_IGO_12061_246

description: single cell


title: WCE-NS1-rep2b

description: Whole-cell extract - Input DNA

source_name: K562 cells transduced with a gRNA targeting MYC enhancer NS1

value: GACAAGCTGCAAGGTGTAAAT


title: Sample_IMQ-5_IGO_12061_198

description: single cell


title: UVA117

description: Explant


title: D17 cells, ChIP-seq, Sfmbt, replicate 1


title: UVA116

description: Explant


title: WCE-Ctrl2-rep2a

description: Whole-cell extract - Input DNA

source_name: K562 cells transduced with a non-targeting control gRNA

value: GACTCGTCACATGGGGTTGCGA


title: WCE-Ctrl1-rep1a

description: Whole-cell extract - Input DNA

value: GATCGCGAGGACCCGTTCCGCC


title: Sample_IMQ-49_IGO_12061_245

description: single cell

source_name: Skin


title: Sample_IMQ-48_IGO_12061_244

description: single cell


title: S2 cells, ChIP-seq, Scm, replicate 2


title: UVA120

description: Explant

value: coronary artery


title: UVA112

description: Explant


title: S2 cells, ChIP-seq, Scm, replicate 1


title: H3K9me3-Ctrl1-rep1b

description: H3K9me3 ChIP-seq


title: UVA113

description: Explant


title: UVA111

description: Explant


title: D17 cells, ChIP-seq, Scm, replicate 2


title: Sample_IMQ-79_IGO_12061_278

description: single cell


title: Sample_IMQ-47_IGO_12061_243

description: single cell


title: NK cells from healthy BALB/C mouse spleen repetition 1

description:
Healthy_Sp_1
3' RNA-seq for digital gene expression quantitation

value: Spleen

value: Primary NK cell


title: H3K9me3-e1-rep1b

description: H3K9me3 ChIP-seq


title: Sample_IMQ-55_IGO_12061_251

description: single cell

value: Skin

value: regulatory T cell


title: UVA110

description: Explant


title: D17 cells, ChIP-seq, Scm, replicate 1


title: H3K9me3-Ctrl1-rep1a

description: H3K9me3 ChIP-seq


title: Sample_IMQ-46_IGO_12061_242

description: single cell


title: Sample_IMQ-45_IGO_12061_241

description: single cell


title: UVA109

description: Explant

source_name: Explant coronary artery, LCX segment


title: Sample_IMQ-44_IGO_12061_240

description: single cell


title: S2 cells, ChIP-seq, Rad21, replicate 1


title: S2 cells, ChIP-seq, Psc, replicate 2


title: UVA108

description: Explant


title: Sample_IMQ-42_IGO_12061_238

description: single cell


title: H3K27ac-NS1-rep2b

description: H3K27ac ChIP-seq


title: UVA107

description: Explant


title: Sample_IMQ-43_IGO_12061_239

description: single cell


title: UVA106

description: Explant


title: H3K9me3-e1-rep1a

description: H3K9me3 ChIP-seq


title: H3K27ac-e7-rep2b

description: H3K27ac ChIP-seq

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e7

value: GCGCCCATGAATGTATAGCAG


title: UVA104

description: Explant


title: H3K27ac-e6-rep2b

description: H3K27ac ChIP-seq

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e6

value: GCTGGTGTCAGCCTCACAAC


title: Sample_IMQ-41_IGO_12061_237

description: single cell

value: Imiquimod


title: Kc167 cells, ChIP-seq, Psc, replicate 2


title: Kc167 cells, ChIP-seq, Psc, replicate 1


title: UVA103

description: Explant


title: UVA102

description: Explant


title: H3K27ac-e5-rep2b

description: H3K27ac ChIP-seq

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e5

value: GCCCATTGGGGTAGAGGCTG


title: D17 cells, ChIP-seq, Psc, replicate 2


title: Sample_IMQ-39_IGO_12061_235

description: single cell


title: Sample_IMQ-4_IGO_12061_197

description: single cell


title: H3K9me3-NS1-rep1a

description: H3K9me3 ChIP-seq


title: S2 cells, ChIP-seq, Rad21, replicate 2


title: Sample_IMQ-38_IGO_12061_234

description: single cell


title: S2 cells, ChIP-seq, Psc, replicate 1


title: S2 cells, ChIP-seq, Pho, replicate 2


title: Sample_IMQ-36_IGO_12061_232

description: single cell


title: Sample_IMQ-37_IGO_12061_233

description: single cell


title: H3K27ac-Ctrl4-rep2b

description: H3K27ac ChIP-seq

value: GGAGAGGCCCCTGTCGCGT


title: UVA099

description: Explant

source_name: Explant coronary artery, RCA segment


title: UVA098

description: Explant


title: H3K27ac-Ctrl2-rep2b

description: H3K27ac ChIP-seq


title: Kc167 cells, ChIP-seq, Pho, replicate 2


title: S2 cells, ChIP-seq, Pho, replicate 1


title: Sample_IMQ-40_IGO_12061_236

description: single cell


title: Sample_IMQ-34_IGO_12061_230

description: single cell


title: H3K27ac-Ctrl1-rep2b

description: H3K27ac ChIP-seq


title: Sample_IMQ-35_IGO_12061_231

description: single cell


title: UVA096

description: Explant

source_name: Explant coronary artery, LAD segment


title: H3K27ac-e4-rep2b

description: H3K27ac ChIP-seq

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e4

value: GAGCTTCCGTGGGCCCCTCC


title: UVA095

description: Explant


title: UVA101

description: Explant


title: H3K27ac-NS1-rep2a

description: H3K27ac ChIP-seq


title: D17 cells, ChIP-seq, Pho, replicate 2


title: H3K27ac-e6-rep2a

description: H3K27ac ChIP-seq


title: D17 cells, ChIP-seq, Psc, replicate 1


title: UVA094

description: Explant


title: Sample_IMQ-33_IGO_12061_229

description: single cell


title: H3K27ac-e3-rep2b

description: H3K27ac ChIP-seq

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e3

value: GACCACGGCAGCCTGCTCTGA


title: Sample_IMQ-32_IGO_12061_228

description: single cell


title: D17 cells, ChIP-seq, Pho, replicate 1


title: H3K27ac-Ctrl3-rep2b

description: H3K27ac ChIP-seq

value: GACGGAGGAAGTACACAGCT


title: UVA100

description: Explant


title: UVA088

description: Normal

source_name: Normal coronary artery, LAD segment


title: S2 cells, ChIP-seq, Ph, replicate 2


title: Kc167 cells, ChIP-seq, Pho, replicate 1


title: S2 cells, ChIP-seq, Ph, replicate 1


title: UVA087

description: Normal


title: Sample_IMQ-31_IGO_12061_227

description: single cell


title: H3K27ac-e4-rep2a

description: H3K27ac ChIP-seq

value: female


title: Sample_IMQ-30_IGO_12061_226

description: single cell


title: H3K27ac-e5-rep2a

description: H3K27ac ChIP-seq


title: H3K27ac-e3-rep2a

description: H3K27ac ChIP-seq


title: Kc167 cells, ChIP-seq, Ph, replicate 2


title: Kc167 cells, ChIP-seq, Ph, replicate 1


title: UVA086

description: Normal


title: Sample_IMQ-29_IGO_12061_225

description: single cell


title: H3K27ac-e2-rep2a

description: H3K27ac ChIP-seq

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e2

value: GGAATCGACCTTCCTTGAGG


title: UVA084

description: Explant


title: D17 cells, ChIP-seq, Ph, replicate 2


title: H3K27ac-e1-rep2a

description: H3K27ac ChIP-seq

value: GGAGCCAGATAAGTCAACGG


title: Sample_IMQ-3_IGO_12061_196

description: single cell


title: Sample_IMQ-28_IGO_12061_224

description: single cell


title: D17 cells, ChIP-seq, Ph, replicate 1


title: UVA083

description: Explant


title: H3K27ac-Ctrl4-rep2a

description: H3K27ac ChIP-seq


title: S2 cells, ChIP-seq, Pcl, replicate 2


title: Sample_IMQ-26_IGO_12061_222

description: single cell


title: S2 cells, ChIP-seq, Pcl, replicate 1


title: UVA081

description: Explant


title: Sample_IMQ-25_IGO_12061_221

description: single cell


title: H3K27ac-Ctrl2-rep2a

description: H3K27ac ChIP-seq

value: GACTCGTCACATGGGGTTGCGA


title: H3K27ac-ctr1-rep2a

description: H3K27ac ChIP-seq

value: GATCGCGAGGACCCGTTCCGCC


title: Sample_IMQ-24_IGO_12061_220

description: single cell


title: UVA085

description: Normal

source_name: Normal coronary artery, RCA segment

value: coronary artery


title: D17 cells, ChIP-seq, Pcl, replicate 1


title: UVA080

description: Normal


title: H3K27ac-NS1-rep1b

description: H3K27ac ChIP-seq

value: GACAAGCTGCAAGGTGTAAAT


title: UVA078

description: Explant


title: Sample_IMQ-23_IGO_12061_219

description: single cell

value: Skin


title: S2 cells, ChIP-seq, Pc, replicate 2


title: Sample_IMQ-22_IGO_12061_218

description: single cell

value: regulatory T cell


title: Sample_IMQ-27_IGO_12061_223

description: single cell


title: H3K27ac-e7-rep1b

description: H3K27ac ChIP-seq

value: GCGCCCATGAATGTATAGCAG


title: Sample_IMQ-21_IGO_12061_216

description: single cell


title: S2 cells, ChIP-seq, Pc, replicate 1


title: Sample_IMQ-20_IGO_12061_215

description: single cell


title: UVA075

description: Explant


title: UVA079

description: Explant


title: H3K27ac-e6-rep1b

description: H3K27ac ChIP-seq

value: GCTGGTGTCAGCCTCACAAC


title: H3K27ac-e5-rep1b

description: H3K27ac ChIP-seq


title: H3K27ac-Ctrl3-rep2a

description: H3K27ac ChIP-seq


title: UVA082

description: Explant


title: Kc167 cells, ChIP-seq, Pc, replicate 2


title: D17 cells, ChIP-seq, Pcl, replicate 2


title: Kc167 cells, ChIP-seq, Pc, replicate 1


title: H3K27ac-e4-rep1b

description: H3K27ac ChIP-seq


title: UVA074

description: Explant


title: D17 cells, ChIP-seq, Pc, replicate 2


title: UVA073

description: Explant


title: D17 cells, ChIP-seq, Pc, replicate 1


title: Sample_IMQ-19_IGO_12061_214

description: single cell

value: Imiquimod


title: UVA072

description: Explant


title: H3K27ac-e3-rep1b

description: H3K27ac ChIP-seq


title: H3K27ac-e2-rep1b

description: H3K27ac ChIP-seq


title: S2 cells, ChIP-seq, Input control


title: UVA070

description: Explant


title: H3K27ac-e1-rep1b

description: H3K27ac ChIP-seq


title: UVA071

description: Explant


title: Sample_IMQ-17_IGO_12061_212

description: single cell


title: Sample_IMQ-18_IGO_12061_213

description: single cell


title: UVA076

description: Explant


title: Kc167 cells, ChIP-seq, Input control


title: H3K27ac-Ctrl4-rep1b

description: H3K27ac ChIP-seq


title: Sample_IMQ-16_IGO_12061_211

description: single cell


title: D17 cells, ChIP-seq, Input control


title: UVA068

description: Explant

source_name: Explant coronary artery, NA segment


title: UVA069

description: Explant


title: S2 cells, ChIP-seq, H3K4me3, replicate 2


title: Sample_IMQ-15_IGO_12061_210

description: single cell


title: H3K27ac-Ctrl3-rep1b

description: H3K27ac ChIP-seq


title: S2 cells, ChIP-seq, H3K4me3, replicate 1


title: H3K27ac-Ctrl1-rep1b

description: H3K27ac ChIP-seq


title: UVA067

description: Explant


title: Sample_IMQ-13_IGO_12061_207

description: single cell


title: Sample_IMQ-2_IGO_12061_195

description: single cell


title: Sample_IMQ-14_IGO_12061_208

description: single cell


title: H3K27ac-Ctrl2-rep1b

description: H3K27ac ChIP-seq


title: Sample_IMQ-12_IGO_12061_206

description: single cell


title: H3K27ac-NS1-rep1a

description: H3K27ac ChIP-seq


title: UVA066

description: Explant


title: D17 cells, ChIP-seq, H3K4me3, replicate 2


title: UVA065

description: Explant


title: H3K27ac-e6-rep1a

description: H3K27ac ChIP-seq


title: Sample_IMQ-10_IGO_12061_204

description: single cell


title: S2 cells, ChIP-seq, H3K4me2, replicate 1


title: H3K27ac-e5-rep1a

description: H3K27ac ChIP-seq

value: GCCCATTGGGGTAGAGGCTG


title: S2 cells, ChIP-seq, H3K4me2, replicate 2


title: H3K27ac-e4-rep1a

description: H3K27ac ChIP-seq


title: D17 cells, ChIP-seq, H3K4me2, replicate 2


title: UVA064

description: Explant


title: UVA062

description: Explant


title: Sample_IMQ-1_IGO_12061_194

description: single cell


title: UVA063

description: Normal


title: D17 cells, ChIP-seq, H3K4me2, replicate 1


title: Sample_CTRL4-4_IGO_12061_313

description: control (no cell)

source_name: Empty well

value: Empty well


title: UVA061

description: Explant


title: H3K27ac-e3-rep1a

description: H3K27ac ChIP-seq


title: Sample_CTRL4-3_IGO_12061_305

description: control (no cell)


title: S2 cells, ChIP-seq, H3K36me3, replicate 2


title: H3K27ac-e2-rep1a

description: H3K27ac ChIP-seq


title: D17 cells, ChIP-seq, H3K4me3, replicate 1


title: Sample_CTRL4-1_IGO_12061_289

description: control (no cell)


title: UVA058

description: Normal


title: Kc167 cells, ChIP-seq, H3K36me3, replicate 2


title: H3K27ac-e7-rep1a

description: H3K27ac ChIP-seq


title: Sample_IMQ-11_IGO_12061_205

description: single cell


title: H3K27ac-e1-rep1a

description: H3K27ac ChIP-seq

source_name: K562 cells transduced with a gRNA targeting MYC enhancer e1


title: S2 cells, ChIP-seq, H3K36me3, replicate 1


title: Sample_CTRL4-2_IGO_12061_297

description: control (no cell)


title: UVA057

description: Normal


title: H3K27ac-Ctrl4-rep1a

description: H3K27ac ChIP-seq

value: GGAGAGGCCCCTGTCGCGT


title: UVA060

description: Explant


title: Kc167 cells, ChIP-seq, H3K36me3, replicate 1


title: UVA055

description: Normal


title: Sample_CTRL3-3_IGO_12061_209

description: control (no cell)


title: D17 cells, ChIP-seq, H3K36me3, replicate 2


title: UVA054

description: Normal


title: H3K27ac-Ctrl3-rep1a

description: H3K27ac ChIP-seq


title: H3K27ac-Ctrl1-rep1a

description: H3K27ac ChIP-seq


title: Sample_CTRL3-2_IGO_12061_201

description: control (no cell)


title: Sample_CTRL3-1_IGO_12061_193

description: control (no cell)


title: H3K27ac-Ctrl2-rep1a

description: H3K27ac ChIP-seq


title: UVA053

description: Normal


title: UVA052

description: Normal


title: S2 cells, ChIP-seq, H3K36me2, replicate 1


title: Sample_CTRL2-4_IGO_12061_121

description: control (no cell)


title: UVA051

description: Normal


title: Mab ATCC19977 △MabwhiB::phspwhiB7N-FLAG - Replicate 2

city: Albany

first: Pallavi

last: Ghosh

address: 150 New Scotland Ave

department: New York State Department of Health

institute: Wadsworth Center

data_processing:
For CHIPseq reads were aligned to the reference genome using the Bowtie2 and SamTools algorithms. Regions of enrichment were identified using a custom Python script as described previously.
CHIPSEq: gff file showing peak location

organism: Mycobacteroides abscessus

extract_protocol:
Immunoprecipitation of DNA-protein complexes as described in methods
NEBNext Ultra II Library Prep kit for Illumina

value: Bacteria


title: Sample_CTRL2-3_IGO_12061_113

description: control (no cell)


title: Mab ATCC19977 △MabwhiB::phspwhiB7N-FLAG - Replicate 1


title: UVA050

description: Normal


title: D17 cells, ChIP-seq, H3K36me2, replicate 2


title: D17 cells, ChIP-seq, H3K36me2, replicate 1


title: UVA048

description: Explant


title: Mab ATCC19977 △MabwhiB::phspwhiB7C-FLAG - Replicate 1


title: Sample_CTRL3-4_IGO_12061_217

description: control (no cell)


title: Mab ATCC19977 △MabwhiB::phspwhiB7C-FLAG - Replicate 2


title: S2 cells, ChIP-seq, H3K27me3, replicate 2


title: D17 cells, ChIP-seq, H3K36me3, replicate 1


title: S2 cells, ChIP-seq, H3K36me2, replicate 2


title: Sample_CTRL-4_IGO_12061_25

description: control (no cell)


title: Mab ATCC19977 △MabwhiB::pnatwhiB7C-FLAG - Replicate 1

value: Tetracycline 16ug/mLfor 2h


title: Mab ATCC19977 △MabwhiB::pnatwhiB7C-FLAG - Replicate 2


title: Sample_CTRL-3_IGO_12061_17

description: control (no cell)


title: S2 cells, ChIP-seq, H3K27me3, replicate 1


title: Kc167 cells, ChIP-seq, H3K27me3, replicate 2


title: UVA045

description: Explant


title: Sample_CTRL-2_IGO_12061_9

description: control (no cell)


title: UVA046

description: Normal


title: Mab ATCC19977 △MabsigH - Tet16 - Replicate 2

data_processing:
Processed files for RNA seq were generated using Rockhopper
RNASeq: Excel File showing  normalized expression of each sample

growth_protocol: Bacteria were grown to an OD of 0.6 in Middle brook 7H9 + OADC

extract_protocol:
RNA prepared using Qiagen kit, 2 microgm total RNA samples were treated with the Ribo-ZeroTM rRNA,
NEBNext Ultra II RNA Library Prep kit

treatment_protocol: 16mg/L of Tet for 45 mins or 2hs whereever indicated

value: dMabsigH

value: Tetracycline 16ug/mLfor 45 mins


title: Mab ATCC19977 △MabsigH - Tet16 - Replicate 1


title: Sample_CTRL2-2_IGO_12061_105

description: control (no cell)


title: Kc167 cells, ChIP-seq, H3K27me3, replicate 1


title: Sample_CTRL-1_IGO_12061_1

description: control (no cell)


title: D17 cells, ChIP-seq, H3K27me3, replicate 2


title: UVA044

description: Explant


title: Sample_CTRL2-1_IGO_12061_97

description: control (no cell)


title: D17 cells, ChIP-seq, H3K27me3, replicate 1


title: UVA043

description: Normal

source_name: Normal coronary artery, LCX segment


title: Mab ATCC19977 △MabwhiB7 - Tet16 - Replicate 4


title: LELab_IHF_manuscript_sample_48

source_name: mixed population, stationary phase

value: mixed population, stationary phase

value: delta_rogA YBE6

value: anti-GafY


title: Mab ATCC19977 △MabwhiB7 - Tet16 - Replicate 3


title: UVA041

description: Explant

value: coronary artery


title: LELab_IHF_manuscript_sample_50

value: delta_rogA rpoD::flag-rpoD

value: anti-FLAG


title: S2 cells, ChIP-seq, H3K27ac, replicate 2


title: UVA040

description: Normal


title: UVA047

description: Explant


title: Mab ATCC19977 △MabwhiB7 - Tet16 - Replicate 2


title: LELab_IHF_manuscript_sample_46

value: delta_rogA gafZ::gafZ-FLAG ZBE5


title: S2 cells, ChIP-seq, H3K27ac, replicate 1


title: Mab ATCC19977 △MabwhiB7 - Tet16 - Replicate 1


title: UVA039

description: Explant


title: UVA038

description: Normal


title: Kc167 cells, ChIP-seq, H3K27ac, replicate 2


title: LELab_IHF_manuscript_sample_45


title: Wt Mab ATCC19977 - Tet16 - Replicate 4

source_name: Wt Mab-Tet16

value: WT


title: UVA036

description: Normal


title: LELab_IHF_manuscript_sample_44


title: Kc167 cells, ChIP-seq, H3K27ac, replicate 1


title: LELab_IHF_manuscript_sample_42

value: delta_rogA gafZ::gafZ-FLAG

value: anti-VSVG


title: UVA034

description: Normal


title: LELab_IHF_manuscript_sample_41


title: UVA033

description: Explant


title: D17 cells, ChIP-seq, H3K27ac, replicate 1


title: D17 cells, ChIP-seq, H3K27ac, replicate 2


title: Wt Mab ATCC19977 - Tet16 - Replicate 2


title: Wt Mab ATCC19977 - Tet16 - Replicate 1


title: LELab_IHF_manuscript_sample_40


title: S2 cells, ChIP-seq, H2AK118ub1, replicate 2


title: UVA032

description: Explant


title: UVA031

description: Explant


title: S2 cells, ChIP-seq, H2AK118ub1, replicate 1


title: Kc167 cells, ChIP-seq, H2AK118ub1, replicate 2


title: A16

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Demultiplex BCL to FastQ using Casava 1.8.2
Raw data was trimmed based on quality score in Partek Flow.
Map to hg38 using STAR 2.7.8a
Features were filtered to exclude features where maximum<=50.
Data were transformed on samples and normalized by median ratio.
DESeq2 was utilized for differential analysis.
Assembly: hg38
Supplementary files format and content: Partek counts file in Excel format

source_name: skin

extract_protocol:
Minced skin biopsy specimens were treated with TRIzol solution (Invitrogen) followed by homogenization.  After addition of the TRIzol-tissue homogenate to chloroform, samples were shaken, and spun down. The supernatants were collected, placed on ice, mixed with an equal volume of 70% ethanol, and loaded onto RNeasy Mini Spin Columns, followed by completion of the RNeasy Mini (QIAGEN) protocol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian kit (Takara Bio USA, Inc.)
Libraries were sequenced on an Illumina HiSeq 3000 (1 x 50bp read length). Libraries were diluted to 3nM and pooled for sequencing.

value: skin

tag: disease

value: Affected

tag: age

tag: Sex

value: M

tag: oncologic diagnosis

value: follicular lymphoma

tag: transplant type

value: sex-mm, HLA-m

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

value: yes

tag: biopsy site

value: thigh

tag: clinical

value: dermal sclerosis, recent onset

tag: histopathology

value: Moderate interface dermatitis, dyskeratosis, dermal sclerosis

tag: sclerotic bsa

tag: skin score

tag: other cgvhd

value: joint, lung

tag: current systemic therapy

value: tacro, MMF

tag: current pred dose

tag: prior systemic therapy

value: pred, ritux

tag: time designation after sclerosis

value: early

tag: degree of infiltrate

value: moderate


title: UVA030

description: Normal

tag: tissue

value: coronary artery


title: Kc167 cells, ChIP-seq, H2AK118ub1, replicate 1

tag: cell line


title: UVA029

description: Explant


title: Wt Mab ATCC19977 - Tet16 - Replicate 3

tag: cell type

value: Bacteria

tag: genotype

value: WT

tag: treatment

value: Tetracycline 16ug/mLfor 45 mins


title: D17 cells, ChIP-seq, H2AK118ub1, replicate 2


title: A14

value: skin

tag: disease

value: Affected

tag: age

tag: Sex

value: F

tag: oncologic diagnosis

value: ALL, pre-T cell-type

tag: transplant type

value: sex-m, HLA-m

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

value: no

value: abdomen

value: dermal sclerosis with scale, stable

value: mild inflammation, dyskeratosis, dermal sclerosis

value: joint, genital, lung, liver, ocular

value: pred, siro, MMF

value: tacro, ritux, ECP

value: mild


title: A15

value: M

value: myelofibrosis

value: sex-mm, HLA-m

value: yes

tag: biopsy site

tag: clinical

value: dermal/subcu sclerosis, stable

tag: histopathology

value: Mild inflammation, interface vacuolization, dermal/subcu sclerosis

tag: sclerotic bsa

tag: skin score

tag: other cgvhd

value: joint, lung, liver, GI, ocular, oral

tag: current systemic therapy

value: pred, siro, ECP

tag: current pred dose

value: 10mg QD

value: cyclo, MMF, ritux, ECP, denileukin diftitox

value: late

value: moderate


title: A13

tag: tissue

value: skin

value: Affected

value: F

value: AML

value: no

value: abdomen

value: dermal sclerosis

value: interface vacuolozation, rare dyskeratosis, dermal/subcu sclerosis

value: joint, genital, liver, ocular

value: tacro, siro, ECP

tag: prior systemic therapy

value: MMF, ritux, pred, imatinib

tag: time designation after sclerosis

value: early

tag: degree of infiltrate


title: UVA028

description: Normal

value: coronary artery


title: D17 cells, ChIP-seq, H2AK118ub1, replicate 1

tag: cell line


title: UVA026

description: Explant


title: A12

tag: disease

tag: age

tag: Sex

tag: oncologic diagnosis

value: multiple myeloma

tag: transplant type

value: sex-m, HLA-m

value: yes

value: mild inflammation, dyskeratosis, dermal/subcu sclerosis

value: joint, lung, liver, ocular, oral

value: pred, MMF, IVIG

value: tacro, cyclo, etan, ritux, ECP

value: mild


title: UVA024

description: Normal


title: S2 cells, ChIP-seq, GAF, replicate 2


title: LELab_IHF_manuscript_sample_39

value: mixed population, stationary phase

tag: genotype

tag: treatment

value: anti-VSVG


title: S2 cells, ChIP-seq, GAF, replicate 1


title: U9

value: skin

value: Unaffected

value: M

value: sex-mm, HLA-m

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

tag: biopsy site

value: abdomen

tag: clinical

value: unaffected

tag: histopathology

value: normal

tag: sclerotic bsa

value: pred, ritux


title: D17 cells, ChIP-seq, GAF, replicate 2


title: A11

tag: tissue

value: Affected

value: F

value: ALL

value: MUD

value: arm

value: dermal/subcu sclerosis, progressive

value: dermal and subcu sclerosis

tag: skin score

tag: other cgvhd

value: joint, lung, liver, ocular

tag: current systemic therapy

value: pred, MMF

tag: current pred dose

tag: prior systemic therapy

value: cyclo, ritux, ECP

tag: time designation after sclerosis

value: early


title: Primary_lung_fibroblasts_Sfrp1_siRNA_rep3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from primary pulmonary fibroblast  treated with control siRNA, biological replicate 3

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

label: biotin

source_name: Primary pulmonary fibroblast  treated with control siRNA, biological replicate 3

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

extract_protocol: Total RNA was isolated using the PEQGold Total RNA Kit (PeqLab) according to the manufacturer’s instructions including gDNA elimination.

treatment_protocol: As described in the paper. Briefly, primary human fibroblasts (phFbs) were cultivated in 24- well plates with a density of 1.0 x105 cells/ well and in 6-well plates with a cell density of 2.5x105 cells/ well.  phFbs were treated with human siRNAs for Sfrp1. siRNAs obtained from Thermo Fisher Scientific were initially resuspended in nuclease-free water to a final concentration of 2µM to prepare a stock solution. For transfection, 10nM final concentration of Sfrp1 siRNA was added to 5µl of Lipofectamine RNAiMax (Invitrogen) diluted in a final volume of 500ml with Opti-MEM media (ThermoFischer). To form siRNA-lipofectamine complexes, the individual solutions were incubated for 20 minutes. In this time-frame, 2.5x104 cells were added in 2ml media (DMEM, 20% FBS without penicillin/streptomycin) per well in a 6-well plate. Next, 250µl of the transfection mix was added in each well. Untreated (UT) conditions were treated with 250µl of Opti-MEM medium and scrambled (sc) and siSfrp1 (si) conditions were treated with scrambled control and Sfrp1 specific siRNAs in lipofectamine solutions respectively. Furthermore, efficiency of siRNA transfection was tested over a period of 6 days, medium exchange was performed after 48 hours and then analyzed further for additional 24, 48 and 96 hours.

tag: cell type

value: Primary pulmonary fibroblast


title: Primary_lung_fibroblasts_untreated_rep3

description: Gene expression data from primary pulmonary fibroblast  untreated, biological replicate 3

source_name: Primary pulmonary fibroblast  untreated, biological replicate 3


title: UVA022

description: Explant

value: coronary artery


title: UVA023

description: Explant


title: Primary_lung_fibroblasts_untreated_rep1

description: Gene expression data from primary pulmonary fibroblast  untreated, biological replicate 1

source_name: Primary pulmonary fibroblast  untreated, biological replicate 1


title: Primary_lung_fibroblasts_Sfrp1_siRNA_rep2

description: Gene expression data from primary pulmonary fibroblast  treated with control siRNA, biological replicate 2

source_name: Primary pulmonary fibroblast  treated with control siRNA, biological replicate 2


title: Primary_lung_fibroblasts_untreated_rep2

description: Gene expression data from primary pulmonary fibroblast  untreated, biological replicate 2

source_name: Primary pulmonary fibroblast  untreated, biological replicate 2


title: D17 cells, ChIP-seq, GAF, replicate 1

tag: cell line


title: UVA021

description: Explant

source_name: Explant coronary artery, LAD segment


title: A10

value: skin

tag: disease

tag: age

tag: Sex

value: M

tag: oncologic diagnosis

value: MGUS

tag: transplant type

value: sex-mm, HLA-m

value: no

value: back

value: dermal sclerosis

value: joint, liver, ocular, oral

value: pred, ECP

value: tacro

tag: degree of infiltrate

value: mild


title: UVA020

description: Normal


title: filamentous fungus deletion strain, lactose + DTT, rep2

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: Dres2 LD2

data_processing:
The analyses were performed using the Eoulsan (version 2.5) pipeline, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Trichoderma reesei QM6a genome (JGI version) using STAR (version 2.7.8a). Alignments from reads matching more than once on the reference genome were removed using htsjdk 1.118. To compute gene expression, a custom Trichoderma reesei QM6a  annotation file was used. All overlapping regions between alignments and referenced CDS were counted  using HTSeq-count 0.5.3. The sample counts were normalized using DESeq2 1.8.1. Statistical treatments and differential analyses were also performed using DESeq2 1.8.1.
Assembly: JGI Trichoderma reesei QM6a genome, 2019 version
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: gff file for custom the custom annotation of Trichoderma reesei QM6a (included in submission as Treesei_QM6a.gff.bz2)

organism: Trichoderma reesei RUT C-30

source_name: mycelia

extract_protocol:
8 mL samples were filtered and immediately frozen in liquid nitrogen. Frozen mycelia were ground by a Fastprep homogenizer for 2 x 40 sec at 6 m/s using Lysis matrix C (MP Bio) with 700 µL of RTL Buffer (Qiagen RNeasy Mini Kit) and 7 µL of β-mercaptoethanol. After removing cell debris by a QIAshredder column, RNA was extracted using the RNeasy Mini Kit and following the instructions of the manufacturer (Qiagen). The RNA concentration was measured with Qubit 2.0, and the quality of the extracted RNAs was evaluated on a Bioanalyzer (Agilent) and agarose gel electrophoresis.
Library preparation and Illumina sequencing were performed at the Ecole normale superieure genomics core facility (Paris, France). Messenger (polyA+) RNAs were purified from 1000 ng of total RNA using oligo(dT). Libraries were performed using the strand specific RNA-Seq library preparation Stranded mRNA Prep, Ligation kit (Illumina) and were multiplexed on two P2 flowcell. (Illumina). A 118 bp single-end read sequencing was performed on a NextSeq 2000 device (Illumina). A mean of 42 million  ± 4 million passing Illumina quality filter reads was obtained for each of the 16 samples

tag: strain

value: mycelia

tag: genotype

value: res-2 deletion strain

tag: treatment

value: lactose fed-batch + 10 mM DTT


title: A9

tag: tissue

value: Affected

value: Hodgkin's lymphoma

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

tag: biopsy site

value: chest

tag: clinical

tag: histopathology

value: mild inflammation, dermal sclerosis

tag: sclerotic bsa

tag: skin score

value: liver, ocular, oral

value: pred

value: tacro, mtx

value: late


title: Primary_lung_fibroblasts_control_siRNA_rep3

description: Gene expression data from primary pulmonary fibroblast  treated with Sfrp1-siRNA, biological replicate 3

source_name: Primary pulmonary fibroblast  treated with Sfrp1-siRNA, biological replicate 3

tag: cell type

value: Primary pulmonary fibroblast


title: A8

value: skin

tag: disease

tag: age

tag: Sex

value: F

value: AML

value: sex-m, HLA-m

value: no

value: shoulder/back

value: dermal sclerosis

tag: other cgvhd

value: joint, genital, lung, GI, ocular, oral

tag: current systemic therapy

value: pred, cyclo, MMF, ECP

tag: current pred dose

value: 10mg QD

tag: prior systemic therapy

value: tacro, siro

tag: time designation after sclerosis

value: early


title: Primary_lung_fibroblasts_control_siRNA_rep1

description: Gene expression data from primary pulmonary fibroblast  treated with Sfrp1-siRNA, biological replicate 1

source_name: Primary pulmonary fibroblast  treated with Sfrp1-siRNA, biological replicate 1


title: S2 cells, ChIP-seq, E(z), replicate 2

tag: cell line


title: filamentous fungus deletion strain, lactose + DTT, rep1

description: Dres2 LD1

tag: strain

value: mycelia

tag: genotype

value: res-2 deletion strain

tag: treatment

value: lactose fed-batch + 10 mM DTT


title: Primary_lung_fibroblasts_Sfrp1_siRNA_rep1

description: Gene expression data from primary pulmonary fibroblast  treated with control siRNA, biological replicate 1

source_name: Primary pulmonary fibroblast  treated with control siRNA, biological replicate 1


title: Primary_lung_fibroblasts_control_siRNA_rep2

description: Gene expression data from primary pulmonary fibroblast  treated with Sfrp1-siRNA, biological replicate 2

source_name: Primary pulmonary fibroblast  treated with Sfrp1-siRNA, biological replicate 2


title: S2 cells, ChIP-seq, E(z), replicate 1


title: filamentous fungus deletion strain, lactose, rep2

description: Dres2 LC2

value: lactose fed-batch


title: D17 cells, ChIP-seq, E(z), replicate 2


title: A7

tag: tissue

value: Affected

value: M

tag: oncologic diagnosis

value: Hodgkin's lymphoma

tag: transplant type

value: sex-mm, HLA-m

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

value: yes

tag: biopsy site

value: flank

tag: clinical

value: subcu sclerosis, possible worsening

value: mild interface vacuolization, dyskeratosis, dermal sclerosis

value: joint, lung, liver, ocular, oral

value: MMF

value: pred, ECP

value: late

tag: degree of infiltrate

value: mild


title: UVA018

description: Normal

source_name: Normal coronary artery, LAD segment

value: coronary artery


title: filamentous fungus deletion strain, lactose, rep1

description: Dres2 LC1

tag: cell type

value: mycelia

value: res-2 deletion strain


title: A6

value: skin

tag: disease

tag: age

tag: Sex

value: AML

value: sex-m, MUD

value: subcu sclerosis

tag: histopathology

value: dermal and subcu sclerosis

tag: sclerotic bsa

tag: skin score

tag: other cgvhd

value: joint, lung

tag: current systemic therapy

value: pred, siro

tag: current pred dose

value: 40mg QOD

value: MMF, tacro, hcq, imatinib, mtx


title: D17 cells, ChIP-seq, E(z), replicate 1

tag: cell line


title: UVA017

description: Normal

source_name: Normal coronary artery, RCA segment

tag: tissue


title: filamentous fungus deletion strain, glucose + DTT, rep2

description: Dres2 GD2

tag: strain

tag: genotype

tag: treatment

value: glucose fed-batch + 10 mM DTT


title: U8

value: Unaffected

value: M

tag: oncologic diagnosis

value: sickle cell

tag: transplant type

value: sex-m, HLA-m

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

value: yes

tag: biopsy site

value: back

tag: clinical

value: unaffected

value: normal

value: lung, GI, ocular, oral

tag: prior systemic therapy

value: tacro, cyclo, MMF, pred

tag: time designation after sclerosis


title: UVA016

description: Normal

value: coronary artery


title: filamentous fungus deletion strain, glucose + DTT, rep1

description: Dres2 GD1

tag: cell type

value: mycelia

value: res-2 deletion strain


title: U7

value: skin

tag: disease

tag: age

tag: Sex

value: CML

value: sex-mm, HLA-m

value: abdomen

tag: histopathology

tag: sclerotic bsa

tag: skin score

tag: other cgvhd

value: lung, oral

tag: current systemic therapy

value: pred, tacro, ECP

value: 30mg QD

value: cyclo, MMF

tag: degree of infiltrate


title: D17 cells, ChIP-seq, En, replicate 2

tag: cell line


title: UVA015

description: Normal

tag: tissue


title: D17 cells, ChIP-seq, En, replicate 1


title: A2

value: Affected

value: F

tag: oncologic diagnosis

value: MDS/AML

tag: transplant type

value: MUD

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

value: no

value: dermal/subcu sclerosis, worsening

value: moderate inflammation, rare dyskeratosis, dermal/subcu sclerosis

value: joint, genital, lung, liver, ocular, oral

tag: current pred dose

value: pred

value: early

value: moderate


title: D17 cells, ATAC-seq, replicate 2

extract_protocol:
ATAC-Seq and library preparation was performed using the Active Motif ATAC-seq kit (#53150) following the manufacturer’s directions.
Libraries were made using either the Thruplex DNA-seq and dual index kits (Takara), or the NEBNext UltraTM II DNA library preparation kit and dual index kits (New England Biolabs). Libraries were made according to the manufacturer’s directions.


title: UVA014

description: Normal

value: coronary artery


title: filamentous fungus deletion strain, glucose, rep2

description: Dres2 GC2

tag: strain

tag: cell type

value: mycelia

tag: genotype

value: res-2 deletion strain

tag: treatment

value: glucose fed-batch


title: UVA012

description: Explant


title: UVA010

description: Explant


title: filamentous fungus reference strain, lactose + DTT, rep2

description: Rut LD2

value: reference

value: lactose fed-batch + 10 mM DTT


title: A17

value: skin

tag: disease

value: Affected

tag: age

tag: Sex

value: ALL

value: sex-mm, HLA-m

value: yes

tag: biopsy site

value: thigh

tag: clinical

value: sclerosis with scale, possibly recent

tag: histopathology

value: mild interface vacuolization, rare dyskeratosis, dermal/subcu sclerosis

tag: sclerotic bsa

value: joint, lung, GI, ocular, oral

value: pred, tacro

value: 10mg QD

tag: prior systemic therapy

value: ECP

tag: time designation after sclerosis

value: mild


title: U6

tag: tissue

value: Unaffected

value: M

tag: oncologic diagnosis

value: mantle cell lymphoma

tag: transplant type

value: sex-m, HLA-m

tag: time since transplant

value: no

value: arm

value: unaffected

value: normal

tag: skin score

tag: other cgvhd

tag: current systemic therapy

value: pred, cyclo, siro

tag: degree of infiltrate


title: UVA019

description: Explant

value: coronary artery


title: D17 cells, ATAC-seq, replicate 1

tag: cell line


title: TR5 [pituitary]

city: Hefei

first: Yanfeng

last: Xue

state: Anhui

address: Changjiang Western Road 130

country: China

institute: Anhui Agricultural University

description: Hu sheep

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oar_v4.0 whole genome.
Fragment per kilobase of exon model per million mapped reads (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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.
Assembly: Oar_v4.0
Supplementary files format and content: Excel files include FPKM values for each Sample.

organism: Ovis aries

source_name: Pituitary

growth_protocol: Ewes at 115 days of gestation.

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Restricted feeding.

value: Pituitary

tag: genotype

value: WT

tag: condition

value: Pregnant (late gestation)

tag: treatment

value: Restricted feeding


title: filamentous fungus reference strain, lactose, rep2

description: Rut LC2

tag: strain

tag: cell type

value: mycelia

value: reference

value: lactose fed-batch


title: TR4 [pituitary]

description: Hu sheep


title: UVA009

description: Explant

source_name: Explant coronary artery, LCX segment


title: TR3 [pituitary]

description: Hu sheep


title: U5

value: skin

tag: disease

value: Unaffected

tag: age

tag: Sex

value: non-Hodgkin lymphoma

value: sex-mm, partial HLA

tag: time since sclerosis

tag: acute skin gvhd

value: unk

tag: biopsy site

value: flank

tag: clinical

tag: histopathology

tag: sclerotic bsa

tag: current pred dose


title: filamentous fungus reference strain, lactose + DTT, rep1

description: Rut LD1

value: lactose fed-batch + 10 mM DTT


title: U4

tag: tissue

value: M

tag: oncologic diagnosis

value: MDS

tag: transplant type

value: sex-mm, HLA-m

tag: time since transplant

value: yes

value: arm

value: unaffected

value: normal

tag: skin score

tag: other cgvhd

value: ocular, oral, renal

tag: current systemic therapy

value: pred, ECP

value: 10mg QD

tag: prior systemic therapy

value: MMF, ritux, IVIG

tag: time designation after sclerosis

tag: degree of infiltrate


title: A1

value: skin

tag: disease

value: Affected

tag: age

tag: Sex

value: F

value: myelofibrosis

value: sex-m, HLA-m

tag: time since sclerosis

value: no

value: subcu sclerosis, stable

value: mild inflammation, rare dyskeratosis, dermal/subcu sclerosis

value: joint, genital, lung, liver, ocular, oral

value: pred, tacro, siro, etan, ECP

value: 40mg QOD

value: MMF, ritux

value: late

value: mild


title: UVA007

description: Explant

value: coronary artery


title: TR2 [pituitary]

description: Hu sheep

value: Pituitary

tag: genotype

value: WT

tag: condition

value: Pregnant (late gestation)

tag: treatment

value: Restricted feeding


title: UVA008

description: Explant

source_name: Explant coronary artery, RCA segment

tag: tissue


title: TR1 [pituitary]

description: Hu sheep


title: filamentous fungus deletion strain, glucose, rep1

description: Dres2 GC1

tag: strain

tag: cell type

value: mycelia

value: res-2 deletion strain

value: glucose fed-batch


title: filamentous fungus reference strain, glucose + DTT, rep1

description: Rut GD1

value: reference

value: glucose fed-batch + 10 mM DTT


title: filamentous fungus reference strain, glucose + DTT, rep2

description: Rut GD2


title: CON5 [pituitary]

description: Hu sheep

value: Normal feeding


title: UVA005

description: Explant


title: U3

source_name: skin

value: skin

value: Unaffected

value: F

tag: oncologic diagnosis

value: peripheral T cell lymphoma

tag: transplant type

value: partial MUD

tag: time since transplant

tag: acute skin gvhd

value: yes

tag: biopsy site

value: abdomen

tag: clinical

value: unaffected

tag: histopathology

value: normal

tag: sclerotic bsa

value: pred

tag: current pred dose

value: 5mg TIW

value: tacro, MMF


title: filamentous fungus reference strain, glucose, rep2

description: Rut GC2

value: mycelia


title: CON4 [pituitary]

description: Hu sheep

value: Pituitary

value: WT

value: Pregnant (late gestation)


title: A4

tag: disease

value: Affected

tag: age

tag: Sex

value: M

value: MDS/AML

value: sex-mm, HLA-m

value: no

value: arm

value: dermal sclerosis, possible softening

value: moderate inflammation, dermal and subcu sclerosis

tag: skin score

tag: other cgvhd

value: joint, ocular

tag: current systemic therapy

value: pred, siro, ECP

value: 10mg QOD

tag: prior systemic therapy

value: tacro, phototherapy, etan, cytoxan, mtx

tag: time designation after sclerosis

value: early

tag: degree of infiltrate

value: moderate


title: filamentous fungus reference strain, glucose, rep1

description: Rut GC1

tag: strain

tag: cell type

value: mycelia

tag: genotype

value: reference

tag: treatment

value: glucose fed-batch


title: A3

tag: tissue

value: skin

value: Affected

tag: oncologic diagnosis

value: systemic mastocytosis/MDS

tag: transplant type

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

tag: biopsy site

value: abdomen

tag: clinical

value: mild inflammation, rare dyskeratosis, dermal/subcu sclerosis

value: joint, lung, liver, GI, ocular, oral

value: pred

value: ECP, ritux, tacro, UVA-1

value: late

value: mild


title: CON3 [pituitary]

description: Hu sheep

value: Pituitary

value: WT

tag: condition

value: Pregnant (late gestation)

value: Normal feeding


title: filamentous fungus reference strain, lactose, rep1

description: Rut LC1

value: mycelia

value: lactose fed-batch


title: U2

tag: disease

value: Unaffected

tag: age

tag: Sex

value: F

value: myelofibrosis

value: sex-m, HLA-m

value: yes

value: unaffected

tag: histopathology

value: normal

tag: sclerotic bsa

tag: skin score

tag: other cgvhd

value: joint, genital, lung, ocular, oral

tag: current systemic therapy

tag: current pred dose

value: tacro


title: UVA001

description: Explant

tag: tissue

value: coronary artery


title: A5

value: skin

value: Affected

value: M

tag: oncologic diagnosis

value: CLL

tag: transplant type

value: sex-mm, HLA-m

value: no

value: flank

value: dermal sclerosis, worsening

value: mild interface vacuolization, dyskeratosis, dermal sclerosis

value: joint, liver, ocular, oral

value: pred, ECP

value: 20mg QOD

tag: prior systemic therapy

value: cyclo, MMF, aza

tag: time designation after sclerosis

value: late

tag: degree of infiltrate

value: mild


title: U1

value: Unaffected

value: AML

value: sex-m, MUD

tag: time since transplant

tag: time since sclerosis

tag: acute skin gvhd

value: yes

tag: biopsy site

value: upper arm

tag: clinical

value: unaffected

value: normal

value: lung, liver, ocular, oral

value: pred

value: 10mg QD

value: mtx, tacro, ATG, siro, MMF


title: NL_M4_Crx

status: Public on Nov 13 2023

city: Los Angeles

first: Yuichiro

last: Itoh

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV. De-multiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic (Bolger et al., 2014) was used for cleaning.
R package “QuasR” (Gaidatzis et al., 2015) was used for the read alignment to the mouse genome (mm10) followed by counting at the gene level.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts

source_name: cortex

extract_protocol:
RNAs were isolated using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: cortex

tag: cell type

value: neuron

tag: Sex

value: Male

tag: disease

value: Normal


title: UVA006

description: Explant

source_name: Explant coronary artery, LAD/RCA segment

extract_protocol:
Frozen tissue samples were pulverized using a mortar & pestle on dry ice, processed in Qiazol in a bullet blender using RINO tubes, then RNA was isolated using the Qiagen miRNeasy mini RNA extraction kit
RNA seq libraries were prepared using manufacturer's instructions for the  Illumina TruSeq Stranded Total RNA Gold kit and barcodes were added using Illumina - TruSeq RNA Unique Dual (UD) Indexes kit
Ribosomal RNA depletion

value: coronary artery


title: PCs, mRNA-derived cDNA [20210910_SK_1_669_S1]

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
cellranger demultiplex and mkfastq
cellranger gene count with Macaca_mulatta.Mmul_10.104.chr.gtf and customized library
Assembly: Macaca_mulatta.Mmul_10.104.chr.gtf
Supplementary files format and content: filtered gene count matrix in h5 generated by cellranger.

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Ex vivo differentiated B cells day 7
3’ chemistry V3.1 dual index kit protocol

value: PBMC

value: B cells

tag: library type

value: mRNA

tag: treatment

value: Ex vivo differentiated


title: PCs, mRNA-derived cDNA [20210910_SK_1_633_S2]


title: NL_M1_Crx


title: NL_M2_Crx


title: NL_F4_Crx

value: Female


title: EAE_M4_Crx

value: EAE


title: UVA004

description: Explant

data_processing:
Raw reads were demultiplexed using bcl2fastq script
Read quality was assessed using FastQC v0.11.9
adapter sequences were trimmed using Trim Galore v0.6.5
Reads with Phred scores <20 were removed
Trimmed reads were mapped to the hg38 human reference genome using STAR v2.7.3a
PCR duplicates were marked using Picard and WASP was used to filter reads prone to mapping bias
Total read counts and RPKM were calculated with RNA-SeQC v1.1.8  with additional flags “-n 1000 -noDoC -strictMode” and GENCODE v32 reference annotation
Transcript and isoform expression levels were estimated using RSEM v1.3.3
we used verifyBamID97 to check whether the reads were contaminated or sample swaps occurred and cross-checked four swaps with NGSCheckMate
Assembly: hg38
Supplementary files format and content: tab-delimited files include TPM values for each individual (column) for each gene (row)


title: NL_F1_Crx


title: EAE_M1_Crx


title: EAE_M5_Crx


title: NL_F2_Crx


title: EAE_M2_Crx


title: EAE_F3_Crx


title: EAE_M3_Crx


title: UVA002

description: Explant


title: EAE_F1_Crx


title: EAE_F4_Crx


title: CON1 [pituitary]

description: Hu sheep

value: Pituitary

tag: genotype

value: WT

tag: condition

value: Pregnant (late gestation)

value: Normal feeding


title: CON2 [pituitary]

description: Hu sheep

tag: tissue


title: NL_M3_Crx


title: RNA-Force2

city: Beijing

first: Yikun

last: Zhou

state: China

address: 22# South Zhongguancun Ave

institute: Peking University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: tab-delimited tey riles include RPKM values for each Sample

source_name: jaw bone

growth_protocol: Mesenchymal cells were maintained in A-MEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% Co2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: jaw bone

tag: cell line

value: mesechymal stem cells

value: stem cells

value: mechanical stimuli


title: RNA-Force1


title: RNA-Control3

value: normal culuture


title: RNA-Force3


title: RNA-Control2


title: NL_F3_Crx

value: cortex

value: neuron

value: Normal


title: colon lamina propria, T cells, vehicle, biol rep 5

city: Aurora

first: Kristine

middle: A

last: Kuhn

state: Colorado

address: 1775 Aurora Ct. Mail Stop B115

department: Medicine

institute: University of Colorado School of Medicine

description: CD3+ indole DESeq

data_processing:
RNA-Sequencing workflow was implemented through the Bioconductor differential expression pipeline
Salmon was used for transcript quantification with GC bias correction, using a human transcript reference index from GENCODE (release 38) and no decoy sequences.
Tximeta was used for importing transcripts which were then analyzed for differential expression with DESeq2
Assembly: GENCODE (release 38)
Supplementary files format and content: .sf files
Supplementary files format and content: DESeq

source_name: colon lamina propria

extract_protocol:
Total RNA was extracted using an RNeasy kit (Qiagen) according to the manufacturer’s protocol.
Libraries were constructed as previously described using the Next Ultra II directional RNA library prep kit with rRNA depletion.

treatment_protocol:
Cryopreserved LPMCs were thawed with DNase and stimulated at 37C with 1mM indole or vehicle for 4 hours.
After 4hr stim, cells were flow sorted as live CD45+CD19+CD3- B cells and live CD45+CD19-CD3+ T cells on a FACSAriaIII cell sorter.

value: colon lamina propria

value: CD3+ T cells

value: vehicle 4hr


title: colon lamina propria, T cells, indole, biol rep 5

description: CD3+ indole DESeq

value: indole 4hr


title: RNA-Control1


title: colon lamina propria, B cells, vehicle, biol rep 5

description: CD19+ indole DESeq

value: CD19+ B cells


title: colon lamina propria, T cells, vehicle, biol rep 4

description: CD3+ indole DESeq


title: colon lamina propria, B cells, indole, biol rep 5

description: CD19+ indole DESeq


title: EAE_F5_Crx

value: Female

value: EAE


title: colon lamina propria, T cells, indole, biol rep 4

description: CD3+ indole DESeq


title: colon lamina propria, T cells, vehicle, biol rep 3

description: CD3+ indole DESeq


title: colon lamina propria, T cells, vehicle, biol rep 2

description: CD3+ indole DESeq


title: colon lamina propria, B cells, indole, biol rep 3

description: CD19+ indole DESeq


title: colon lamina propria, B cells, vehicle, biol rep 3

description: CD19+ indole DESeq


title: colon lamina propria, B cells, vehicle, biol rep 2

description: CD19+ indole DESeq


title: colon lamina propria, T cells, indole, biol rep 2

description: CD3+ indole DESeq


title: colon lamina propria, T cells, vehicle, biol rep 1

description: CD3+ indole DESeq


title: colon lamina propria, B cells, indole, biol rep 2

description: CD19+ indole DESeq


title: colon lamina propria, T cells, indole, biol rep 1

description: CD3+ indole DESeq


title: colon lamina propria, B cells, vehicle, biol rep 1

description: CD19+ indole DESeq


title: colon lamina propria, B cells, indole, biol rep 1

description: CD19+ indole DESeq


title: h2az_Gen3_Line2_sib

city: Klosterneuburg

first: Daniel

last: Zilberman

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

data_processing:
Assembly: Araport 11
GFF files containing C/T counts for cytosines in the CG context

organism: Arabidopsis thaliana

source_name: leaf tissue

extract_protocol:
Genomic DNA (gDNA) was extracted from 1-month-old Arabidopsis thaliana rosette leaves with the DNeasy plant mini kit (Qiagen, cat. no. 69104) per the manufacturer’s instructions.
Libraries were produced with the Ultra II DNA Library prep kit according to manufacturer’s instructions (New England Biolabs, cat. no. E7645L). Bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Zymo, EZ DNA Methylation Lightning Kit, cat. no. D5046). DNA was converted twice to ensure complete bisulfite conversion of unmethylated cytosine.

value: leaf tissue

tag: generation

tag: lineage


title: GFP-(GR)50_1

city: Chicago

first: Evangelos

last: Kiskinis

state: IL

address: 233 E Erie St #500

institute: Northwestern University

description: CLIP-Seq -- Huppertz et. al. (Methods. 2014 Feb; 65(3): 274–287. doi: 10.1016/j.ymeth.2013.10.011)

data_processing:
Basecalling and quality scores were generated with the MiSeq Real Time Analysis (RTA) software.
Barcoded sequencing libraries were demultiplexed allowing 1 nt barcode mismatch, and adapter sequences and low-quality bases were filtered using iCount (version 2.0)
Trimmed, single-end reads were aligned to the hg38 genome (Gencode V32) using Novoalign (version 4.03.03). Parameters for alignment included: score threshold (-t) set to 15,3, the minimum number of bases for alignment (-l) set to 20, the gap penalty (-x) set to 4, gap opening penalty (-g) set to 20, trimming step size (-s) set to 1, score difference (-R) set to 0 and multimapping reporting (-R) set to ALL.
Samples were deduplicated using UMI-tools (version 1.1.2) with multi-mapping detection.
To determine the location of CLIP peaks, overlapping reads were collapsed to create a list of genomic regions using bedtools (version 2.30.0). Peaks found within 50 nt of one another were combined to a single feature. Reads associated with CLIP peaks were counted using FeatureCounts (version 2.0.2) with the following parameters: the minimum number of overlapping bases in a read required for assignment as 1, and strand specific read counting was performed. Analysis was performed without multi-mapped reads (unique reads only) and with multi-mapped reads included (unique + multi-mapped reads). Multi-mapped reads were assigned a fractional count of 1/x, where x is the total number of alignments reported for the same read. CLIP peaks with > 5 unique + fractional multi-mapped reads were annotated with overlapping genomic features. Protein coding and ncRNA features were identified from the Gencode hg38 V32 while ncRNA and repeat regions were identified from hg38/GRCh38 Repeatmasker annotations and rRNA annotations were identified from RefSeq GRCh38.p13 (GCF_000001405.39).
Genome_build: hg38
Supplementary_files_format_and_content: .txt tables were generated indicating the number of unique and unique + fractional multimapping reads present at sites containing > 5 unique + fractional multimapping reads. These sites were then annotated.

growth_protocol: HEK-293 cells were grown to 70% confluence under standard growth conditions in high glucose DMEM + 10% FBS.

extract_protocol:
Cells were crosslinked with 100 mJ/cm2 UVC (254 nm). Cells were lysed in 50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS with EDTA-free complete mini protease inhibitor cocktail and 1 mM phenylmethylsulfonyl fluoride. Lysates were incubated with 4 U/ml Turbo DNase and 0.04 (library1) or 0.02 (library2) units/ml of RNase I. Immunoprecipitation was performed by incubating the lysates with GFP-Trap Magnetic beads for 1.5 hours at 4°C. 3’ linker ligation was performed on beads overnight at 16°C. After labeling with [γ-32P]-ATP, RNPs were resolved on NuPAGE 4-12% Bis-Tris gels. After gel fractionation, RNPs were transferred to nitrocellulose and labeled complexes visualized using a storage phosphor screen. RNA-protein complexes of the expected size were excised from the nitrocellulose membranes, along with the same size region from GFP, GFP-(GP)10, or untransfected control experiments. Associated proteins were removed by digesting with proteinase K and the associated RNA was extracted with phenol chloroform.
Extracted 3' linker ligated RNA was used as input for reverse transcription performed using Superscript III. RT primers used were as described in Huppertz et. al. (Methods. 2014 Feb; 65(3): 274–287. doi: 10.1016/j.ymeth.2013.10.011) library 1 GPF - Rt1clip, GFP-(GR)50 - Rt6clip; library 2 untransfected - Rt1clip, GFP-(GP)10 - Rt6clip, GFP-(GR)50 - Rt9clip. cDNA was size selected and circularized with Circligase II. Circularized cDNA was cut with BamHI and amplified using Accuprime Supermix I. The PCR cycle number was optimized to prevent over amplification of the library. Amplified samples were sequenced on the Illumina MiSeq platform in single end read mode with 110 nt reads.

treatment_protocol: Cells were transfected with GFP, GFP-(GR)50 or GFP-(GP)10 using lipofectamine 3000.

tag: transfection

tag: ip

value: anti-GFP using GFP-Trap Magnetic beads (Chromotek cat:gtd-10)

tag: molecule subtype

value: CLIP-Seq RNA


title: untransfected

value: untransfected


title: GFP-(GP)10


title: GFP

value: GFP


title: GFP-(GR)50_2


title: h2az_Gen3_Line1_sib


title: h2az_Gen3_Line2


title: h2az_Gen2_Line2_sib


title: colon lamina propria, B cells, vehicle, biol rep 4

description: CD19+ indole DESeq


title: h2az_Gen2_Line1_sib


title: h2az_Gen2_Line2


title: h2az_Gen1_Line2


title: colon lamina propria, T cells, indole, biol rep 3

description: CD3+ indole DESeq


title: h2az_Gen2_Line1


title: h2az_Gen0_rep2


title: h2az_Gen1_Line1


title: colon lamina propria, B cells, indole, biol rep 4

description: CD19+ indole DESeq


title: ros1_Gen3_Line1_sib


title: ros1_Gen3_Line1


title: ros1_Gen2_Line2_sib


title: h2az_Gen0_rep1


title: ros1_Gen3_Line2


title: ros1_Gen2_Line1