title: Mouse mPFC, LTG-2_biol rep 2

city: Hannover

first: Maximilian

last: Lenz

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

data_processing:
Data analysis was performed at the Galaxy platform (usegalaxy.eu; (Galaxy, 2022)). All files contained more than 10 M high-quality reads (after mapping to the reference genomes) with a phred quality of at least 30 (>90% of total reads).
RNA sequencing data were uploaded to the galaxy web platform (public server: usegalaxy.eu; Afgan et al., 2018; Jalili et al., 2020; Afgan et al., 2016) and transcriptome analysis was performed using the Galaxy platform in accordance with the reference-based RNA-seq data analysis tutorial (Batut et al., 2021).
Adapter sequences, low quality, and short reads were removed via the CUTADAPT tool.
Reads were mapped using RNA STAR with the mm10 (Mus musculus) or the hg38 (Human) reference genome.
The evidence-based annotation of the mouse genome (GRCm38), version M25 (Ensembl 100) or the human genome (GRCh38), version 40 (Ensembl 106) served as gene model (GENCODE). For an initial assessment of gene expression, unstranded FEATURECOUNT analysis was performed from RNA STAR output.
Assembly: mm10
Supplementary files format and content: RNA STAR output (mapped BAM-files)
Supplementary files format and content: FEATURE COUNT output (tabular files)

source_name: Brain, adult, medial prefrontal cortex

extract_protocol:
For experiments in organotypic tissue cultures, 5-6 cultures of the same mouse were collected and used per sample. For in vivo experiments, the mPFC of treated and untreated adult mice was dissected and the mPFC of the left hemisphere was used as one sample. In experiments with human material, the tissue of each patient was seen as one biological sample. RNA was isolated using the Monarch® Total RNA Miniprep Kit (#T2010S; New England Biolabs) according to the manufacturer's instructions. RNA quantity and quality were assessed using an Agilent RNA 6000 Pico Kit (#5067-1513; Agilent) with a 2100 Bioanalyzer (#G2939BA; Agilent). After RNA isolation from TTX-treated tissue cultures, library preparation and RNA sequencing was performed using the genome sequencer Illumina HiSeq technology in NovaSeq 6000 S4 PE150 XP sequencing mode (service provided by Eurofins). After RNA isolation from the mPFC of mouse in vivo experiments and human neocortical samples, poly(A)- selection was performed using a poly(A)-selection mRNA magnetic isolation module (#E7490; New England Biolabs) according to the manufacturer’s instructions. For non-directional library preparation, NEBNext Ultra II RNA Library Preparation Kit for Illumina (#E7770; New England Biolabs) was used.
After fragmentation and adaptor ligation, dual index primers (New England Biolabs, #E7600S) were ligated in a library amplification step using 10 PCR cycles. Libraries were finally cleaned up with 0.8X SPRI beads following a standard bead purification protocol. Library purity and size distribution were assessed with a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). We quantified the libraries using the NEBNext Library Quant Kit for Illumina (New England Biolabs, #E7630) based on the mean insert size provided by the Bioanalyzer. A 10 nM sequencing pool (120 µl in Tris-HCl, pH 8.5) was generated for sequencing on the NovaSeq6000 sequencing platform (Illumina; service provided by CeGaT GmbH, Tübingen, Germany). We performed a paired-end sequencing with 100 bp or 150 bp read length.

value: Brain, adult, medial prefrontal cortex

value: Lamotrigine (LTG, 20 mg/kg, daily i.p. injections) treatment for 2 days


title: Benign Breast Disease Biopsy Fresh Frozen [sample64_FFzn_Exome]

status: Public on Sep 29 2023

type: SRA

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

country: USA

institute: Mayo Clinic

description: Benign Breast Disease Biopsy

library_source: transcriptomic

data_processing:
Paired-end sequencing reads were mapped to reference genome hg38 using STAR aligner
Gene and exon counts were generated using FeatureCounts using gene definition files from Ensembl v78
Quality control was carried out using RSeQC
Gene counts were normalized to counts per million (CPM) and transcript per million (TPM) using TMM method as implemented in edgeR.
Assembly: hg38
Supplementary files format and content: count_table.tsv : Gene count table

molecule: total RNA

organism: Homo sapiens

source_name: Breast

extract_protocol:
RNA was extracted from FFPE biopsy benign breast disease tissue
40–100ng of experimental FFPE RNA, FFPE control RNA, or 20ng fresh frozen control RNA was used for library preparation using the TruSeq RNA Library Prep for Enrichment and the Illumina Exome Panel-Enrichment Oligos kit. Additionally, 20–100 ng of FFPE RNA and paired fresh frozen RNA was used for library preparation using the NEBNext rRNA Depletion Kit

tag: tissue

value: Breast

tag: cell type

value: Biopsy

tag: genotype

value: Benign Breast Disease


title: RV-Failing_9

city: Bad Nauheim

first: Fatemeh

last: Khassafi

address: Parkstrasse

country: Germany

institute: Max Planck Institute

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_9

data_processing:
Raw fastqs were assessed for quality, adapter content, and duplication rates using FastQC. Trimmomatic version 0.39 was employed to trim reads following a quality drop (below a mean of Q15) in a window of five nucleotides
STAR mapping-b1: --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair --outFilterMultimapNmax 1 --genomeDir GRCh38/indices/star_GRCh38_gencode.v27
STAR mapping-b2: mode: single-end, keep duplicates: no, keep multi-mapping: no, keep ribosomal: no, keep mitochondria: no --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair --outMultimapperOrder Random --limitOutSAMoneReadBytes 10000000 --outFilterMultimapNmax 1 --genomeDir GRCh38/indices/star_GRCh38_gencode.v27
The number of reads that aligned to genes was counted using featureCounts version 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were aggregated and counted per gene. Reads aligning to multiple regions or genes were excluded. -t exon -g gene_id -s 2; multi-mapping: no; duplicates: no
Raw count values for each organism were normalized separately using DESeq2 version 1.30.0, then transformed into regularized logarithm values for further analysis. Because we had two different batches of human samples, we performed a batch effect correction on this data using the sva package. The normalized and batch-corrected data were the basis of downstream analysis.
Assembly: hg38; (GRCh38.27)
Supplementary files format and content: excel file containing sheet 1: sample labels and mapping parameters
Supplementary files format and content: excel file containing sheet 2: matrix of raw read counts for genes*samples

source_name: Right ventricle

extract_protocol:
Human RV tissues were manually dissected in cardiac biopsy or autopsy, according to the previously described protocol ( doi: 10.1161/CIRCULATIONAHA.120.047626 ), and Total RNA from each batch of RV samples were isolated separately using the RNeasy Mini Kit (Qiagen, Germantown, MA, USA) and snap-frozen. Purification of total RNA was performed as described in the RNeasy handbook, using DNase I digestion (RNase-Free DNase Set, Qiagen).
Following the RNA integrity measurement, approximately 10 ng of total RNA were used as starting material for library preparation using the SMARTer® Stranded Total RNA-seq Kit - Pico Input Mammalian, following manufacturers’ protocols

value: Right ventricle

tag: Sex

value: M

tag: primary disease_characterization

value: Decompensated RV

tag: secondary group_characterization

value: Decompensated-1 RV


title: Mouse mPFC, LTG-1_biol rep 1

department: Institute of Neuroanatomy and Cell Biology

molecule: polyA RNA

organism: Mus musculus

tag: treatment


title: RV-Failing_6

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_6

value: F

value: Compensated-2 RV


title: CRC_69T

city: Wuhan

first: Bin

last: Li

address: Donghu Road 115

country: China

institute: Department of Epidemiology and Biostatistics, School of Public Health; Wuhan University

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low-quality reads from raw data.
Trimmed reads were aligned against human transcriptome using the Genome Reference Consortium human reference 38 assembly (GRCh38/hg38) with Hisat (v2.0.5) software using Ensemble release annotations,
Assembly: hg38
Supplementary files format and content: Gene and transcript expression were quantified using FPKM.

source_name: colorectal cancer

extract_protocol:
154 CRC tissues removed tumors or biopsy specimens, flash freozen by dry ice, and RNA was harvested using TRIzol (Invitrogen, USA)
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). For library preparation, the Illumina RNA Library Prep kit (NEBNext® UltraTM) was used. The libraries were tagged with unique adapter indexes. Final libraries were validated on the Agilent 2100 Bioanalyzer, quantified via qRT-PCR, pooled at equimolar ratios, diluted, denatured, and loaded onto an Illumina novaseq 6000.

value: colorectal cancer

tag: gender

value: Male

tag: age

tag: diagnosis

value: Colon cancer

tag: tnm stage


title: Mouse mPFC, LTG-3_biol rep 3


title: CRC_70T

value: Female

value: Rectal cancer


title: Benign Breast Disease Biopsy FFPE [sample64_FFPE_Exome]

description: Benign Breast Disease Biopsy


title: Mouse mPFC, CONTROL-4_biol rep 4

value: vehicle-only (corn oil with 5% DMSO; daily i.p. injections) treatment for 2 days


title: CRC_67T


title: P3_5_Bmal

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie version 1.2.2 with parameters -p 30 -m 1 -S -q
peaks were called using MACS2 version 2.2.7.1 with parameters callpeak -g mm -B --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.2.7.1, reprsenting fold enrichment for each sites

molecule: genomic DNA

source_name: MOUSE FIBROBLAST

growth_protocol: MAF was cultured under 5% CO2,20% O2,37 ℃ with DMEM (10% FBS, 1% PS)

extract_protocol:
Unsynchronized and confluent pika/rat Epas1 knock-in MAF cells in 15 cm dishes were treated with 1 mM DMOG for 16 h. After treatment, cells were cross-linked in DMEM containing 1 mM DMOG, PMSF, and 1% formaldehyde for 12 min at room temperature. The cross-link was stopped by adding glycine to a final concentration of 125 mM and incubated at room temperature for 5 min. ChIP assay and DNA sample preparation were performed strictly following the ChIP-IT High Sensitivity Kit instructions (Active Motif). Eluted DNA was analyzed with quantitative PCR and high-throughput sequencing.
Libraries were prepared according to Illumina's instructions

treatment_protocol: After growing to 60% confluency, cells were changed fresh culture medium with 1mM DMOG. After 12h, cells were harvested.

tag: chip-grade antibody

value: Abcam (Cat #ab3350)

tag: 2nd antibody

value: anti-rabbit IgG

value: 12h 1 mM DMOG treatment


title: Benign Breast Disease Biopsy Fresh Frozen [sample64_FFzn_Depletion]

description: Benign Breast Disease Biopsy

value: Breast

value: Biopsy


title: RV-Failing_7

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_7

value: Right ventricle


title: CRC_68T


title: Mouse mPFC, CONTROL-3_biol rep 3

value: Brain, adult, medial prefrontal cortex


title: Benign Breast Disease Biopsy FFPE [sample64_FFPE_Depletion]

description: Benign Breast Disease Biopsy

value: Benign Breast Disease


title: CRC_66T


title: RV-Failing_2

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_2

value: M

value: Decompensated RV


title: Mouse mPFC, CONTROL-2_biol rep 2


title: Benign Breast Disease Biopsy Fresh Frozen [sample63_FFzn_Exome]

description: Benign Breast Disease Biopsy


title: CRC_65T


title: CRC_64T


title: RV-Failing_5

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_5

value: Compensated RV

value: Compensated-2 RV


title: Benign Breast Disease Biopsy Fresh Frozen [sample63_FFzn_Depletion]

description: Benign Breast Disease Biopsy


title: RV-Compen_3

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_3

value: Compensated-1 RV


title: CRC_63T

value: colorectal cancer

value: Male

value: Colon cancer


title: Benign Breast Disease Biopsy FFPE [sample63_FFPE_Exome]

description: Benign Breast Disease Biopsy


title: RV-Failing_4

description:
processed-data-human.xlsx
count matrix column name: RV-Failing_4

value: F


title: Mouse OTC, TTX-3, biol rep 3

source_name: Brain, organotypic entorhino-hippocampal culture

value: TTX (tetrodotoxin, 2 uM) treatment for 2 days


title: RV-Compen_5

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_5


title: Benign Breast Disease Biopsy FFPE [sample63_FFPE_Depletion]

description: Benign Breast Disease Biopsy


title: RV-Compen_6

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_6


title: Benign Breast Disease Biopsy FFPE [sample61]

description: Benign Breast Disease Biopsy


title: CRC_62T

value: Female


title: Benign Breast Disease Biopsy FFPE [sample62]

description: Benign Breast Disease Biopsy


title: RV-Compen_10

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_10


title: Mouse OTC, TTX-2, biol rep 2

value: Brain, organotypic entorhino-hippocampal culture


title: Benign Breast Disease Biopsy FFPE [sample60]

description: Benign Breast Disease Biopsy

value: Breast


title: CRC_61T

value: Rectal cancer


title: Mouse OTC, TTX-1, biol rep 1


title: CRC_60T


title: RV-Compen_9

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_9

value: Right ventricle


title: Mouse OTC, control-4, biol rep 4

value: vehicle-only (water; 1:1000) treatment for 2 days


title: RV-Compen_4

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_4

value: Decompensated-1 RV


title: CRC_59T


title: Benign Breast Disease Biopsy FFPE [sample6]

description: Benign Breast Disease Biopsy

value: Biopsy

value: Benign Breast Disease


title: Mouse mPFC, CONTROL-1_biol rep 1

value: Brain, adult, medial prefrontal cortex

value: vehicle-only (corn oil with 5% DMSO; daily i.p. injections) treatment for 2 days


title: Mouse OTC, control-3, biol rep 3


title: Mouse OTC, TTX-4, biol rep 4


title: CRC_58T


title: RV-Compen_8

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_8

value: Compensated RV


title: Mouse OTC, control-2, biol rep 2


title: CRC_57T

value: colorectal cancer


title: RV-Compen_7

description:
processed-data-human.xlsx
count matrix column name: RV-Compen_7

value: Compensated-2 RV


title: Mouse OTC, control-1, biol rep 1


title: Benign Breast Disease Biopsy FFPE [sample59]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample58]

description: Benign Breast Disease Biopsy


title: RV-Normal_4

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_4

value: M

value: Normal RV


title: CRC_56T

value: Male

value: Colon cancer


title: WT_GroundState_3

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

data_processing:
FASTQ files generated by paired end sequencing (150 bp paired-end) were aligned to the mouse genome using bowtie2 v2.2.6 (parameters: --local --threads 3; mm9 genome build).
Mapped RNA-seq data was processed using tools from the HOMER suite (v4.8). SAM files were converted into tag directories using ‘makeTagDirectory’ (parameters: -format sam -sspe). Genomic intervals which extended beyond the end of the chromosomes was removed using ‘removeOutOfBoundsReads.pl’. bigWig browser track files were generated using ‘makeUCSCfile’ (parameters: -fsize 1e20-strand+ -norm 1e8). bigWig browser track files are included.
For gene expression analysis, read depths were quantified for all annotated refseq genes using analyzeRepeats.pl (parameters: rna mm9 -strand both -count exons -rpkm -normMatrix 1e7 -condenseGenes). For repeat analysis, read coverage was quantified for each repeat and then condensed to a single value for each named entry (parameters: repeats mm9 -strand both -rpkm -normMatrix 1e7 -condenseL1). Read depths were then corrected for the number of instances of each repeat prior to expression analysis. Raw quantitation files for genes and repeats are included.
Quantified RNA-seq data was processed using the limma package (R/Bioconductor)(Team, 2017). Following the addition of an offset value (1 RPKM) to each gene or repeat, data was normalised across all samples using 'normalizeBetweenArrays' with method='quantile'. Normalised read counts for all Refseq genes are included as a supplimentary tab-delimited files (Normalised_Gene_Expression.txt).
Assembly: mm9
Supplementary files format and content: ‘.bigWig’ files. Non-strand specific genome coverage track normalised to 100 Million reads per samples (genome build – mm9).
Supplementary files format and content: ‘ID_FPKMExon.txt’. Tab-delimited text file including read counts for each RefSeq genes (mm9). Column Names and content: Gene_ID – Refseq Gene ID, Chr – Gene Chromosome, Start – Gene Start, End – Gene End, Strand – Gene Strand, Length – Gene Length (including introns), Copies – Number of gene copies, Annotation_Divergence – Annotation Divergence (see Homer Package for details) and Expression – read depth.
Supplementary files format and content: ‘ID_Repeat_FPKM.txt’. Tab-delimited text file includes read counts for each annotated repeat (mm9). Column Names and content: Repeat_ID, Chr – Repeat Chromosome, Start – Repeat Start, End – Repeat End, Strand – Repeat Strand, Length – Repeat Length, Copies – Number of repeat copies, Annotation_Divergence – Annotation Divergence (see Homer Package for details) and Expression – read depths are corrected for the number of instances of each repeat.
Supplementary files format and content: Normalised_Gene_Expression.txt: Tab-delimited text file which includes normalised RPKM values for each RefSeq genes (mm9). Column Names and content: Gene_ID – Refseq Gene ID, Chr – Gene Chromosome, Start – Gene Start, End – Gene End, Strand – Gene Strand, Length – Gene Length (sum of exon length excluding introns), Copies – Number of gene copies, Annotation_Divergence – alternatibve gene annotations and Expression values (multiple columns containing normalised RPKM values for each sample named as per GEO sample title).

growth_protocol: ESCs grown in 2i + Vitamin C. ESCs were cultured in Neurobasal:DMEM/F-12 (50:50, Gibco) medium, supplemented with N2 and B-27 supplements (Gibco), BSA fraction V (0.05%Gibco), 1-thioglycerol (1.5x10-4M, Sigma) and ESGRO 2 inhibitors (GSK3i and MEKi) and LIF (Merck). Vitamin C (L-ascorbic acid 2-phosphate, Sigma) was added at a concentration of 100 µg/mL (Blaschke et al., 2013). Cells were grown on 0.1% gelatin-coated plates at 37°C with 5% CO2. Medium was changed daily. Cells were passed every 2 days at 1:4 ratio for the first passage then at a 1:6 ratio.

extract_protocol:
Total RNA was extracted using RNeasy extraction kit (Qiagen) according to manufacturer’s instructions including a DNAseI treatment step for 15 min at room temperature (Qiagen)
Prior to library construction, purified RNA was quantified by nanodrop and quality assessed by agarose gel electrophoresis and agilent bioanalyser 2100 (to determine RNA integrity and quantity). mRNA was enriched using oligo(dT) beads and then depleted for rRNA using the Ribo-Zero kit (Illumina; according to manufacturer’s instructions). The resulting mRNA was converted into sequencing libraries using Illumina protocols performed by Novogene. Briefly, RNA was randomly fragmented by incubation in fragmentation buffer. First strand cDNA synthesis was performed using random hexamer oligonucleotides. Second-strand synthesis was performed using second-strand synthesis buffer (Illumina) containing dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was then taken through terminal repair, A-base ligation, adaptor ligation and size selection steps prior to library amplification. PCR enrichment was performed using illumina barcoding primers and the resulting libraries were quality controlled using a Qubit 2.0, Agilent 2100 bioanalyser and quantitative-PCR.

tag: cell line

value: embryonic stem cells

value: wildtype

value: Ground State ESCs (2i +VitaminC)


title: CRC_55T


title: WT_GroundState_2


title: Benign Breast Disease Biopsy FFPE [sample57]

description: Benign Breast Disease Biopsy

value: Breast


title: Benign Breast Disease Biopsy FFPE [sample56]

description: Benign Breast Disease Biopsy


title: RV-Normal_7

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_7

value: Right ventricle

value: F


title: CRC_53T


title: CRC_54T


title: WT_GroundState_1


title: Benign Breast Disease Biopsy FFPE [sample55]

description: Benign Breast Disease Biopsy

value: Biopsy


title: Benign Breast Disease Biopsy FFPE [sample54]

description: Benign Breast Disease Biopsy

value: Benign Breast Disease


title: WT_Serum_3

growth_protocol: ESCs grown in Serum + LIF. ESCs were cultured in DMEM (Gibco) supplemented with 10% of ESC-certified FBS (Gibco), 2-mercaptoethanol (0.05mM, Gibco), Glutamax (Gibco), MEM non-essential amino acids (0.1mM, Gibco), Penn-Strep (100units/mL, Gibco) and LIF (1000units/mL). Cells were grown on 0.1% gelatin-coated plates or stem cell plates (Stem Cell technology) at 37°C with 5% CO2. Medium was changed every day and cells were passaged every 2 to 3 days.

value: ESCs (Serum+LIF)


title: RV-Normal_2

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_2


title: WT_Serum_2


title: Benign Breast Disease Biopsy FFPE [sample53]

description: Benign Breast Disease Biopsy


title: CRC_51T


title: RV-Normal_10

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_10


title: WT_Serum_1


title: RV-Normal_1

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_1


title: RV-Normal_8

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_8


title: WT_Diff_3

growth_protocol: Neural differentiation of mESCs. ESCs were maintained in Serum + LIF media as follows. ESCs were cultured in DMEM (Gibco) supplemented with 10% of ESC-certified FBS (Gibco), 2-mercaptoethanol (0.05mM, Gibco), Glutamax (Gibco), MEM non-essential amino acids (0.1mM, Gibco), Penn-Strep (100units/mL, Gibco) and LIF (1000units/mL). Cells were grown on 0.1% gelatin-coated plates or stem cell plates (Stem Cell technology) at 37°C with 5% CO2. Medium was changed every day and cells were passaged every 2 to 3 days. ESCs were differentiated by culturing them for 24 h in ESC media without LIF, then for a further four days in -LIF media supplemented with retinoic acid (10 µM).

value: neuronal differentiation (Retinoic Acid -LIF)


title: Benign Breast Disease Biopsy FFPE [sample52]

description: Benign Breast Disease Biopsy


title: CRC_50T

value: Female


title: RV-Normal_6

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_6


title: CRC_49T

value: colorectal cancer


title: Benign Breast Disease Biopsy FFPE [sample50]

description: Benign Breast Disease Biopsy


title: RV-Normal_9

description:
processed-data-human.xlsx
count matrix column name: RV-Normal_9


title: Benign Breast Disease Biopsy FFPE [sample51]

description: Benign Breast Disease Biopsy


title: CRC_48T

value: Rectal cancer


title: RV-Decompensated_5

description:
processed-data-human.xlsx
count matrix column name: Decompensated_5

value: Decompensated RV

value: Decompensated-2 RV


title: CRC_47T

value: Male


title: Benign Breast Disease Biopsy FFPE [sample5]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample49]

description: Benign Breast Disease Biopsy


title: CRC_52T


title: WT_Diff_1


title: WT_Diff_2


title: RV-Decompensated_3

description:
processed-data-human.xlsx
count matrix column name: Decompensated_3


title: Benign Breast Disease Biopsy FFPE [sample48]

description: Benign Breast Disease Biopsy


title: DaxxKO_GroundState_3

value: Daxx Knockout


title: DaxxKO_GroundState_2

value: embryonic stem cells


title: CRC_46T

value: Colon cancer


title: CRC_45T


title: DaxxKO_GroundState_1

value: Ground State ESCs (2i +VitaminC)


title: RV-Decompensated_2

description:
processed-data-human.xlsx
count matrix column name: Decompensated_2


title: CRC_44T


title: RV-Decompensated_1

description:
processed-data-human.xlsx
count matrix column name: Decompensated_1

value: Decompensated-1 RV


title: CRC_43T


title: Benign Breast Disease Biopsy FFPE [sample46]

description: Benign Breast Disease Biopsy

value: Breast


title: DaxxKO_Serum_3


title: RV-Decompensated_4

description:
processed-data-human.xlsx
count matrix column name: Decompensated_4

value: Right ventricle

value: M


title: CRC_42T


title: Benign Breast Disease Biopsy FFPE [sample45]

description: Benign Breast Disease Biopsy

value: Biopsy

value: Benign Breast Disease


title: DaxxKO_Serum_2

value: ESCs (Serum+LIF)


title: RV-Compensated_5

description:
processed-data-human.xlsx
count matrix column name: Compensated_5

value: F

value: Compensated RV


title: DaxxKO_Serum_1


title: Benign Breast Disease Biopsy FFPE [sample44]

description: Benign Breast Disease Biopsy


title: RV-Compensated_4

description:
processed-data-human.xlsx
count matrix column name: Compensated_4


title: CRC_41T

value: colorectal cancer

value: Rectal cancer


title: DaxxKO_Diff_3

value: neuronal differentiation (Retinoic Acid -LIF)


title: Benign Breast Disease Biopsy FFPE [sample43]

description: Benign Breast Disease Biopsy


title: RV-Compensated_2

description:
processed-data-human.xlsx
count matrix column name: Compensated_2


title: Benign Breast Disease Biopsy FFPE [sample42]

description: Benign Breast Disease Biopsy


title: RV-Compensated_3

description:
processed-data-human.xlsx
count matrix column name: Compensated_3


title: DaxxKO_Diff_2


title: RV-Compensated_1

description:
processed-data-human.xlsx
count matrix column name: Compensated_1


title: Benign Breast Disease Biopsy FFPE [sample47]

description: Benign Breast Disease Biopsy


title: DaxxKO_Diff_1


title: CRC_39T

value: Male


title: Benign Breast Disease Biopsy Fresh Frozen [sample65_FFzn_Exome]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample41]

description: Benign Breast Disease Biopsy


title: RV-Control_5

description:
processed-data-human.xlsx
count matrix column name: Control_5

value: Normal RV


title: CRC_38T


title: oxLDL_KO, rep2 (ApoE KO)

city: Ann Arbor

first: Yang

last: Zhao

address: 2800 Plymouth Rd

institute: University of Michigan

data_processing:
We use FastQC(FastQC)(v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore(TrimGalore)(v0.4.5) and cutadapt(Martin)(v1.15) with the following parameters: –nextera -e 0.1 –stringency 6 –length 20 –nextseq 20.
We align trimmed reads to mm10 with Bowtie2(Langmead and Salzberg, 2012)(v2.3.4.1) with the following parameters: -X 2000 –no-mixed –no-discordant, and defaults multi-seed length of 20bp with 0 mismatches.
Alignments to autosomes are kept (i.e.sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard are removed, and alignments below a MAPQ threshold are removed. These filtering steps are performed with samtools(Liet al., 2009)(v1.2) and the parameters: -q 10 -F 1024.
Reads completely overlapping blacklisted regions(ENCODE Blacklist Regions)are removed with bedtools(Quinlan and Hall, 2010)(v2.28.0).
Sample-wise peaks are called with macs2 with flags: -f BAMPE –nomodel –shift -100 –extsize 200 –gsize mm.
Assembly: mm10
Supplementary files format and content: bed(peak)

source_name: Bone marrow

extract_protocol:
Cryopreserved BMDM were sent to CD Genomics for ATAC-Seq nuclei preparation following internal QC and nuclei prep propotocl in the company.
The libraries were constructed using Nextera DNA perp kit, followed byquantitation with the Qubit 2.0 DNA HS Assay kit, and quality assessment on a TapeStation HS D1000 kit. The libraries were pooled and sent for PE-150 sequencing on a shared flowcell on the NovaSeq6000.

value: Bone marrow

value: Primary

value: BMDM

value: Baf60af/f, Lyz2 Cre+, ApoE KO

value: oxLDL(50ug/ml, 48h)


title: Benign Breast Disease Biopsy FFPE [sample40]

description: Benign Breast Disease Biopsy

value: Breast


title: oxLDL_KO, rep1 (ApoE KO)


title: CRC_37T

value: Colon cancer


title: Benign Breast Disease Biopsy FFPE [sample4]

description: Benign Breast Disease Biopsy

value: Biopsy


title: RV-Control_4

description:
processed-data-human.xlsx
count matrix column name: Control_4

value: Right ventricle


title: CRC_40T


title: RV-Control_3

description:
processed-data-human.xlsx
count matrix column name: Control_3


title: CRC_36T


title: oxLDL_WT, rep1 (ApoE KO)

value: Baf60af/f, Lyz2 Cre-, ApoE KO


title: RV-Control_2

description:
processed-data-human.xlsx
count matrix column name: Control_2

value: M


title: KO, rep2 (ApoE KO)


title: CRC_34T

value: Female


title: KO, rep1 (ApoE KO)


title: CRC_35T

value: colorectal cancer


title: RV-Control_1

description:
processed-data-human.xlsx
count matrix column name: Control_1


title: WT, rep2 (ApoE KO)


title: CRC_33T

value: Rectal cancer


title: WM989_ATAC_NGFR-High-3

city: Philadelphia

first: Sydney

middle: M.

last: Shaffer

state: PA

address: 421 Curie Blvd

department: Department of Pathology

institute: University of Pennsylvania

data_processing:
For scRNA-seq we processed the data using 10X Cell Ranger software. For ATAC seq we used alligned reads with bowtie2 v2.3.4.1, filtered out low quality read alignments using samtools v1.1, and used MACS2 2.1.1.20160309 for peak calling.
Assembly: hg38
Supplementary files format and content: Tab-separated values and matrix files.

extract_protocol:
For scRNA-seq we followed protocols from 10X genomics for cell lines. For ATAC we followed the OMNI-ATAC protocol.
For scRNA-seq library construction we followed protocols from 10X genomics. For ATAC seq we used the Illumina Tagment DNA Enzyme kit protocol.

value: melanoma

value: NGFR-High


title: WM989_ATAC_NGFR-High-2


title: WM989_ATAC_NGFR-High-1


title: Benign Breast Disease Biopsy FFPE [sample37]

description: Benign Breast Disease Biopsy

value: Benign Breast Disease


title: Benign Breast Disease Biopsy FFPE [sample38]

description: Benign Breast Disease Biopsy


title: WT, rep1 (ApoE KO)

value: Bone marrow


title: Benign Breast Disease Biopsy FFPE [sample34]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample35]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample36]

description: Benign Breast Disease Biopsy


title: CRC_30T

value: Male


title: Benign Breast Disease Biopsy FFPE [sample39]

description: Benign Breast Disease Biopsy


title: WM989_ATAC_Mix-3

value: Mix


title: oxLDL_WT, rep2 (ApoE KO)

value: Primary

value: BMDM


title: PDX-sp-3 [TCR]

city: Tarrytown

first: Gabrielle

last: Choonoo

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals, Inc

data_processing:
library strategy: TCR-seq
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq and V(D)J libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)
Assembly: GRCh38
Supplementary files format and content: Seurat R data object includes CD4 cell counts, clustering, and TCR across all samples

source_name: PDX spleen

extract_protocol:
mCD45-hCD45+hCD2+hCD4+hCD8- cells were flow sorted from cell suspensions prepared from spleens and skins of recipient mice and collected into tubes containingPBSwith 0.04%BSA.
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq and V(D)J libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)

value: Spleen

tag: strain

value: SIRPA KI Rag2-/- Il2rg-/- IL15 KO


title: WM989_ATAC_Mix-2


title: PDX-sp-3 [GEX]

data_processing:
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq and V(D)J libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)
Assembly: GRCh38
Supplementary files format and content: Seurat R data object includes CD4 cell counts, clustering, and TCR across all samples


title: Benign Breast Disease Biopsy FFPE [sample32]

description: Benign Breast Disease Biopsy

value: Breast

value: Biopsy


title: CRC_29T

value: Colon cancer


title: Benign Breast Disease Biopsy FFPE [sample31]

description: Benign Breast Disease Biopsy


title: CRC_28T


title: PDX-sp-2 [TCR]


title: CRC_32T


title: Benign Breast Disease Biopsy Fresh Frozen [sample65_FFzn_Depletion]

description: Benign Breast Disease Biopsy


title: WM989_ATAC_EGFR-NGFR-High-3

value: EGFR-NGFR-High


title: CRC_31T

value: Female


title: PDX-sp-2 [GEX]


title: WM989_ATAC_EGFR-NGFR-High-2


title: Benign Breast Disease Biopsy FFPE [sample30]

description: Benign Breast Disease Biopsy


title: CRC_26T

value: colorectal cancer


title: Benign Breast Disease Biopsy FFPE [sample3]

description: Benign Breast Disease Biopsy


title: WM989_ATAC_EGFR-NGFR-High-1


title: CRC_25T


title: CRC_24T

value: Rectal cancer


title: WM989_ATAC_EGFR_High_3

value: melanoma


title: Benign Breast Disease Biopsy FFPE [sample28]

description: Benign Breast Disease Biopsy


title: PDX-sp-1 [GEX]


title: Benign Breast Disease Biopsy FFPE [sample33]

description: Benign Breast Disease Biopsy


title: CRC_23T


title: Benign Breast Disease Biopsy FFPE [sample29]

description: Benign Breast Disease Biopsy


title: PDX-skin-4 [TCR]

source_name: PDX skin

value: Skin


title: WM989_ATAC_EGFR_High_2


title: PDX-skin-4 [GEX]


title: CRC_22T


title: WM989_ATAC_Mix-1


title: WM989_ATAC_EGFR_High_1


title: Benign Breast Disease Biopsy FFPE [sample27]

description: Benign Breast Disease Biopsy

value: Benign Breast Disease


title: CRC_27T


title: PDX-skin-3 [TCR]


title: Benign Breast Disease Biopsy FFPE [sample26]

description: Benign Breast Disease Biopsy


title: CRC_21T


title: PDX-skin-3 [GEX]


title: WM989TreatementEffect_PrimedTGFBRi_scRNAseq

description:
10x_exp3_barcodes.tsv.gz
10x_exp3_genes.tsv.gz
10x_exp3_matrix.mtx.gz
10x_exp3_metadata.tsv.gz

library_source: transcriptomic single cell

value: PrimedTGFBRi


title: Benign Breast Disease Biopsy FFPE [sample25]

description: Benign Breast Disease Biopsy


title: CRC_20T

value: Male


title: PDX-sp-1 [TCR]


title: WM989TreatementEffect_PrimedTGFB1_scRNAseq


title: PDX-skin-2 [TCR]


title: WM989TreatementEffect_PrimedPI3Ki_scRNAseq


title: PDX-skin-2 [GEX]


title: Benign Breast Disease Biopsy FFPE [sample23]

description: Benign Breast Disease Biopsy


title: CRC_19T


title: Benign Breast Disease Biopsy FFPE [sample22]

description: Benign Breast Disease Biopsy


title: CRC_17T


title: Benign Breast Disease Biopsy FFPE [sample24]

description: Benign Breast Disease Biopsy


title: WM989TreatementEffect_MixTGFBRi_scRNAseq

value: MixTGFBRi


title: Benign Breast Disease Biopsy FFPE [sample21]

description: Benign Breast Disease Biopsy


title: CRC_18T


title: WM989TreatementEffect_MixTGFB1_scRNAseq


title: CRC_16T


title: PDX-skin-1 [GEX]


title: Benign Breast Disease Biopsy FFPE [sample20]

description: Benign Breast Disease Biopsy


title: CRC_15T


title: WM989TreatementEffect_MixPI3Ki_scRNAseq


title: ATAC-Seq oxLDL_WT

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) with the following parameters: –nextera -e 0.1 –stringency 6 –length 20 –nextseq 20.
We align trimmed reads to mm10 with Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4.1) with the following parameters: -X 2000 –no-mixed –no-discordant, and defaults multi-seed length of 20bp with 0 mismatches.
Alignments to autosomes are kept (i.e. sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard are removed, and alignments below a MAPQ threshold are removed. These filtering steps are performed with samtools (Li et al., 2009) (v1.2) and the parameters: -q 10 -F 1024.
Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) are removed with bedtools (Quinlan and Hall, 2010) (v2.28.0).
Sample-wise peaks are called with macs3 with flags: -f BAM –nomodel –shift -100 –extsize 200 –gsize mm.
Assembly: mm10
Supplementary files format and content: bed(peak)

source_name: Primary

extract_protocol:
Cell suspensions were brought to the UM Epigenomics Core for ATAC-Seq library preparation. We used the Omni-ATAC-Seq protocol (Corces et al., 2017).
The final libraries were cleaned using Qiagen MinElute columns and AMPure XP beads before quantitation with the Qubit HS dsDNA kit, and quality assessment on a TapeStation HS D1000 kit. The libraries were pooled and quantitated by qPCR using KAPA’s Illumina Library quantitation kit before PE-150 sequencing on a shared flowcell on the NovaSeq6000 at the Advanced Genomics Core

value: Primary

value: oxLDL(50ug/ml, 48h)


title: Benign Breast Disease Biopsy FFPE [sample2]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample19]

description: Benign Breast Disease Biopsy


title: ATAC-Seq KO

description: KO

value: BMDM


title: CRC_13T


title: Untreated_Replicate_WM983B_scRNAseq

value: untreated


title: ATAC-Seq WT

description: WT


title: CRC_12T


title: Benign Breast Disease Biopsy FFPE [sample18]

description: Benign Breast Disease Biopsy

value: Breast


title: WM989TreatementEffect_PrimedControl_scRNAseq

value: PrimedControl


title: PDX-skin-1 [TCR]

value: SIRPA KI Rag2-/- Il2rg-/- IL15 KO


title: ChIP-Seq oxLDL_KO

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie2.
Peaks were called using MACS3 with parameters: -f BAMPE -g mm --SPMR -q 0.05.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Chromatin immunoprecipitation was performed with the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling, #9003), according to the manufacturer's recommendation. BRG1 (Abcam, ab110641, 1:100 dilution).
The DNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the DNA library was prepared with NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 150bp pair-end reads.

tag: chip antibody

value: BRG1 (Abcam, ab110641)


title: Benign Breast Disease Biopsy FFPE [sample17]

description: Benign Breast Disease Biopsy

value: Biopsy


title: ChIP-Seq oxLDL_WT


title: CRC_10T

value: colorectal cancer

value: Colon cancer


title: ATAC-Seq oxLDL_KO


title: ChIP-Seq KO

description: KO


title: CRC_14T

value: Rectal cancer


title: Benign Breast Disease Biopsy FFPE [sample15]

description: Benign Breast Disease Biopsy


title: CD3ζ-TIR-CAR-iMAC, scRNAseq

city: Hangzhou

first: Hua

last: Yu

address: No.18 Shilongshan Road

institute: Westlake University

description: 10x Genomics

data_processing:
The "cellrange count" program, a subcommand included in the 10×single-cell gene expression analysis pipeline (https://support.10xgenomics.com/single-cell-gene-expression/), was used to produce a gene-cell barcode expression matrix.
The single-cell gene expression matrix was analyzed with Seurat v3.2.1 (https://satijalab.org/seurat/). To guarantee the quality of genes and cells used for downstream analysis, we excluded genes expressed in fewer than 3 cells and cells expressing less than 200 genes or more than 30000.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human iPSC-derived CAR-macrophage

growth_protocol: Matured CAR-iMACs  growed in StemSpanXF medium  containing M-CSF (100 ng/mL) and GM-CSF (100 ng/mL). U87MGEGFRvIII cells were cultured in MEM  medium supplemented with 10% FBS, 1×Non-Essential Amino Acids , 1mM Sodium Pyruvate, and 1×Pen Strep.

extract_protocol:
After co-incubation of CAR-iMACs with U87MGEGFRvIII cells for 24 hours, cells were harvested through trypsin digestion. DPBS was used to wash the cells  3 times to remove the residual medium.  Subsequently, the cells were processed with  10X Single Cell 3' Solution Reagents V2 to construct an RNA library.
We used 10X Single Cell 3' Solution Reagents V2 following the manufacturer’s protocol (10x Genomics)

treatment_protocol: Before co-incubation with U87MGEGFRvIII cells, CAR-iMACs were maintained in  StemSpanXF medium containing IFN-γ/LPS for 24 hours. MEM  medium containing 10% FBS, 1×Non-Essential Amino Acids , 1mM Sodium Pyruvate, and 1×Pen Strep was used as a medium for the co-incubation of CAR-iMACs with U87MGEGFRvIII cells.

value: human iPSC-derived CAR-macrophage


title: Benign Breast Disease Biopsy FFPE [sample14]

description: Benign Breast Disease Biopsy

value: Benign Breast Disease


title: ChIP-Seq WT

description: WT


title: CRC_9T


title: CRC_8T


title: WM989TreatementEffect_MixControl_scRNAseq

value: melanoma

value: MixControl


title: CRC_7T

value: Male


title: Truncated CAR-iMAC, scRNAseq

description: 10x Genomics


title: Benign Breast Disease Biopsy FFPE [sample13]

description: Benign Breast Disease Biopsy


title: Benign Breast Disease Biopsy FFPE [sample12]

description: Benign Breast Disease Biopsy


title: TIR-CAR-iMAC, scRNAseq

description: 10x Genomics


title: Untreated_WM989_scRNAseq


title: Benign Breast Disease Biopsy FFPE [sample11]

description: Benign Breast Disease Biopsy


title: RNA-Seq_Eahy_WT_hypoxia_24h_clone12

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Sequencing reads were pre-processed by trimming and filtering using Trim Galore (v.0.4.4) with a Phred quality score cutoff 30. Processed reads were aligned to GRCh37 using STAR and Salmon.
Genome browser shots were created using UCSC genome browser using representative bigWigs created using the wiggletools (1.2.10) mean function from TMM normalised bigWig files created using deeptools2 (3.5.1).
Assembly: hg19
Supplementary files format and content: ChIP-Seq bigWigs
Supplementary files format and content: raw RNA-Seq count matrix

source_name: Eahy 926

growth_protocol: EA.hy926 cells were cultured in DMEM (#D6429, Sigma) supplemented with 10% FBS and Penicillin/Streptomycin as above. Cells were maintained in 5% CO2 and either normoxia (ambient 21% O2) or in hypoxia (Invivo2 400 workstation, Ruskinn Technology Ltd, Bridgend, UK) at 1% O2.

extract_protocol:
ChIP-seq libraries were prepared as previously described (Kaikkonen et al, Nucleic Acids Res., 2014, 42, 12570–84). Briefly, 1% formaldehyde fixed cells were collected, sonicated and H3K4me3 complexes were precipitated using rabbit polyclonal antisera to H3K4me3 (Abcam, #ab8580) with rabbit IgG used as a negative control. DNA was purified, blunted, and used for library preparation with ligation to NEXTflex DNA barcode adaptors and indexes (Bioo Scientific Corporation) were incorporated and amplified using PCR. Library fragments were size selected on 10% polyacrylamide gel and sequenced on a NextSeq 500 (Illumina) using single-end 75 cycles in high output mode.
RNA was isolated using RNeasy minikit (Qiagen) and DNase treated with the RNase-free DNase set (Qiagen). RNA-Seq library preparation was carried out using a NEBNext Ultra II directional RNA library prep kit for Illumina (New England BioLabs) according to the manufacturer’s instructions. The resultant library was quantified using a Qubit double-stranded-DNA HS assay kit (Thermo Fisher Scientific), and quality checked with a Bioanalyzer (Agilent Technologies). Individual libraries were pooled in equimolar amounts (4 nM for each) and sequenced with the NextSeq 550 sequencer (Illumina, San Diego, CA) using 75 single-end cycles for 10 million reads per sample.

treatment_protocol: For CRISPR-Cas9 ablation of the HIF1A-AS in EAhy.926 cells, gRNAs were designed to target the flanks of the 460bp promoter (as determined by GRO-seq, H3K4me3 and ENCODE TFBS ChIP data). The crRNA:tracrRNA duplex was formed by denaturing 1μM of each at 95°C for 5 minutes and left to hybridise at room temperature. Equimolar quantities of Alt-R S.p. HiFi Cas9 Nuclease (IDT) and gRNA were then complexed at room temperature for 15 minutes. RNP complexes were reverse transfected into 8x104 EAhy.926 cells on 96 well plates using Lipofectamine CRISPRMAX (Invitrogen) according to the manufacturer’s instructions. Three independent clonal cell lines (clone 5, 7 and 12) of EAhy.926 ΔHIF1A-AS were established through single cell isolation where colonies were confirmed to have the HIF1A-AS deletion using PCR with primers targeting the HIF1A-AS promoter flanks and visualisation with gel electrophoresis combined with sanger sequencing.

value: Eahy 926

value: HIF1a-AS TSS deletion, clone 12

value: hypoxia 24h


title: Benign Breast Disease Biopsy FFPE [sample16]

description: Benign Breast Disease Biopsy


title: CRC_11T


title: RNA-Seq2 KO Rep3

description:
KO Rep3
Sample_3135-HL-49

data_processing:
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
The reference was indexed with Salmon v 1.2.0, and gene expression quantification was performed using Salmon in its nonalignment-based mode.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (74106, QIAGEN, Hilden, Germany)
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 6000 platform (Illumina) to generate pair-end 51 bp reads according to the manufacturer’s recommendation. In total, ~360 million reads were generated with an average of 30 million paired-reads per sample.

value: Primary

value: BMDM

value: Baf60a KO

value: BMDM differentiation

tag: time

value: Day 7


title: ChIP-Seq Input

description: Input


title: RNA-Seq2 KO Rep4

description:
KO Rep4
Sample_3135-HL-50


title: CRC_6T

tag: tissue


title: CRC_5T

value: Female


title: RNA-Seq2 KO Rep2

description:
KO Rep2
Sample_3135-HL-48

tag: cell type


title: CRC_4T

value: colorectal cancer


title: RNA-Seq_Eahy_WT_normoxia_clone12

tag: genotype

value: normoxia


title: RNA-Seq2 KO Rep1

description:
KO Rep1
Sample_3135-HL-47


title: CRC_3T

value: Colon cancer


title: RNA-Seq2 WT Rep4

description:
WT Rep4
Sample_3135-HL-46

value: WT


title: RNA-Seq_Eahy_WT_hypoxia_24h_clone7

value: HIF1a-AS TSS deletion, clone 7


title: Benign Breast Disease Biopsy FFPE [sample10]

description: Benign Breast Disease Biopsy

value: Breast

value: Biopsy

value: Benign Breast Disease


title: RNA-Seq_Eahy_WT_hypoxia_8h_clone7

value: Eahy 926

value: hypoxia 8h


title: CRC_2T

value: Male


title: CRC_1T

value: Rectal cancer


title: RNA-Seq2 WT Rep2

description:
WT Rep2
Sample_3135-HL-44

value: Primary

value: BMDM


title: RNA-Seq_Eahy_WT_normoxia_clone7


title: RNA-Seq_Eahy_WT_hypoxia_8h_clone5

value: HIF1a-AS TSS deletion, clone 5


title: RNA-Seq_Eahy_WT_hypoxia_8h_clone12

value: HIF1a-AS TSS deletion, clone 12


title: RNA-Seq_Eahy_WT_hypoxia_24h_clone5

value: hypoxia 24h


title: RNA-Seq2 WT Rep1

description:
WT Rep1
Sample_3135-HL-43

value: BMDM differentiation

value: Day 7


title: RNA-Seq_Eahy_WT_normoxia_clone5

value: normoxia


title: RNA-Seq1 KO Rep5

description:
KO Rep5
Sample_2445-YZ-12

value: Baf60a KO


title: Benign Breast Disease Biopsy FFPE [sample1]

description: Benign Breast Disease Biopsy


title: RNA-Seq1 KO Rep4

description:
KO Rep4
Sample_2445-YZ-11


title: TA(d2/-)104_RRBS

city: Yokosuka

first: Iyoko

last: Katoh

address: 82 Inaoka-cho

country: Japan

institute: Kanagawa Dental University

data_processing:
FASTQ Processing: Single-end 75 nucleotide sequencing reads are generated by Illumina sequencing using NextSeq 500.
Bismark Alignment: Reads are mapped to the genome using Bismark v0.23.0 and Bowtie 2 allowing for no mismatches (-N 0) and a seed substring length of 20 (-L 20). Following alignment, PCR duplicates are removed using a custom analysis script. Each read has a randomized 6-mer barcode and if more than one read has the same start and end coordinates and the same barcode, all but one of the reads are discarded. Alignment information of the remaining reads are stored in BAM files. Methylation at CpG sites is then extracted from the BAM files using Bismark.
MethylKit Analysis: CpG reports from the Bismark alignment are processed with the methylKit 1.18.0, and only CpG sites covered with at least 10 reads are retained for the downstream analyses.
Assembly: hg38
Supplementary files format and content: XLSX, gene methylation rates

source_name: TAp63-knockout cell line derived from FaDu

extract_protocol:
Genomic DNA was purified with the NucleoSpin Tissue (MACHEREY-NAGEL) kit. Cell (10^7) suspension in T1 buffer was incubated with RNase A (1mg/mL) at room temperature for 5 min before addition of proteinase K. Subsequent steps of incubation, loading onto the column, washing and elution were carried out according to the protocol of NucleoSpin Tissue.
gDNA (100 ng) was digested with TaqaI (NEB R0149) at 65°C for 2h followed by MspI (NEB R0106) at 37°C overnight. Digested DNA was randomly ligated, end-repaired and bisulfite-converted with the EpiTect Fast DNA Bisulfite Kit (Qiagen 59824). After the bisulfite conversion and clean-up, library amplification and purification were carried out with the Ovation RRBS Methyl-Seq System (Tecan 0353-32). Libraries were analyzed with Agilent 2200 TapeStation System and quantified with the KAPA Library Quantification Kit ABI Prism qPCR Mix (Roche KK4835) for sequencing on the Illumina NextSeq 550 system with SE75 workflow.

value: TAp63 knockout cell line derived from FaDu

tag: tumor type

value: Phenotype influenced by genome editing


title: FaDu_RRBS

source_name: FaDu, ATCC HTB-43

value: FaDu

value: Well-differentiated squamous cell carcinoma


title: RNA-Seq_Eahy_WT_hypoxia_24h_rep3

value: Eahy 926

value: WT


title: RNA-Seq1 KO Rep3

description:
KO Rep3
Sample_2445-YZ-10


title: RNA-Seq_Eahy_WT_hypoxia_24h_rep2


title: RNA-Seq1 KO Rep2

description:
KO Rep2
Sample_2445-YZ-5


title: RNA-Seq2 WT Rep3

description:
WT Rep3
Sample_3135-HL-45


title: RNA-Seq_Eahy_WT_hypoxia_24h_rep1


title: RNA-Seq1 KO Rep1

description:
KO Rep1
Sample_2445-YZ-4


title: RNA-Seq_Eahy_WT_hypoxia_8h_rep3

value: hypoxia 8h


title: RNA-Seq1 WT Rep7

description:
WT Rep7
Sample_2445-YZ-9


title: Decompensated RV [Decomp_3]

description: processed-data-pab.xlsx

data_processing:
Raw reads were assessed for quality, adapter content, and duplication rates using FastQC. Trimmomatic was employed to trim reads following a quality drop (below a mean of Q15) in a window of five nucleotides
STAR mapping: mode: single-end, keep duplicates: no, keep multi-mapping: no, keep ribosomal: no, keep mitochondria: no --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignEndsProtrude 10 ConcordantPair --alignMatesGapMax 2000 --limitOutSAMoneReadBytes 10000000 --outMultimapperOrder Random --sjdbOverhang 100 --alignIntronMax 200000 --outFilterMultimapNmax 999 --outSAMmultNmax -1 --genomeDir /rattus_norvegicus/104/index_star
FEATURE COUNT: The number of reads that aligned to genes was counted using featureCounts version 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were aggregated and counted per gene. Reads aligning to multiple regions or genes were excluded. -t exon -g gene_id -s 2; multi-mapping: no; duplicates: no
Raw count values were normalized using DESeq2 version 1.30.0, then transformed into regularized logarithm values for further analysis. The normalized data were the basis of downstream analysis.
Assembly: Rn06/104/
Supplementary files format and content: excel file containing sheet 1: sample labels and mapping parameters
Supplementary files format and content: excel file containing sheet 2: matrix of raw read counts for genes*samples

organism: Rattus norvegicus

source_name: Decompensated RV

extract_protocol:
RV tissues from PAB-treated rats were harvested after RHC measurements and snap-frozen. Total RNA was isolated from RV samples using miRNeasy Micro Kit (Qiagen) and snap-frozen. Purification of total RNA was performed as described in the RNeasy handbook, using DNase I digestion (RNase-Free DNase Set, Qiagen).
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer), and 2 µg of total RNA was used as input forVAHTS Stranded mRNA-seq Librarypreparation following manufacture’s protocol (Vazyme).

value: Right ventricle

tag: Sex

value: male

tag: tissue type

value: Decompensated RV


title: Compensated RV [Comp_5]

description: processed-data-pab.xlsx

source_name: Compensated RV

value: Compensated RV


title: Decompensated RV [Decomp_4]

description: processed-data-pab.xlsx


title: Compensated RV [Comp_2]

description: processed-data-pab.xlsx


title: Compensated RV [Comp_1]

description: processed-data-pab.xlsx


title: Compensated RV [Comp_4]

description: processed-data-pab.xlsx


title: Decompensated RV [Decomp_2]

description: processed-data-pab.xlsx


title: Decompensated RV [Decomp_5]

description: processed-data-pab.xlsx


title: Compensated RV [Comp_3]

description: processed-data-pab.xlsx


title: RNA-Seq_Eahy_WT_hypoxia_8h_rep2

tag: treatment


title: Control RV [CTRL_4]

description: processed-data-pab.xlsx

source_name: Control RV

value: Control RV


title: iPSCS+ EC Diff Day 0 RNA-seq

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: iPSCS EC Diff Day 0 RNA-seq SRM ID 2600073

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human (hg38)  genome assembly   (STAR v2.7.1a).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (human release 31)
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
RNA was harvested from cells using miRNeasy micro kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

value: iPSC

value: p53 KO

value: Day 0


title: P3F+ iPSC EC Diff Day 15 RNA-seq

description: P3F+ iPSC EC Diff Day 15 RNA-seq SRM ID 2600092

value: Day 15


title: iPSC EC Diff Day 0 IgG C&R

description: iPSC EC Diff Day 0 IgG C&R SRM ID 2542612

data_processing:
library strategy: CUT&RUN
Paired-end CUT&RUN-seq reads were aligned first to the E. coli reference genome using bowtie (version 1.2.2) in paired-end with parameters -k 1 –best and –un to retain unmapped reads. Because of nonbiological variability among samples, the numbers of E. coli reads were not used for cell-number-normalization hereafter. Retained non-E. coli reads were then mapped to the mouse reference genome (mm10) or human reference genome (hg38) using bowtie in paired-end mode with parameters -p 20 -k 2 -m 2 –best. A BAM file containing CUT&RUN-seq fragments was computationally created from each aligned read-pair using samtools sort -n, bedtools bamToBed -bedpe, a manual conversion from BEDPE to BED3, and bedtools bedToBam. For display, the reference genomes were binned into 50bp windows using bedtools makewindows, and coverage of those bins by fragments was calculated using bedtools intersect -c. Fragment coverage was normalized per million mapped fragments, converted to bedGraph using bedGraphToBigWig, converted to wiggle using bigWigToWig, converted to TDF using igvtools toTDF, and then visualized in the IGV(version 2.16.2.) browser in hg38 for human samples.
MACS1.4  was used to identify regions significantly enriched in CUT&RUN-seq reads. Prior to peak-calling, individual reads from each paired-end alignment were discarded if they overlapped the ENCODE-defined Problematic Regions list corresponding to the reference genome in use, and further filtered in mouse if they overlapped the region chr1:24611436-24616256, because of an observed genomically amplified region in all samples near the Col19a1 gene.  Retained reads were used for peak-calling against each sample’s corresponding, identically processed, control IgG. In mouse, parameters –keep-dup=auto and –p 0.001 were used; in human, parameters –keep-dup=auto and -p 1e-9 were used. To compare TCP vs. MCP coverage at regions of interest, we collapsed peaks called separately in each sample (N=3 TCP and N=4 MCP in mouse) using bedtools merge. Bedtools closest -t first was used to annotate each peak with the name of the gene whose transcript has the nearest transcription start site from mm10_refGene.gtf downloaded from the UCSC Genome Browser. Individual read coverage in each of the seven samples was separately quantified using bedtools intersect -c. For comparative analyses (Fig.5c), read coverage in each sample was normalized to the millions of mapped reads (RPM), and the average RPMs from each condition were calculated. For statistical analysis (Fig. 5d) of differential coverage, raw reads from the three TCP samples and three representative MCP samples (MCP20_1, MCP20_2, and MCP_38) were used as input for DEseq2. Peaks were considered differentially covered if they had DEseq2 adjusted log2 fold-change >1 or <-1 and adjusted p value of 0.05.
We used ROSE (https://bitbucket.org/young_computation/rose) to separately identify super-enhancers from each sample of MCP, TCP, Day 15 Untransduced p53KO iPSC, and Day 15 Lenti-P3F transduced p53KO iPSC CUT&RUN-seq data targeting H3K27ac, as previously described. Each sample was separately processed with its corresponding IgG. For each sample, we used MACS1.4 to identify two sets of peaks from each read set filtered as above. In mouse, we used parameter sets –keep-dup=auto –p 0.001 and –keep-dup=all –p 0.001; in human, we used parameter sets –keep-dup=auto -p 1e-9 and –keep-dup=all -p 1e-9. These two peak sets from each sample were collapsed into a per-sample set of peaks using bedtools merge; these collapsed peaks were used as input for ROSE with parameters -s 12500 -t 1000.
Assembly: hg38
Supplementary files format and content: bigWig, bed (for Untransduced Day 15 and P3F Day 15 H3K27ac data)

extract_protocol:
Nuclei were isolated by incubating cells in Nuclear Extraction Buffer (NEB) which consists of 20mM HEPES KOH pH7.9, 10mM KCl, 0.1% Triton X-100, 20% Glycerol, EDTA-free Protease Inhibitor (11836170001, Roche) and water for 10 minutes on ice. Aliquots of 250,000 nuclei were spun down then resuspended in nuclear extraction buffer and slowly frozen at -80°C in a Mr. Frosty freezing container (C1562, Sigma-Aldrich).
Libraries were prepared with the xGen ssDNA & Low-Input DNA Library Prep Kit (#10009859, IDT) and quantified using the Agilent 4150 TapeStation and Agilent Bioanalyzer before sequencing with NovaSeq6000 (Illumina).

tag: cut&run antibody

value: IgG (#13-0042k, EpiCypher)


title: P3F + iPSC EC Diff Day 15 IgG C&R

description: P3F + iPSC EC Diff Day 15 IgG C&R SRM ID 2572648


description: Untransduced iPSC EC Diff Day 15 IgG C&R SRM ID 2572644


title: P3F + iPSC EC Diff Day 15

description: P3F + iPSC EC Diff Day 15 FOXO1 C&R SRM ID 2572650

value: FOXO1 (#2880, Cell Signaling Technology)


title: Control RV [CTRL_5]

description: processed-data-pab.xlsx


title: iPSC EC Diff Day 0 FOXO1 C&R

description: iPSC EC Diff Day 0 FOXO1 C&R SRM ID 2572614


title: RNA-Seq1 WT Rep6

description:
WT Rep6
Sample_2445-YZ-8

value: Primary

value: BMDM

value: BMDM differentiation

value: Day 7


title: Control RV [CTRL_3]

description: processed-data-pab.xlsx


title: Untransduced iPSC EC Diff Day 15

description: Untransduced iPSC EC Diff Day 15 FOXO1 C&R SRM ID 2572646


title: RNA-Seq_Eahy_WT_normoxia_rep3

value: Eahy 926

value: WT

value: normoxia


title: RNA-Seq_Eahy_WT_hypoxia_8h_rep1

value: hypoxia 8h


title: RNA-Seq1 WT Rep2

description:
WT Rep2
Sample_2445-YZ-2


title: RNA-Seq_Eahy_WT_normoxia_rep1


description: Untransduced iPSC EC Diff Day 15 RNA-seq SRM ID 2600081

value: Untransduced


title: RNA-Seq1 WT Rep5

description:
WT Rep5
Sample_2445-YZ-7


title: H3K4me3_ChIP_Eahy_input_rep1

tag: antibody


title: RNA-Seq1 WT Rep4

description:
WT Rep4
Sample_2445-YZ-6


title: PLPmut

city: Würzburg

first: Fabian

last: Imdahl

state: Bavaria

address: Josef-Schneider Str. 2

department: Single-cell-center

institute: helmholtz institute for RNA based infection research

description: 10x Genomics

data_processing:
Data were demultiplexed using the CellRanger software v.2.0.2 based on 8 bp 10x sample indexes; paired-end FASTQ files were generated. The cell barcodes and transcript unique molecular identifiers were processed as described previously. The reads were aligned to the University of California, Santa Cruz mouse mm10 reference genome using STAR aligner v.2.5.1b. The alignment results were used to quantify the expression level of mouse genes and generate the gene-barcode matrix. Subsequent data analysis was performed using the R package Seurat v.4.0. Doublets and potentially dead cells were removed based on the percentage of mitochondrial genes (cutoff set at 60%) and the number of genes (cells with >100 and <6,000 genes were used) expressed in each cell as quality control markers. The gene expression of the remaining cells (13,522, 9,898, and 12,170 cells from Wt, PLPmut, and PLPtg mice, respectively) was log-normalized. Highly variable genes were detected with Seurat and the top 2,000 of these genes were used as the basis for downstream clustering analysis. Data were scaled, principle component analysis was used for dimensionality reduction and the number of principal components was identified using the built-in Elbow plot function. Cells were clustered based on the identified principal components (10) with a resolution of 0.5; uniform manifold approximation and projection was used for data visualization in two dimensions. Microglia and oligodendrocyte clusters were subset based on marker gene expression and reanalyzed, resulting in 9,484, 8,405, and 8,419 cells from Wt, PLPmut, and PLPtg mice, respectively. These were reanalyzed and reclustered based on 14 principal components and a resolution of 0.6. Contribution of the samples to each microglia cluster in absolute numbers was calculated by extrapolating their frequencies to the number of CD45lowSiglec-H+ cells per brain. Differentially expressed genes were identified using the FindMarkers function with min.pct = 0.25. Complete lists of differentially expressed genes (p_val_adj > 0.05 after Bonferroni or FDR correction) are included in Supplementary Table 1. Marker gene scores for feature expression programs were calculated using the AddModuleScore function in Seurat. Gene-set enrichment analysis was performed using Metascape v.3.5 (http://metascape.org).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Brain

extract_protocol:
Mice were euthanized with CO2 (according to the guidelines by the State Office of Health and Social Affairs Berlin) and blood was thoroughly removed by transcardial perfusion with PBS containing heparin. Brains including optic nerves, leptomeninges and choroid plexus were dissected, collected in ice‐cold PBS and cut into small pieces. Tissue was digested in 1 ml of Accutase (Merck Millipore) per brain at room temperature for 15 min and triturated through 70-μm cell strainers, which were rinsed with 10% FCS in PBS. Cells were purified by a linear 40% Percoll (GE Healthcare) centrifugation step at 650 g without brakes for 25 min and the myelin top layer and supernatant were discarded. Mononuclear cells were resuspended in 1% BSA in PBS and isolated cells were counted for each brain. For scRNA-seq, cells from the brains of 3 adult (10-month-old) Wt, 3 PLPmut, and 3 PLPtg mice were pooled into 3 separate samples. Viable cells were identified by Calcein blue AM stain (catalog no. ABD-22007; Biomol), Fc receptors were blocked for 15 min with rat anti‐CD16/32 (1:200, catalog no. 553141; BD Biosciences) and cells were washed and labeled with the following antibodies for 30 min at 4 °C: rat anti-CD45 PerCP/Cyanine5.5 (1:100, catalog no. 130-102-469; Miltenyi Biotec); rat anti-SiglecH PE (1:100, catalog no. 12-0333-82; eBioscience); rat anti-O1 AF700 (1:100, FAB1327N-100UG; R&D Systems). Cells were washed twice, single viable cells were gated and CD45-O1+ and CD45lowSiglec-H+ cells were collected using a FACSAria III and corresponding software (FACSDiva, v.6; BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
10x Genomics 3' v2 Protocol

value: Microglia, oligodendrocytes

value: Brain

value: PLPmut

tag: age


title: P3F + iPSC EC Diff Day 15 H3K27ac C&R

description: P3F + iPSC EC Diff Day 15 H3K27ac C&R SRM ID 2572649

value: iPSC

value: H3K27ac (#39133, Active Motif)


title: RNA-Seq_Eahy_WT_normoxia_rep2


title: SGC996_NC3

city: Fuzhou

first: Yanling

last: Chen

address: xinquan road

department: Hepatobiliary surgery

institute: Fujian medical university union hospital

description:
gene_fpkm.txt
gene_count.txt

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: disease state

value: gallblader cancer

value: gallblader cancer cell

value: untreated


title: Control RV [CTRL_2]

description: processed-data-pab.xlsx

value: Right ventricle

value: male

value: Control RV


description: Untransduced iPSC EC Diff Day 15 H3K27ac C&R SRM ID 2572645


title: Control RV [CTRL_1]

description: processed-data-pab.xlsx


title: iPSC EC Diff Day 0 H3K27ac C&R

description: iPSC EC Diff Day 0 H3K27ac C&R SRM ID 2572613


title: H3K4me3_ChIP_Eahy_input_rep2


title: RNA-Seq1 WT Rep3

description:
WT Rep3
Sample_2445-YZ-3

value: Primary

value: BMDM

value: BMDM differentiation

value: Day 7


title: SGC996_OE3

description:
gene_fpkm.txt
gene_count.txt

value: FOXA2 overexpression


title: Decompensated RV male (Decomp-m_6)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-m_6

data_processing:
Raw reads were assessed for quality, adapter content, and duplication rates using FastQC59. Trimmomatic version 0.39 was employed to trim reads following a quality drop (below a mean of Q15) in a window of five nucleotides
STAR mapping: mode: single-end, keep duplicates: no, keep multi-mapping: no, keep ribosomal: no, keep mitochondria: no --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignEndsProtrude 10 ConcordantPair --alignMatesGapMax 2000 --limitOutSAMoneReadBytes 10000000 --outMultimapperOrder Random --sjdbOverhang 100 --alignIntronMax 200000 --outFilterMultimapNmax 999 --outSAMmultNmax -1 --genomeDir rattus_norvegicus/104/index_star
FEATURE COUNT: The number of reads that aligned to genes was counted using featureCounts version 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were aggregated and counted per gene. Reads aligning to multiple regions or genes were excluded. -t exon -g gene_id -s 2; multi-mapping: no; duplicates: no
Raw count values for each organism were normalized separately using DESeq2 version 1.30.0, then transformed into regularized logarithm values for further analysis. The normalized data were the basis of downstream analysis.
Assembly: Rn06/104/
Supplementary files format and content: excel file containing sheet 1: sample labels and mapping parameters
Supplementary files format and content: excel file containing sheet 2: BATCH 1. matrix of raw read counts for genes*samples
Supplementary files format and content: excel file containing sheet 2: BATCH 2. matrix of raw read counts for genes*samples

extract_protocol:
MCT tissues from MCT-treated rats were harvested after RHC measurements and snap-frozen. Total RNA from each batch of RV samples were isolated separately using the RNeasy Mini Kit (or miRNeasy Micro Kit, when less sample provided-Qiagen) and snap-frozen. Purification of total RNA was performed as described in the RNeasy handbook, using DNase I digestion (RNase-Free DNase Set, Qiagen).
Following the RNA integrity measurement, approximately 2 µg of total RNA were used as starting material for library preparation using the VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme)

value: M

tag: condition

value: Decompensated RV

tag: batch

value: batch 2


title: Tomato high aP2-Cre [scRNA-seq]

description: Top 50 tom positive ATOM - 2449249

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38(mm10)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: FACS sorted tomato positive cells from the sternocleidomastoid muscle

extract_protocol:
For tumors, tumor samples were manually dissected from normal surrounding tissue.
For sorted cells, tissues were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
RNA extraction and library preparation was performed according to manufacturer's instructions (single cell 3' v3.1 protocol, 10x Genomics)


title: Decompensated RV male (Decomp-m_4)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-m_4

source_name: Right ventricle


title: SGC996_OE2

description:
gene_fpkm.txt
gene_count.txt

tag: cell line


title: RNA-Seq1 WT Rep1

description:
WT Rep1
Sample_2445-YZ-1

value: WT


title: PLPtg

description: 10x Genomics

value: Microglia, oligodendrocytes

value: Brain

value: PLPtg


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_clone7_rep1

value: Eahy 926

value: HIF1a-AS TSS deletion, clone 7

value: hypoxia 8h


title: Decompensated RV female (Decomp-f_3)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-f_3

value: Right ventricle

value: F


title: SGC996_OE1

description:
gene_fpkm.txt
gene_count.txt

value: gallblader cancer

value: gallblader cancer cell

value: untreated


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_clone12_rep2

value: HIF1a-AS TSS deletion, clone 12


title: Decompensated RV male (Decomp-m_3)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-m_3


title: Tek-Cre Tomato+  [scRNA-seq]

description: TT tom+ SCM - 2227298

value: FACS sorted tomato positive cells from the sternocleidomastoid muscle


title: Decompensated RV female (Decomp-f_2)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-f_2


title: Donor-patient-1

description:
1412876
Sezary_Seurat_Clustering_Data.RData
1412876

data_processing:
library strategy: RNA-seq and TCR-seq
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq and V(D)J libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)
Assembly: GRCh38
Supplementary files format and content: Seurat R data object includes CD4 cell counts, clustering, and TCR across all samples

source_name: PBMC

extract_protocol:
mCD45-hCD45+hCD2+hCD4+hCD8- cells were flow sorted from PBMCs of a healthy control, a Sezary patient, and collected into tubes containingPBSwith 0.04%BSA.
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq and V(D)J libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)

value: PBMC

tag: strain

value: SIRPA KI Rag2-/- Il2rg-/- IL15 KO

tag: subject status

value: Patient


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_clone12_rep1


title: Wt

description: 10x Genomics

value: Wt


title: Decompensated RV male (Decomp-m_1)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-m_1

value: M

value: Decompensated RV

value: batch 2


title: SGC996_NC2

description:
gene_fpkm.txt
gene_count.txt

value: WT


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_clone7_rep2

value: Eahy 926

value: HIF1a-AS TSS deletion, clone 7


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_rep4

value: hypoxia 8h


title: SGC996_NC1

description:
gene_fpkm.txt
gene_count.txt


title: P53 KO IPSCS 2

description: p53 KO BJFF.6 iPSCs p5 - 2440991

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human (hg38) or mouse (mm10) genome assembly   (STAR v2.7.1a).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (human release 31  for human sampls or mouse release 22 for mouse samples).
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM text file

source_name: BJFF.6 iPSC

extract_protocol:
For tumors, tumor samples were manually dissected from normal surrounding tissue.
For sorted cells, tissues were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
RNA from tumors was harvested using miRNeasy mini plus kit (Qiagen) and RNA from sorted cells was harvested using miRNeasy micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

value: BJFF.6 iPSC

value: Trp53 null iPSCs


title: Fabp4-Cre Tomato+ 1 [scRNA-seq]

description: FTom female SCM tom+ - 2361328


title: Decompensated RV male (Decomp-m_2)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-m_2

value: Right ventricle


title: Donor-healthy-1

description:
1412877
Sezary_Seurat_Clustering_Data.RData
1412877

value: Healthy


title: Compensated RV male (Comp-m_2)

description:
processed-data-mct.xlsx
count matrix column name: Comp-m_2

value: Compensated RV


title: Decompensated RV female (Decomp-f_1)

description:
processed-data-mct.xlsx
count matrix column name: Decomp-f_1

value: F


title: TCP 1 [scRNA-seq]

description: TCP 83 - 2280152

source_name: FACS sorted Tomato positive tumor cells

value: FACS sorted Tomato positive tumor cells


title: iPSC xeno tumor 9

description: EC diff iPSCs xenograft 2/24 tumor 3 - 2421338

value: Trp53 null iPSCs transduced with P3F while undergoing directed differentiation to the endothelial lineage


title: Compensated RV male (Comp-m_3)

description:
processed-data-mct.xlsx
count matrix column name: Comp-m_3


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_clone5_rep2

value: HIF1a-AS TSS deletion, clone 5


title: aP2-Cre Tomato+ 2 [scRNA-seq]

description: adult ATOM male tom+ SCM - 2122763

value: FACS sorted tomato positive cells from the sternocleidomastoid muscle


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_clone5_rep1


title: Ec EMBR Rep3

city: Santa Barbara

first: Kellie

last: Heom

state: California

address: UC Santa Barbara

department: Chemical Engineering

institute: University of California Santa Barbara

description: EMBR-seq

data_processing:
In the sequencing libraries, read 1 contains the sample barcode. Read 2 is mapped to the bacterial or fungal transcriptome. Prior to mapping, read 1 was trimmed to 25 bases, read 2 was trimmed to 51 bases, and only reads containing valid sample barcodes on read 1 were retained. Next, the reads were mapped to the appropriate reference transcriptome using Burrows-Wheeler Aligner (BWA) version 0.7.15 with default parameters.
Assembly: Escherichia coli K12 substr. MG1655 (ASM584v2); Geobacter metallireducens GS-15 (ASM1292v1); Fibrobacter succinogenes strain UWB7 (GCA_900142945.1); Anaeromyces robustus (Anaeromyces robustus v1.0); Caecomyces churrovis (Caecomyces churrovis A v1.0)
Supplementary files format and content: Text file where column 1 contains gene names or gene IDs and column 2 contains gene counts.

organism: Escherichia coli

extract_protocol:
For E. coli and G. metallireducens monocultures, total RNA extractions were performed using Trizol according to the manufacturer’s protocol. RNA was extracted from F. succinogenes strain UWB7 monoculture & co-culture pellets using the RNeasy Mini Kit following the protocol for purification of total RNA from plant cells and tissues and filamentous fungi, using liquid N2 method of cell lysis, QIAshredder homogenization, on-column DNase I digestion, and elution in 30 µL of RNAse-free water.
(1) Overview: EMBR-seq libraries were prepared according to the protocol described in Wangsanuwat et al. 100 ng of total RNA were used as input material for all libraries. For the libraries denoted “EMBR-seq” and “EMBR-seq+”, blocking primers were added during the polyadenylation step and reverse transcription step. For the libraries denoted “No depletion” and “RNase H”, water was added instead of blocking primers during these two steps. In the libraries denoted “RNase H” and “EMBR-seq+”, the RNase H treatment was performed as described below. In the libraries denoted “No depletion” and “EMBR-seq”, the RNase H treatment was skipped; the amplified RNA (aRNA) product of in vitro transcription (IVT) was used directly for the library reverse transcription step as described in Wangsanuwat et al. (2) Polyadenylation: 2 μL of total RNA (50 ng/μL) was mixed with 1 μL of 5x first strand buffer [250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2, comes with Superscript II reverse transcriptase, Invitrogen Cat. # 18064014], 1 uL of blocking primer mix, 0.1 μL 10 mM ATP, and 0.1 μL E. coli poly-A polymerase (New England Biolabs, Cat. # M0276S). The samples were incubated at 37°C for 10 mins. In the “No depletion” and “RNase H” libraries, 1 μL of nuclease-free water was added instead of the blocking primer mix. (3) Reverse transcription: The polyadenylation product was mixed with 0.5 μL 10 mM dNTPs (New England Biolabs, Cat. # N0447L), 1 μL reverse transcription primers (25 ng/μL, Supplementary Table 2), and 1.3 μL blocking primer mix, and heated to 65°C for 5 mins, 58°C for 1 min, and then quenched on ice. In the “No depletion” and “RNase H” libraries, 1.3 μL of nuclease-free water was added instead of the blocking primer mix. This product was then mixed with 1.2 μL 5x first strand buffer, 1 μL 0.1 M DTT, 0.5 μL RNaseOUT (Thermo Fisher Scientific, Cat. #10777019), and 0.5 μL Superscript II reverse transcriptase, and then incubated at 42°C for 1 hr. Immediately afterwards, the samples were heat-inactivated at 70°C for 10 mins. (4) Second strand synthesis: The reverse transcription product was mixed with 33.5 μL nuclease-free water, 12 μL 5x second strand buffer [100 mM Tris-HCl (pH 6.9), 23 mM MgCl2, 450 mM KCl, 0.75 mM β-NAD, 50 mM (NH4)2SO4, Invitrogen, Cat. # 10812014], 1.2 μL 10 mM dNTPs, 0.4 μL E. coli ligase (Invitrogen, Cat. # 18052019), 1.5 μL DNA polymerase I (Invitrogen, Cat. # 18010025), and 0.4 μL RNase H (Invitrogen, Cat. # 18021071), and incubated at 16°C for 2 hrs. The cDNA was purified with 1x AMPure XP DNA beads (Beckman Coulter, Cat. # A63881) and eluted in 24 μL nuclease-free water that was subsequently concentrated to 6.4 μL. (5) In vitro transcription: The product from the previous step was mixed with 9.6 μL of in vitro transcription mix (1.6 μL of each ribonucleotide, 1.6 μL 10x T7 reaction buffer, 1.6 μL T7 enzyme mix, MEGAscript T7 Transcription Kit, Thermo Fisher Scientific, Cat. # AMB13345) and incubated at 37°C for 13 hrs. The IVT product was mixed with 6 μL ExoSAP-IT PCR Product Cleanup Reagent (Thermo Fisher Scientific, Cat. # 78200.200.UL) and incubated at 37°C for 15 mins. Next, it was treated with 5.5 μL fragmentation buffer (200 mM Tris-acetate (pH 8.1), 500 mM KOAc, 150 mM MgOAc) at 94°C for 3 mins and immediately quenched with 2.75 μL stop buffer (0.5 M EDTA) on ice. The fragmented aRNA was size-selected with 0.8x AMPure RNA beads (RNAClean XP Kit, Beckman Coulter, Cat. # A63987) and eluted in 18 μL nuclease-free water. In the libraries denoted “No depletion” and “EMBR-seq”, the fragmented and cleaned-up in vitro transcription product was used directly for Illumina library preparation by reverse transcription and PCR, as described previously (18, 30). In the “RNase H” and “EMBR-seq+” libraries, the RNase H treatment was performed before proceeding to Illumina library preparation. (6) RNase H treatment for monocultures: After ExoSAP treatment, RNA fragmentation, and bead-based size selection, the aRNA concentration was measured on a NanoDrop One spectrophotometer. 1000 ng of aRNA was mixed with 500 ng (3.2 μL) of RNase H probe mix, 3.2 μL of RNase H buffer mix, and nuclease-free water to reach a total volume of 15 μL for each reaction. This mixture was preheated at 65°C for 5 mins and quenched on ice. 1 μL of RNase H (Invitrogen, Cat. # 18021071) was added and the reaction was incubated at 16°C for 30 mins. Finally, the RNase H product was size-selected with 1x AMPure RNA beads and eluted in 15 μL nuclease-free water, and then concentrated to 5 μL volume for Illumina library preparation. (7) RNase H reaction for co-cultures: For co-culture samples, the RNase H probe mix was altered to include probes for depleting fungal rRNA along with bacterial rRNA. 1000 ng of aRNA derived from co-culture samples was mixed with 850 ng (5.5 μL) of co-culture RNase H probe mix, which consisted of: 100 ng each of the two fungal 28S probes with 50 ng each of the two fungal 18S, fungal 5.8S, and ten bacterial RNase H probes. The aRNA and probes were mixed with 3.2 μL RNase H buffer mix and nuclease-free water to reach a total volume of 15 μL for each reaction. The reactions were preheated at 65°C for 5 mins and quenched on ice. 1 μL of RNase H was added and the reaction was incubated at 16°C for 30 mins. The RNase H product was size-selected with 1x AMPure RNA beads and eluted in 15 μL nuclease-free water, and then concentrated to 5 μL volume for Illumina library preparation.
OTHER (EMBR-seq+). Method is detailed in Heom, Wangsanuwat et al.

tag: input material_for_library_preparation

value: total RNA (Trizol)


title: aP2-Cre Tomato+ 1 [scRNA-seq]

description: adult ATOM female tom+ SCM - 2122762


title: Compensated RV male (Comp-m_5)

description:
processed-data-mct.xlsx
count matrix column name: Comp-m_5

tag: tissue

value: M


title: Compensated RV male (Comp-m_4)

description:
processed-data-mct.xlsx
count matrix column name: Comp-m_4

value: batch 2


title: Fabp4-Cre Tomato+ 2 [scRNA-seq]

description: Ftom female HL tom+ - 2361329

tag: cell type


title: P53 KO IPSCS 3

description: p53 KO BJFF.6 iPSCs p6 - 2440992

tag: genotype


title: Compensated RV male (Comp-m_1)

description:
processed-data-mct.xlsx
count matrix column name: Comp-m_1


title: iPSC xeno tumor 7

description: EC diff iPSCs xenograft 2/24 tumor 1 - 2421336


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_rep3

value: WT


title: P53 KO IPSCS 1

description: p53 KO BJFF.6 iPSCs p4 - 2440990


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_rep2

value: Eahy 926


title: H3K4me3_ChIP_Eahy_WT_hypoxia_8h_rep1


title: TCP 2 [scRNA-seq]

description: TCP 93 - 2280153


title: iPSC xeno tumor 6

description: EC diff iPSCs xenograft 2/21 tumor 3 - 2421335


title: Compensated RV female (Comp-f_7)

description:
processed-data-mct.xlsx
count matrix column name: Comp-f_7


title: MCP 5 [scRNA-seq]

description: MCP 48 - 2315613


title: MCP 2 [scRNA-seq]

description: MCP 299 - 2177145


title: Compensated RV female (Comp-f_3)

description:
processed-data-mct.xlsx
count matrix column name: Comp-f_3


title: iPSC xeno tumor 8

description: EC diff iPSCs xenograft 2/24 tumor 2 - 2421337


title: Ec EMBR Rep2

description: EMBR-seq


title: iPSC xeno tumor 4

description: EC diff iPSCs xenograft 2/21 tumor 1 - 2421333


title: Ec Control Rep2

description: No depletion


title: MCP 4 [scRNA-seq]

description: MCP 46 - 2315612


title: MCP 1 [scRNA-seq]

description: MCP 375 - 2177143


title: iPSC xeno tumor 3

description: EC diff iPSCs xenograft tumor 3 - 2421332


title: Ec Control Rep1

description: No depletion


title: Compensated RV female (Comp-f_6)

description:
processed-data-mct.xlsx
count matrix column name: Comp-f_6


title: Ec EMBR Rep1

description: EMBR-seq


title: MCP 3 [scRNA-seq]

description: MCP 13 - 2315611


title: iPSC xeno tumor 5

description: EC diff iPSCs xenograft 2/21 tumor 2 - 2421334


title: Ec Control Rep3

description: No depletion


title: Compensated RV female (Comp-f_1)

description:
processed-data-mct.xlsx
count matrix column name: Comp-f_1


title: iPSC xeno tumor 2

description: EC diff iPSCs xenograft tumor 2 - 2421331


title: control RV male (CTRL-m_3)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-m_3

value: control RV


title: Compensated RV female (Comp-f_5)

description:
processed-data-mct.xlsx
count matrix column name: Comp-f_5


title: Compensated RV female (Comp-f_2)

description:
processed-data-mct.xlsx
count matrix column name: Comp-f_2


title: aP2-Cre tdTomato+ 1

description: ATom tom+ SCM - 2156406

source_name: FACS sorted Tomato positive cells from the sternocleidomastoid muscle


title: Tek-Cre tdTomato- 4

description: TT tom- SCM - 2064741

source_name: FACS sorted Tomato negative cells from the sternocleidomastoid muscle

value: Tek-Cre;tdTom


title: Inhibitor, DN3, ChIP, input

city: Shanghai

first: Mingyuan

last: Hu

address: 320, Yueyang Road

institute: Chinese Academy of Science

data_processing:
The sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to mm10 genome using the BWA algorithm with default settings.
Peaks were called using the MACS 2.1.0 algorithms with the following setting: band width = 200, model fold = [5, 50], pvalue cutoff = 1.00e-07, Broad region calling is off.
bigWig files were generated using Active Motive software.
The tag number of all samples (within a comparison group) is reduced by random sampling to the number of tags present in the smallest sample.
To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Active Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Active Region.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak (except for Input samples)

source_name: double negative thymocytes

growth_protocol: Isolated HSCs  were co-cultured with OP9-DL1 cells in complete αMEM supplied with 5 ng/mL Flt-3L and 2 ng/mL IL-7. Cells are havested when developed into DN3 stage.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using a Active Motive ChIP-IT ChIP-Seq kit (Cat# 53041). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, dNTP mix, DNA polymerase I Klenow and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligate adapter to DNA fragments in a cocktail containing DNA, quick ligation buffer, adapter oligo mix and T4 DNA ligase for 20 minutes at room temperature. After adapter ligation DNA was PCR amplified with PCR primers mix for 18 cycles and library fragments of 200-300 bp were band isolated from an agarose gel.

treatment_protocol: HSCs were developed in the presence or absence of SCD1 inhibitor A939572

value: double negative thymocytes

tag: chip antibody

value: SCD1 inhibitor A939572


title: Control, DN3, ChIP, input

value: DMSO


title: MA-D

city: Guwahati

first: Narayana

middle: H

last: Mohan

state: Assam

address: Rani

department: ICAR-National Research Centre on Pig

country: India

institute: Indian Council of Agricultural Research

data_processing:
The quality of the raw sequences generated from MeDIP sequencing were assessed with FastQC (version 0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). With respect to the FastQC report, the low quality bases were removed using custom made perl script and the adaptor sequences were removed using cutadapt (version 3.3). The pre-processed reads were mapped to the Sus scrofa genome v11.1 downloaded from UCSC (http://genome.ucsc.edu/) with Burrows–Wheeler alignment. Uniquely mapped reads with high mapping quality (reads with a mapping quality score of ≥10) were analyzed using the MEDIPS software package (version 1.44) (BWA) (version 0.7.17).
The wiggle files were generated using "exportWIG" function in MEDIPS to export genome wide coverage profiles for visualization in the UCSC genome browser
Genome_build: Sus scrofa 11.1 reference genome
Supplementary_files_format_and_content: tab-delimited text files containing chromosome wise differentially methylated regions
Supplementary_files_format_and_content: CPG informtion in DNA isolated two different breeds of animals

organism: Sus scrofa

source_name: Muscle

extract_protocol:
A was isolated from muscle tissues using a commercial kit (Thermofisher, USA) .The methylated regions were precipitated and used for sequencing.
MeDIP libraries were prepared for sequencing using standard Illumina protocols
The enriched fragments with methylation were purified and amplified through adaptor-mediated PCR. Later, 8.5pmol of the MeDIP library was subjected to paired-end sequencing using an Illumina HiSeq 2500 and a 100-bp read length.

treatment_protocol: Muscle tissues were removed using biopsy from pigs belonging to Hampshire and Mali breeds of pigs

tag: breed

value: Mali breed


title: HA-D

value: Hampshire breed


title: aP2-Cre tdTomato+ 3

description: ATom tom+ SCM - 2156418

value: FACS sorted Tomato positive cells from the sternocleidomastoid muscle


title: aP2-Cre tdTomato+ 2

description: ATom tom+ SCM - 2156414


title: iPSC xeno tumor 1

description: EC diff iPSCs xenograft tumor 1 - 2421330

value: BJFF.6 iPSC


title: PC3_RNAseq_siFANCI_rep3

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: LNCaP and PC-3 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using TriPure Isolation Reagent (Roche, cat. no. 11667165001) following manufacturer’s protocol.
mRNA was enriched using oligo(dT) beads and fragmented randomly by adding fragmentation buffer. The cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: LNCaP and PC-3 cells were transfected with siRNA using Opti-MEM and Lipofectamine RNAiMAX reagent 48 h before extraction of RNA.

value: Bone Metastasis Prostate Cancer 3

tag: sirna treatment

value: FANCI silencing RNA (siFANCI, Dharmacon, cat.no. L-022320-01-0005)

tag: sirna concentration

value: 25 nM

tag: sirna time


title: Inhibitor, DN3, ChIP

value: H3K79me2 (Active Motif, cat no. 39143)

tag: treatment


title: control RV male (CTRL-m_1)

first: Fatemeh

last: Khassafi

description:
processed-data-mct.xlsx
count matrix column name: CTRL-m_1

value: Right ventricle

tag: Sex

value: M