title: Blood, donor 3

city: Oxford

first: Nicholas

last: Provine

address: Roosevelt Way

department: Pandemic Sciences Institute

country: United Kingdom

institute: University of Oxford

description: 10x Genomics

data_processing:
CellRanger v7.0.0
Assembly: GRCh38
Supplementary files format and content: features.tsv file (tsv format) contains the list of features from CellRanger
Supplementary files format and content: barcodes.tsv (tsv format) contains the list of cell barcodes from CellRanger
Supplementary files format and content: matrix.mtx (MEX format) contains the feature counts from CellRanger

source_name: peripheral blood

extract_protocol:
CD45+ non-naïve T, non-naïve B, and non-T/B cells were isolated by FACS and input into the 10x Genomics 5' NextGEM v2 dual-index pipeline
10x Genomics 5' NextGEM v2 dual-index pipeline

value: peripheral blood

value: PBMC


title: Blood, donor 2

status: Public on Feb 23 2024

type: SRA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Lymph node FNA, donor 2

description: 10x Genomics

source_name: lymph node

value: lymph node

value: MNCs


title: Lymph node FNA, donor 1

description: 10x Genomics


title: Blood, donor 4

description: 10x Genomics


title: Lymph node FNA, donor 3

description: 10x Genomics


title: Blood, donor 1

description: 10x Genomics


title: Lymph node FNA, donor 4

description: 10x Genomics


title: Antrum_2

city: Marburg

first: Laura

last: Koebbe

address: Baldingerstraße

country: Germany

institute: University of Marburg

library_source: transcriptomic

data_processing:
Quality control of sequencing data was performed with FastQC v0.11.7.
For adaptor trimming bbduk from the BBMap v37.44 was used.
The read alignment against GRCh38 was performed with STAR Aligner 2.5.2b.
FeatureCounts v1.5.1 was used for quantification of gene expression using the Ensembl annotation GRCh38.89 as reference.
Further QC was performed using RSeQC.
Assembly: GRCh38
Supplementary files format and content: gastric_expression_unique_counts.csv: comma-separated file with number of unique counts per gene and sample (columns = samples, rows = genes (Ensembl Ids))

source_name: Antrum

extract_protocol:
Tissue samples were mechanically homogenized with ceramic beads and a Precellys tissue homogenizer. Total RNA (and genomic DNA) was extracted using the Allprep DNA/RNA Mini Kit from Qiagen.
RNA libraries for RNA-Seq were prepared using Lexogen's QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina following manufacturer's protocol.

value: Antrum


title: Antrum_1


title: CUT&RUN A204 H3K4me1 rep2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

country: USA

institute: Vanderbilt University Medical Center

library_source: genomic

data_processing:
library strategy: CUT&RUN
CUT&RUN analysis: CUT&RUNTools was used for CUNT&RUN data analysis including adapter trimming, alignment, duplication marking, and peak calling. DiffBind was then applied to get consensus peaks for H3K4me3 and H3K27ac
ATAC-seq anaysis: After adaptor trimming by Cutadapt, ATAC-seq reads were aligned to the human genome hg19 using Bowtie2. Peaks were called using MACS2 with q-value of 0.05. Peaks present in at least two replicates per condition were included, and peaks identified across conditions were combined into a final peak set and ATAC-seq read counts were calculated for the final peak set. Differential enriched peaks were identified using DiffBind with a FDR < 0.05
RNA-seq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
Assembly: hg19
Supplementary files format and content: CUT&RUN: peak file for each condition
Supplementary files format and content: ATAC-seq: peak file for each condition
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample

molecule: genomic DNA

growth_protocol: JMU-RTK-2 cells were maintained in DMEM supplemented with 10% FBS and 1%Penicillin/Streptomycin. A204 and TTC-549 were maintained in RPMI supplemented with 10% FBS and 1%Penicillin/Streptomycin. This maintenance media was also the same media that DMSO, cis-ACBI1, or ACBI1 was diluted in.

extract_protocol:
For ATAC-seq, 100,000 cells were harvested and nuclei were treated with the Active Motif transposase included in the Active Motif ATAC-seq kit. All subsequent processing following the Active motif protocol. For RNA-seq, RNA was extracted from 2-3 million cells using Trizol and the Direct-zol RNA mini prep kit by Zymo Research. For CUT&RUN, 500,000 cells were bound to ConA beads and processed following the Cell Signaling CUT&RUN kit protocol.
For ATAC-seq, libraries were made using the Active Motif ATAC-seq kit, which included index primers and all PCR reagents. For RNA-seq, libraries were made at Vanderbilt University Medical Center VANTAGE core using their standard methods with ribosomal RNA depletion. For CUT&RUN, we made libraries of DNA fragments using the NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiple Oligos for Illumina.

treatment_protocol: All cells were treated with indicated amounts of DMSO, cis-ACBI1, or ACBI1 for 24 hours (ATAC-seq and RNA-seq). For CUT&RUN, no treatment was performed prior to collection.

tag: cell line

value: rhabdoid tumor cell line

value: No treatment


title: P6975_169

city: La Jolla

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
Sequence data for RNA-Seq were quality controlled using FastQC and summarized with multiQC
Trimmomatic was used to trim low-quality bases and sequencing adapters from the reads
The CHO-K1 reference genome was extended to incorporate the transgene sequences so that the transcripts of the heterologous secretome can be quantified
Reads were then quasi-mapped to the extended CHO-K1 genome and quantified with Salmon
Assembly: CHO-K1
Supplementary files format and content: CSV (comma-separated values) file with gene counts for each Sample
Supplementary files format and content: CSV (comma-separated values) file with TPMs for each Sample
Supplementary files format and content: CSV (comma-separated values) file with transgene abundance for each Sample

molecule: total RNA

organism: Cricetulus griseus

source_name: Icosagen QMCF

extract_protocol:
RNA was extracted using RNeasy plus Mini Kit (Qiagen) according to manufacturer’s guidelines and the quality of the isolated RNA was evaluated by BIOanalyzer 2100 (Agilent, Santa Clara, CA) using the Agilent RNA 6000 Nano Kit.
Library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103), according to manufacturer’s protocol

value: Icosagen QMCF

value: expressing BCHE


title: P6975_168

value: expressing HMGB1


title: Organoid AKP rep2

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Organoid AKP rep2

data_processing:
Reads were aligned to the mouse genome (GRCm39) using star (version 2.7.0e).
R (version 4.1.2) was used to perform the differential expression analyses. Count values were imported and processed using edgeR.
Expression values were normalized using the trimmed mean of M values (TMM) method and lowly-expressed genes (< 1 counts per million) were filtered out.
Differentially expressed genes were identified using linear models (Limma-Voom), and P values were adjusted for multiple comparisons by applying the Benjamini-Hochberg correction method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include count values for each sample

organism: Mus musculus

source_name: Colon

extract_protocol:
Cells were collected using TrypLE Express Enzyme, lysed in RLT buffer (QIAGEN, Catalog No. 74004), and the RNA was extracted using the QIAGEN RNeasy Micro Kit (QIAGEN, Catalog No. 74004) according to the manufacturer’s instructions.
Purified RNA was quality checked using a TapeStation 4200 (Agilent), and 500 ng were used for QuantSeq 3′ mRNA-Seq library construction according to the manufacturer’s instructions (Lexogen, Catalog No. 015.96).

value: Colon

value: Organoid AKP

value: AKP

value: OptoCre activation


title: shRNAseq in NC350 roots Rep2

city: Cold Spring Harbor

first: Jonathan

last: Cahn

state: NY

address: 1 Bungtown Rd

institute: CSHL

data_processing:
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to NC350 NAM genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to NC350 NAM with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: NC350 NAM
Supplementary files format and content: For RNAseq: count table on all NC350 NAM genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)

organism: Zea mays

source_name: root tips

growth_protocol: For collecting immature ears, NC350 maize inbreds were grown in the CSHL Uplands Farm field in the summer until they reached the appropriate stage. The plants were collected from the field, and 5-10mm primary and secondary ear primordia were dissected in the lab then frozen in LN2 and stored at -80°C. For pollen samples, shedding tassels of field-grown plants as described above were bagged in the evening and mature pollen was collected the following day. After passing through a sieve to remove anthers, pollen was frozen in LN2 and stored at -80°C. For endosperm samples, ears of field-grown plants were sib-pollinated and collected 15 DAP. Endosperm was dissected in the lab, frozen in LN2 and stored in -80°C. For root tips samples, seeds were germinated on wet paper towels in a Pyrex dish kept in the incubator at 26°C in continuous darkness. After 5 days, 1-3 mm root tips were cut off with a razor blade on ice, frozen in LN2 and stored at -80°C. For coleoptilar nodes samples, seeds were germinated in flats in a long day (8h dark/16h light) growth chamber, 27°C day and 24°C night, and light at 130 μmoles at the top flat. After 5 days, seedlings were unearthed and 5 mm sections around coleoptilar nodes were dissected on ice, frozen in LN2 and stored at -80°C.

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep Kit (Zymo Reserach).
RNAseq libraries were constructed from 1ug of total RNA with TruSeq Stranded Total RNA LT Kit, including RiboZero Plant depletion and oligo(dT) and random probes for cDNA synthesis. RAMPAGE libraries were constructed from 5ug total RNA following published protocol (Batut and Gingeras 2013) using RiboMinus Plant depletion. shRNAseq libraries were constructed from 5ug of total RNA using TruSeq Small RNA protocol after RiboMinus Plant depletion and size selection of 100 to 205nt with BluePippin (Sage Science).

value: root tips

tag: inbred line

value: WT

tag: developmental stage

value: 5 DAG


title: CUT&RUN A204 H3K4me1 rep1


title: P6975_167

value: expressing LGALS3


title: P6975_166

value: expressing KL


title: shRNAseq in NC350 roots Rep1


title: 24_siPKP2_4_D8  [V24]

city: South San Francisco

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

data_processing:
Adapter trimming by FASTP (ver. 0.23.3)
Read alignment by Salmon (ver. 1.8.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 107
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT

source_name: iCell Cardiomyocytes2

extract_protocol:
Total RNA was extracted from iPSC-CMs using the RNeasy Mini or Universal Mini Kit (Qiagen Sciences, 74106 and 73404), cDNA synthesized (Invitrogen SuperScript III First-Strand Synthesis SuperMix for RT) and analyzed by qPCR using Taqman probes to human genes.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina Inc.. RNA quality control was performed before library prep using Agilent TapeStation instrument. The RNA libraries were prepared using a TruSeq RNA Library Prep Kit (Illumina), which also removes ribosomal RNA. The libraries were sequenced as 100 base pair single-end reads using Illumina NovaSeq 6000 using V1.5 reagent kit on S1 flow cell with an average of 40.37 million reads per sample.

treatment_protocol: TN-401 or AAV9:PKP2 was given as a single dose via retro-orbital injection 1 week before animals were induced with tamoxifen.  HBSS, as vehicle control, was injected to WT or non-AAV treated Pkp2-cKO animals.  Tamoxifen injection activates Cre recombinase in Cre-positive animals and induces homozygous deletion of Pkp2 gene.  Pkp2fl/fl Cre-negative littermates were used as controls.

value: iCell Cardiomyocytes2

value: Cardiomyocyte


title: Organoid AKP rep1

description: Organoid AKP rep1


title: shRNAseq in NC350 pollen Rep2

source_name: pollen

value: pollen

value: mature pollen


title: P6975_165

value: expressing VIP


title: Control rep5

description: Control rep5

value: Control

value: Non-induced AKP

value: No treatment (control)


title: 22_siPKP2_2_D8 [V22]


title: Organoid AKP rep4

description: Organoid AKP rep4

value: Colon


title: shRNAseq in NC350 pollen Rep1


title: 21_siPKP2_1_D8 [V21]


title: P6975_164

value: Icosagen QMCF

value: expressing PPY


title: 20_siNeg_D8 [V20]

value: siNeg


title: Control rep3

description: Control rep3


title: shRNAseq in NC350 endosperm Rep2

source_name: endosperm

value: endosperm

value: 15 DAP


title: P6975_162

value: expressing SHH


title: shRNAseq in NC350 endosperm Rep1

value: WT


title: Organoid AKP rep3

description: Organoid AKP rep3

value: Organoid AKP

value: AKP

value: OptoCre activation


title: P6975_163

value: expressing PAMR1


title: 18_siPKP2_4_D6 [V18]

value: iCell Cardiomyocytes2

value: Cardiomyocyte


title: Control rep2

description: Control rep2

value: Control


title: Control rep4

description: Control rep4

value: Non-induced AKP


title: shRNAseq in NC350 ears Rep2

source_name: immature ears

value: immature ears


title: shRNAseq in NC350 ears Rep1


title: Control rep1

description: Control rep1

value: Colon

value: No treatment (control)


title: P6975_160

value: Icosagen QMCF

value: expressing PCSK1


title: 16_siPKP2_2_D6 [V16]


title: 17_siPKP2_3_D6 [V17]


title: 23_siPKP2_3_D8 [V23]


title: P6975_159

value: expressing FURIN_1


title: shRNAseq in NC350 coleoptilar node Rep2

source_name: coleoptilar nodes

value: coleoptilar nodes

value: 5 DAG


title: 15_siPKP2_1_D6 [V15]

value: WT


title: Control rep6

description: Control rep6


title: shRNAseq in NC350 coleoptilar node Rep1


title: 14_siNeg_D6 [V14]

value: siNeg


title: P6975_157

value: expressing AGPS


title: P6975_158

value: expressing ST6GAL1


title: RAMPAGE in NC350 roots Rep2

library_source: other

data_processing:
library strategy: RAMPAGE
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to NC350 NAM genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to NC350 NAM with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: NC350 NAM
Supplementary files format and content: For RNAseq: count table on all NC350 NAM genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)

molecule: other

value: root tips


title: 12_siPKP2_4_D4 [V12]

value: iCell Cardiomyocytes2


title: P6975_155

value: expressing FGFBP3


title: P6975_161

value: expressing FN1


title: P6975_156

value: expressing NCF1


title: 11_siPKP2_3_D4 [V11]

value: Cardiomyocyte


title: 10_siPKP2_2_D4 [V10]


title: RAMPAGE in NC350 pollen Rep2

value: pollen

value: mature pollen


title: 9_siPKP2_1_D4 [V9]


title: RAMPAGE in NC350 roots Rep1


title: RAMPAGE in NC350 endosperm Rep2

value: endosperm

value: 15 DAP


title: RAMPAGE in NC350 pollen Rep1


title: P6975_154

value: Icosagen QMCF

value: expressing SVEP1


title: 8_siNeg_D4 [V8]


title: P6975_152

value: expressing IL22


title: P6975_153

value: expressing ASGR1


title: RAMPAGE in NC350 ears Rep2

value: immature ears

value: WT


title: P6975_151

value: expressing HSP90B1


title: M337V-Rep2

city: Sangareddy

first: Ashish

last: Misra

state: Telangana

address: Kandi

department: Biotechnology

country: India

institute: Indian Institute of Technology Hyderabad

description:
Patient derived induced pluripotent Cell Line with M337V TDP-43 mutation
TDP-43(M337V) mutant cell line

data_processing:
Images were analyzed using OLB 1.9 and CASAVA_v1.8.2
TopHat v2.0.9 (bowtie2/2.1.0) was used to map the sequences to human genome hg19
Reads counts were processed by DEXSeq v 1.10.6
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include exon level count values for each Sample

source_name: iPS Cell Line

extract_protocol:
RNA was isolated from TDP-43 (WT) and TDP-43(M337V) ALS iPSCs using RNeasy mini kit (qiagen) according to manufacturer's protocol
Library was prepared using Illumina TrueSeq kit

treatment_protocol: Cells were cultured in mTeSR1 media (STEMCELL Technologies) on matrigel-coated plates.

tag: genotype/variation

value: M337V TDP-43 mutation


title: M337V-Rep1


title: 5_siPKP2_3_D2 [V5]

value: iCell Cardiomyocytes2


title: P6975_150

value: expressing MAN2B1


title: WT-Rep2

description:
Patient derived induced pluripotent Cell Line with WT TDP-43 mutation
TDP-43 WT iPS cel line

value: WT TDP-43 mutation


title: RAMPAGE in NC350 ears Rep1


title: 4_siPKP2_2_D2 [V4]


title: RAMPAGE in NC350 coleoptilar node Rep2

value: coleoptilar nodes

value: 5 DAG


title: WT-Rep1


title: P6975_148

value: expressing MFAP4


title: P6975_149

value: expressing H6PD


title: RAMPAGE in NC350 coleoptilar node Rep1


title: FABP5 hKO

city: New Haven

last: Sun

address: 10 Amistad St

institute: Yale University

data_processing:
Reads were aligned against mouse genome mm9 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R (version 3.0) using Seurat v3. Cells were filtered for more than 500 genes detected in each cell, 20,000 or less total number of molecules detected within a cell and 5% or less mitochondrial gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test, and clusters were calculated with 30 PCs
Differential expression analysis was done using wilcox
Assembly: mmp10
Supplementary files format and content: Cell-gene-barcode matrices

source_name: Tumor

growth_protocol: 6-8 weeks old littermates WT and FABP5hKO mice were injected with tamoxifen (100mg/Kg every 3 days, after 16h fasting) five times. 2 weeks after last tamoxifen injection, mice were fed a CD-HFD for 15 months.

extract_protocol:
Singlle-cell suspensions were obtained from a pull of 2-3 freshly isolated HCC tumor. Tissue digestion was performed by digesting in collagenase at 37 degrees for 1 hour, followed by passing through a 40um filter to generate single cell suspension.
Single cells were encapsulated into droplets and processed following standard manufacturer’s specification, using 10X Genomics GemCode technology. Cells were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMS) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the single-Cell 3’ Regent Kits version 2 (10X Genomics). Libraries were sequenced on an Illumina HiSeq 4000 as 2x 100 paired-end reads.

tag: strain

value: Liver

tag: genetype

value: FABP5 hKO

value: 15month CD-HFD


title: 2_siNeg_D2 [V2]

value: Cardiomyocyte

value: siNeg


title: RNAseq in NC350 roots Rep2

description:
RNAseq_counts_NC350_NAM.txt
NC350_roots_RNAseq_Rep2

value: root tips


title: P6975_147

value: Icosagen QMCF

value: expressing CTF1


title: RAMPAGE in NC350 endosperm Rep1

value: endosperm

value: WT

value: 15 DAP


title: WT


title: 6_siPKP2_4_D2  [V6]

value: iCell Cardiomyocytes2


title: MCF7/CAF, 24h, rep D

city: Lund

first: Kristian

last: Pietras

address: Sheelevägen 2

department: Division of Translational Cancer Research

country: Sweden

institute: Lund University

data_processing:
Sequencing and processing was performed by the Center for Translational Genomics, Lund.
Demultiplexing raw data to FASTQ files was performed using bcl2fastq (Illumina).
HISAT2 was used to align the reads to the human reference genome.
StringTie was used for the assembly of full transcripts and quantification of the expression levels at the gene and transcript level.
Assembly: GRCh38. Reference genome and annotation (GTF file) were downloaded from the Ensemble database release 94.
Supplementary files format and content: Comma-separated values file including raw counts for all samples.
Supplementary files format and content: Comma-separated values file including normalized counts (TPM) for all samples.

growth_protocol: MCF7 cells were seeded in Transwells and CAF2 in 6-well plates in a 1:3 ratio in growth medium overnight. MCF7 cells were starved for 24 hours before adding Transwells to the CAF2 for a further 2 days.

extract_protocol:
RNeasy kit (Qiagen #74106)
TruSeq Stranded mRNA Library Prep

treatment_protocol: Cultures were stimulated with 100 nM Estradiol at 6 and 24 hours before all being lysed in RLT at the same endpoint.

value: Breast cancer cell line

value: precultured with CAFs (48h) and estrogen stimulation (24h)


title: P6975_146

value: expressing FCN2


title: RNAseq in NC350 pollen Rep2

description:
RNAseq_counts_NC350_NAM.txt
NC350_pollen_RNAseq_Rep2

value: pollen

value: mature pollen


title: RNAseq in NC350 roots Rep1

description:
RNAseq_counts_NC350_NAM.txt
NC350_roots_RNAseq_Rep1

value: 5 DAG


title: P6975_145

value: expressing C6


title: MCF7/CAF, 24h, rep C


title: TSC_08, scRNA-seq

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19-A1038

department: Department of Biomedicine

country: Estonia

institute: Institute of Biomedicine and Translational Medicine

data_processing:
The raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline with the GRCh38 reference. The scRNA-seq alignment and quantification were carried out on the Tartu University High Performance Computing Center Rocket cluster.
Assembly: GRCh38

extract_protocol:
PBMCs from four patients and four controls were thawed slowly using RPMI 1640 media (Corning) supplemented with Penicillin-Streptomycin (Corning, cat. 30-002-CI) and Fetal Bovine Serum (Gibco, cat. 10270106).
After washing with media, cells were stained with antibodies against CD3, CD25, CD14, CD56, CD127, CD8a, CD21, CD4 and CD19. Tregs were sorted out as CD4+CD25+CD127low cells using a Sony MA900 Cell Sorter (Sony Biotechnology, USA) and counted using Luna FL Automated Cell Counter and Acridine Orange/ Propidium Iodide Stain (Logos Biosystems). Two thousand carefully counted Tregs were loaded onto a Chromium controller and cDNA was generated using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, cat. 1000128) and Chromium Next GEM Chip G Single Cell Kit (10X Genomics, cat. 1000127) according to the manufacturer’s instructions.

value: peripheral blood

value: Healthy


title: TSC_07, scRNA-seq


title: 1 - CH Pat.31

type: RNA

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);  Affymetrix Genechip® fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Arrays were scanned using Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (4.0.0) using Affymetrix default analysis settings for generation of CEL-files.

label: biotin

source_name: Bone-marrow stromal cells derived cartilage discs

label_protocol: Samples were labeled using Affymetrix WT PLUS Reagent Kit P/N 703147 Rev5, (Cat No. 902280);

growth_protocol: Primary human bone marrow-derived BMSCs were isolated and cultivated. The cell culture medium was Dulbecco’s modified Eagle’s medium (DMEM) low glucose (Sigma Aldrich, D5546, USA) with 10% fetal calf serum ‘superior’ (Biochrom, S0615, Germany), 2 mM GlutaMAX™ (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), penicillin (10 U/mL)/streptomycin (10 µg/mL) (Biochrom, Germany). Sub-cultured cells were seeded at 2400 cells/cm2 in cell culture flasks. Cells were counted by using CasyTT for standard cell culture and cryopreserved until further use.

extract_protocol: Ribonucleic acid (RNA) was isolated from snap-frozen cartilage organoid discs using RNeasy Mini kit (Qiagen) . Discs were homogenized prior RNA extraction with a Minilys homogenizer using ceramic beads (Precellys lysing kit; Bertin Technologies). RNA concentrations and quality were assessed using a Bioanalyzer (Agilent)

treatment_protocol: Chondrogenic Differentiation  Chondrocyte phenotype was determined under re-differentiation. For chondrogenic re-differentiation, a pellet culture assay with chondrogenic differentiation media (ChM) was performed for 21 days in a 96 deep-well format. Briefly, 3 × 105 cells per pellet were used, and cultured in ChM composed of high glucose DMEM including L-glutamine (Sigma Aldrich, D6546, USA), dexamethasone (0.1 µM, Sigma Aldrich, D2915, USA), L-ascorbic acid (50 µg/mL, Sigma Aldrich, A8960, USA), L-proline (40 µg/mL, Sigma Aldrich, P5607, St. Louis, MO, USA) sodium pyruvate (0.1 mg/mL, AppliChem, A4859, Darmstadt, Germany) ITS (6.25 µg/mL, Sigma Aldrich, I1884, St. Louis, MO, USA), BSA (1.25 mg/mL, Sigma Aldrich, A9418, St. Louis, MO, USA), linoleic acid (5.35 µg/mL, Sigma Aldrich, L1012, St. Louis, MO, USA), penicillin (10 U/mL)/streptomycin (10 µg/mL) (Biochrom, A2213, Berlin, Germany) and recombinant human TGF-ß1 (10 ng/mL, Peprotech, 100-21-5, Cranbury, NJ, USA). Negative controls were cultured in the same medium but without TGF-ß1. Media change was performed every 3–4 days. Chondrogenic phenotype was determined by proteoglycan assay, type II collagen immunostaining, Alcian blue staining, as well as by expression of type II collagen, type X collagen, MMP13, Sox9 and aggrecan mRNAs.

value: Bone-marrow stromal cells


title: 3 - CH Pat.12


title: 8 - CH Pat.20


title: TSC_06, scRNA-seq


title: TSC_05, scRNA-seq


title: 2 - CH Pat.18


title: RNAseq in NC350 endosperm Rep2

description:
RNAseq_counts_NC350_NAM.txt
NC350_endosperm_RNAseq_Rep2


title: MCF7 alone, 24h, rep D

value: estrogen stimulation (24h)


title: RNAseq in NC350 pollen Rep1

description:
RNAseq_counts_NC350_NAM.txt
NC350_pollen_RNAseq_Rep1


title: P6975_144

value: Icosagen QMCF

value: expressing ENG


title: TSC_04, scRNA-seq


title: RNAseq in NC350 endosperm Rep1

description:
RNAseq_counts_NC350_NAM.txt
NC350_endosperm_RNAseq_Rep1

value: endosperm


title: P6975_143

value: expressing PINLYP


title: P6975_142

value: expressing CXCL5


title: MCF7/CAF, 6h, rep D

value: WT

value: precultured with CAFs (48h) and estrogen stimulation (6h)


title: 3_siPKP2_1_D2 [V3]

value: iCell Cardiomyocytes2

value: Cardiomyocyte


title: MCF7 alone, 24h, rep C

description: MCF_24h_ C

value: Breast cancer cell line


title: RNAseq in NC350 ears Rep2

description:
RNAseq_counts_NC350_NAM.txt
NC350_ears_RNAseq_Rep2

value: immature ears


title: TSC_03, scRNA-seq


title: TSC_02, scRNA-seq


title: P6975_141

value: expressing COL2A1


title: P6975_140

value: expressing PZP


title: RNAseq in NC350 ears Rep1

description:
RNAseq_counts_NC350_NAM.txt
NC350_ears_RNAseq_Rep1


title: RNAseq in NC350 coleoptilar node Rep2

description:
RNAseq_counts_NC350_NAM.txt
NC350_cn_RNAseq_Rep2

value: coleoptilar nodes

value: 5 DAG


title: P6975_139

value: expressing EPYC


title: P6975_138

value: expressing CCL21


title: RNAseq in NC350 coleoptilar node Rep1

description:
RNAseq_counts_NC350_NAM.txt
NC350_cn_RNAseq_Rep1


title: MCF7 alone, 6h, rep C

value: estrogen stimulation (6h)


title: MCF7/CAF, 0h, rep D

value: MCF7 precultured with CAFs (for 48 hours)


title: RNA-seq TTC-549 cis-ACBI1 rep2

data_processing:
CUT&RUN analysis: CUT&RUNTools was used for CUNT&RUN data analysis including adapter trimming, alignment, duplication marking, and peak calling. DiffBind was then applied to get consensus peaks for H3K4me3 and H3K27ac
ATAC-seq anaysis: After adaptor trimming by Cutadapt, ATAC-seq reads were aligned to the human genome hg19 using Bowtie2. Peaks were called using MACS2 with q-value of 0.05. Peaks present in at least two replicates per condition were included, and peaks identified across conditions were combined into a final peak set and ATAC-seq read counts were calculated for the final peak set. Differential enriched peaks were identified using DiffBind with a FDR < 0.05
RNA-seq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
Assembly: hg19
Supplementary files format and content: CUT&RUN: peak file for each condition
Supplementary files format and content: ATAC-seq: peak file for each condition
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample

value: rhabdoid tumor cell line

value: 250 nM cis-ACBI1


title: P6975_137

value: Icosagen QMCF

value: expressing CD6


title: MCF7/CAF, 0h, rep C

value: WT


title: RNA-seq TTC-549 cis-ACBI1 rep1


title: P6975_136

value: expressing NAMPT


title: shRNAseq in B73 roots Rep1

data_processing:
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to B73 NAM genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to B73 NAM with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: B73 NAM
Supplementary files format and content: For RNAseq: count table on all B73 NAM genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)

growth_protocol: For collecting immature ears, B73 maize inbreds were grown in the CSHL Uplands Farm field in the summer until they reached the appropriate stage. The plants were collected from the field, and 5-10mm primary and secondary ear primordia were dissected in the lab then frozen in LN2 and stored at -80°C. For pollen samples, shedding tassels of field-grown plants as described above were bagged in the evening and mature pollen was collected the following day. After passing through a sieve to remove anthers, pollen was frozen in LN2 and stored at -80°C. For endosperm samples, ears of field-grown plants were sib-pollinated and collected 15 DAP. Endosperm was dissected in the lab, frozen in LN2 and stored in -80°C. For root tips samples, seeds were germinated on wet paper towels in a Pyrex dish kept in the incubator at 26°C in continuous darkness. After 5 days, 1-3 mm root tips were cut off with a razor blade on ice, frozen in LN2 and stored at -80°C. For coleoptilar nodes samples, seeds were germinated in flats in a long day (8h dark/16h light) growth chamber, 27°C day and 24°C night, and light at 130 μmoles at the top flat. After 5 days, seedlings were unearthed and 5 mm sections around coleoptilar nodes were dissected on ice, frozen in LN2 and stored at -80°C.

value: root tips


title: MCF7 alone, 0h, rep D

value: Breast cancer cell line

value: MCF7 alone (control)


title: MCF7/CAF, 6h, rep C

value: precultured with CAFs (48h) and estrogen stimulation (6h)


title: TSC_01, scRNA-seq

value: peripheral blood


title: RNA-seq TTC-549 ACBI1 rep3

value: 250 nM ACBI1


title: MCF7 alone, 6h, rep D


title: shRNAseq in B73 pollen Rep1

value: pollen

value: mature pollen


title: RNA-seq TTC-549 ACBI1 rep2


title: MCF7 alone, 0h,  rep C


title: RNA-seq TTC-549 ACBI1 rep1


title: shRNAseq in B73 pollen Rep2


title: P6975_134

value: expressing RETN


title: shRNAseq in B73 endosperm Rep2

value: endosperm

value: 15 DAP


title: MCF7/CAF, 24h, rep A

value: precultured with CAFs (48h) and estrogen stimulation (24h)


title: RNA-seq TTC-549 cis-ACBI1 rep3

value: rhabdoid tumor cell line

value: 250 nM cis-ACBI1


title: MCF7/CAF, 24h, rep B

description: CAF_24h_ B


title: P6975_133

value: Icosagen QMCF

value: expressing SERPINA5


title: RNA-seq TTC-549 DMSO rep3

value: DMSO


title: shRNAseq in B73 roots Rep2

value: root tips

value: WT

value: 5 DAG


title: RNA-seq TTC-549 DMSO rep2


title: shRNAseq in B73 endosperm Rep1


title: shRNAseq in B73 ears Rep2

value: immature ears


title: MCF7 alone, 24h, rep B

value: Breast cancer cell line

value: estrogen stimulation (24h)


title: P6975_132

value: expressing SERPINA6


title: P6975_131

value: expressing SERPINE2


title: P6975_135

value: expressing LACTB


title: MCF7 alone, 24h, rep A


title: shRNAseq in B73 ears Rep1


title: MCF7/CAF, 6h, rep B

value: precultured with CAFs (48h) and estrogen stimulation (6h)


title: P6975_130

value: expressing AGA


title: RNA-seq A204 cis-ACBI1 rep3


title: shRNAseq in B73 coleoptilar node Rep2

value: coleoptilar nodes


title: P6975_129

value: expressing IL17B


title: MCF7/CAF, 6h, rep A


title: P6975_128

value: expressing BTBD17


title: P6975_127

value: Icosagen QMCF

value: expressing MMP9


title: MCF7 alone, 6h, rep B

value: estrogen stimulation (6h)


title: RNA-seq A204 cis-ACBI1 rep2

value: rhabdoid tumor cell line

value: 250 nM cis-ACBI1


title: RNA-seq A204 cis-ACBI1 rep1


title: MCF7 alone, 6h, rep A

value: WT


title: shRNAseq in B73 coleoptilar node Rep1

value: 5 DAG


title: RAMPAGE in B73 roots Rep2

data_processing:
library strategy: RAMPAGE
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to B73 NAM genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to B73 NAM with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: B73 NAM
Supplementary files format and content: For RNAseq: count table on all B73 NAM genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)

value: root tips


title: MCF7/CAF, 0h, rep B

value: Breast cancer cell line

value: precultured with CAFs (48h)


title: RNA-seq A204 ACBI1 rep2

value: 250 nM ACBI1


title: P6975_126

value: expressing CTSL


title: P6975_125

value: expressing PROC


title: RAMPAGE in B73 roots Rep1


title: RAMPAGE in B73 pollen Rep2

value: pollen

value: mature pollen


title: P6975_124

value: expressing ITIH4


title: RAMPAGE in B73 pollen Rep1


title: RNA-seq A204 ACBI1 rep1


title: RNA-seq TTC-549 DMSO rep1

value: DMSO


title: MCF7 alone, 0h, rep B

value: alone (control)


title: MCF7/CAF , 0h, rep A


title: RAMPAGE in B73 endosperm Rep2

value: endosperm

value: 15 DAP


title: RNA-seq A204 DMSO rep3

value: rhabdoid tumor cell line


title: MCF7 alone , 0h (no estrogen stimulation), rep A


title: RNA-seq A204 DMSO rep2


title: RAMPAGE in B73 endosperm Rep1


title: P6975_122

value: Icosagen QMCF

value: expressing ADIPOQ


title: RNA-seq A204 ACBI1 rep3


title: RNA-seq A204 DMSO rep1


title: RAMPAGE in B73 ears Rep2

value: immature ears

value: WT


title: ATAC-seq JMU-RTK-2 ACBI1 rep3

value: 2.5 μM ACBI1


title: HDMBO3_A485_6H_bio_rep4

city: Memphis

first: Brian

middle: J

last: Abraham

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Built a reference genome sequence that contains the sequences of the ERCC spike-in probes as additional chromosomes.
Sequencing reads were aligned to the hg19-ERCC reference index with default parameters by Hisat2, and the resulting aligned reads file was converted to a sorted, indexed BAM file using Samtools.
Created a positional gene reference GTF from RefSeq (hg19) by adding GTF-formatted positions of ERCC probes. Quantified coverage of all genes using Htseq-count.
Assembly: hg19
Supplementary files format and content: tab-delimited text files that contain gene name and raw counts for each sample

growth_protocol: HDMB03 and MB002 cells were cultured in neurosphere media in low-attachment flasks, in standard conditions of 37°C, and 5% humidified oxygen.

extract_protocol:
Cells were spun at 1200rpm x 5 minutes at 4°C and counted using trypan blue exclusion. 250,000 cells were resuspended in 1mL of TRIZOL, including relevant concentrations of ERCC spike in mix 1 (Thermo-Fisher), normalized to cell number. RNA was extracted using the TRIZOL extraction protocol, with DNAse 1 treatment (Thermo-Fisher Scientific), prior to resuspension in sterile, nuclease free water for library preparation.
Total RNA was subjected to ribosomal RNA depletion prior to library preparation using the TruSeq Stranded Total Library Prep Gold Kit (Illumina).

treatment_protocol:
500,000 cells were treated with relevant compound (JQ1, A485, CCS1477 or DMSO) at the day 3 IC50 dose determined by cell-titer glo analysis, for 6h in neurosphere media.
N/A

value: medulloblastoma cells


title: RAMPAGE in B73 ears Rep1


title: ATAC-seq JMU-RTK-2 ACBI1 rep2


title: P6975_120

value: expressing NXPH1


title: P6975_119

value: expressing SRPX


title: HDMBO3_CCS1477_6hr_bio_rep4


title: RAMPAGE in B73 coleoptilar node Rep2

value: coleoptilar nodes

value: 5 DAG


title: ATAC-seq JMU-RTK-2 ACBI1 rep1


title: P6975_118

value: expressing OIT3


title: ATAC-seq JMU-RTK-2 DMSO rep3


title: RAMPAGE in B73 coleoptilar node Rep1


title: HDMBO3_A485_6H_bio_rep3


title: P6975_117

value: expressing ACVR2A


title: P6975_123

value: expressing COL1A2


title: RNAseq in B73 roots Rep1

description:
B73_roots_RNAseq_Rep1
RNAseq_counts_B73_NAM.txt

value: root tips


title: ATAC-seq JMU-RTK-2 DMSO rep2

value: DMSO


title: P6975_116

value: expressing CER1


title: RNAseq in B73 pollen Rep2

description:
B73_pollen_RNAseq_Rep2
RNAseq_counts_B73_NAM.txt

value: pollen

value: mature pollen


title: HDMBO3_CCS1477_6hr_bio_rep3


title: P6975_115

value: Icosagen QMCF

value: expressing EDDM3B


title: HDMBO3_JQ1_6hr_bio_rep4

value: JQ1 6h


title: P6975_121

value: expressing BSG


title: ATAC-seq TTC-549 ACBI1 rep3

value: rhabdoid tumor cell line

value: 250 nM ACBI1


title: HDMBO3_DMSO_bio_rep3

value: medulloblastoma cells


title: RNAseq in B73 pollen Rep1

description:
B73_pollen_RNAseq_Rep1
RNAseq_counts_B73_NAM.txt

value: WT


title: P6975_114

value: expressing ALB


title: HDMBO3_DMSO_bio_rep4


title: P6975_113

value: expressing NCAM1


title: RNAseq in B73 roots Rep2

description:
B73_roots_RNAseq_Rep2
RNAseq_counts_B73_NAM.txt

value: 5 DAG


title: HDMBO3_A485_6H_bio_rep2


title: ATAC-seq TTC-549 ACBI1 rep2


title: RNAseq in B73 endosperm Rep2

description:
B73_endosperm_RNAseq_Rep2
RNAseq_counts_B73_NAM.txt

value: endosperm

value: 15 DAP


title: RNAseq in B73 endosperm Rep1

description:
B73_endosperm_RNAseq_Rep1
RNAseq_counts_B73_NAM.txt


title: HDMBO3_JQ1_6hr_bio_rep3


title: P6975_112

value: expressing FST


title: ATAC-seq TTC-549 ACBI1 rep1


title: HDMBO3_JQ1_6hr_bio_rep2


title: HDMBO3_CCS1477_6hr_bio_rep2


title: ATAC-seq TTC-549 DMSO rep3

value: DMSO


title: P6975_111

value: expressing ANGPTL2


title: RNAseq in B73 ears Rep2

description:
B73_ears_RNAseq_Rep2
RNAseq_counts_B73_NAM.txt

value: immature ears


title: HDMBO3_DMSO_bio_rep2


title: P6975_110

value: Icosagen QMCF

value: expressing CD209


title: RNAseq in B73 ears Rep1

description:
B73_ears_RNAseq_Rep1
RNAseq_counts_B73_NAM.txt


title: ATAC-seq TTC-549 DMSO rep2


title: ATAC-seq JMU-RTK-2 DMSO rep1


title: MBOO2_A485_6H_bio_rep3


title: RNAseq in B73 coleoptilar node Rep2

description:
B73_cn_RNAseq_Rep2
RNAseq_counts_B73_NAM.txt

value: coleoptilar nodes


title: ATAC-seq A204 ACBI1 rep2

value: 2.5 μM ACBI1


title: MBOO2_JQ1_6hr_bio_rep3

value: JQ1 6h


title: P6975_109

value: expressing WFDC12


title: RNAseq in B73 coleoptilar node Rep1

description:
B73_cn_RNAseq_Rep1
RNAseq_counts_B73_NAM.txt


title: P6975_108

value: expressing CHIT1


title: ATAC-seq A204 ACBI1 rep1

value: rhabdoid tumor cell line


title: MBOO2_CCS1477_6hr_bio_rep3

value: medulloblastoma cells


title: P6975_107

value: expressing NXPH4


title: sorted NeuN- nuclei from pooled prefrontal cortex white matter from middle aged (10 m) Olig2-SRF cKO male and female

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

description: 10x Genomics

data_processing:
Conversion to FASTQ using bcl2fastq v2.20.0.422.
Genome mapping with CellRanger v7.0.0 and reference refdata-gex-mm10-2020-A to generate cell-to-gene count matrices.
Contaminating ambient RNA removal using SoupX v1.6.2 to yield strained and filtered cell-to-gene matrices.
Assembly: mm10
Supplementary files format and content: Output of Cellranger count, respective SoupX routine; For each sample nine files are provided containing the raw, filtered, and strained (SoupX) cell-barcodes, the mapped reference features, and the raw counts: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.

molecule: nuclear RNA

source_name: brain

growth_protocol: Olig2-CRE (cKO) and non CRE (Floxed) mice were grown 10 months without any treatments

extract_protocol:
Prefrontal cortex was punched out using a 1.5mm biopsy punch (Hahn et al., 2023). Nuclei from two punches (one male and one female)  h were isolated with EZ Prep lysis buffer (Sigma, NUC-101) on ice following the manufacturer protocol. After removing supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235) and spun at 500g for 5min. After removing supernatant, nuclei were stained with anti-NeuN and anti-Olig2 and Hoechst. NeuN negative nuclei were sorted on a Sony800 to tubes.
Nuclei were sorted and loaded on a standard Chromium Controller (10X Genomics) according to manufacturer protocols. We applied 12 PCR cycles to generate cDNA. Library construction was conducted using Chromium Single Cell 3’ Library Construction Kit v3  using 14 PCR cycles for library generation (10X Genomics). All reaction and quality control steps were carried out according to the manufacturer’s protocol and with recommended reagents, consumables, and instruments. Quality control of cDNA and libraries was conducted using a TapeStation (Agilent) at the Stanford Knight Initiative core.

treatment_protocol: Male and female mice were euthanized, perfused  and brains were flash frozen.

value: brain

value: Neun negative nuclei

value: cKO

tag: age

value: 10 months


title: ATAC-seq A204 DMSO rep3

value: DMSO


title: MBOO2_DMSO_bio_rep3


title: P6975_106

value: expressing NXPH3


title: MBOO2_A485_6H_bio_rep2


title: SRF-KO OL replicate 4

data_processing:
Raw sequencing files were demultiplexed and known adapters were trimmed with bcl2fastq. Data analysis of raw sequencing data was performed using the nextflow-core RNA-seq pipeline v3.0. Briefly, the core workflow of the pipeline maps filtered reads against the species reference genome using STAR and computes transcript counts using RSEM. For nuclear RNA-seq data, a custom reference genome was created where exon sequences in GTF files were modified to include all introns per transcript and used for the mapping instead.
Assembly: For mouse and rat sequencing data the reference genome GRCm38 and Rnor 6.0 provided by Illumina igenomes were used, respectively. All gene annotations were based on the Ensembl database.

growth_protocol: Mouse OPCs were purified from brains of SRF floxed by immunopanning as described above for rat OPCs.

extract_protocol:
For RNA extraction, cells were scraped with RLT buffer and RNA was extracted with the RNeasy Plus Micro kit (Qiagen, 74034).
cDNA and library synthesis were done inhouse using the Smart-seq2 protocol as previously described 14 (detailed protocol at https://doi-org.laneproxy.stanford.edu/10.17504/protocols.io.2uvgew6) with several modifications.
Libraries were pooled and sequenced on a Nextseq550 sequencer (Illumina) using single end 63bp for Read 1 and 12bp for index 1 with a high output 75bp kit (20024906, Illumina).  Libraries were sequenced to a depth of at least >10 million reads per sample.

treatment_protocol: On day 3 of the culture, SRF-f/f OPCs were split and plated in 12-well plates at a density of 30K per well. When the cells were in suspension in proliferation media before plating, 1*1010 viral genomes of AAV DJ-CMV eGFP-deleted cre (GVVC-AAV-62) or AAV DJ-CMV eGFP-cre (GVVC-AAV-63) (both generated by the Stanford Gene Vector and Virus Core). The following day, media was fully replaced and 48hrs after infection media was removed and the plate was flash frozen on dry ice and kept in -80 deg. For CRE induction in oligodendrocytes, on day 5 after isolation, SRF-f/f OPCs were plated at a density of 35,000 cells per well in a 12-well plate. On day 6, cells were infected with 5.6-6.6 x 10^8 viral units of a lentivirus-CRE-IRES-GFP or GFP control. On day 7, media was replaced to differentiation media and on day 3 of differentiation the media was removed and plates were frozen at -80.

value: primary mouse OPC culture allowed to differentiate fro 3 days

value: SRF-floxed/floxed mice

value: lentivirus-CRE-IRES-GFP control


title: sorted NeuN- nuclei from pooled prefrontal cortex white matter from middle aged (10 m) floxed male and female

description: 10x Genomics

value: flox


title: ATAC-seq A204 DMSO rep2


title: P6975_105

value: Icosagen QMCF

value: expressing NXPH2


title: MBOO2_JQ1_6hr_bio_rep2

value: JQ1 6h


title: ATAC-seq A204 DMSO rep1


title: CUT&RUN TTC-549 IgG rep2

data_processing:
library strategy: CUT&RUN
CUT&RUN analysis: CUT&RUNTools was used for CUNT&RUN data analysis including adapter trimming, alignment, duplication marking, and peak calling. DiffBind was then applied to get consensus peaks for H3K4me3 and H3K27ac
ATAC-seq anaysis: After adaptor trimming by Cutadapt, ATAC-seq reads were aligned to the human genome hg19 using Bowtie2. Peaks were called using MACS2 with q-value of 0.05. Peaks present in at least two replicates per condition were included, and peaks identified across conditions were combined into a final peak set and ATAC-seq read counts were calculated for the final peak set. Differential enriched peaks were identified using DiffBind with a FDR < 0.05
RNA-seq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
Assembly: hg19
Supplementary files format and content: CUT&RUN: peak file for each condition
Supplementary files format and content: ATAC-seq: peak file for each condition
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample

value: No treatment


title: MBOO2_CCS1477_6hr_bio_rep2


title: SRF-KO OL replicate 2


title: CUT&RUN TTC-549 IgG rep1

value: rhabdoid tumor cell line


title: P6975_103

data_processing:
Sequence data for RNA-Seq were quality controlled using FastQC and summarized with multiQC
Trimmomatic was used to trim low-quality bases and sequencing adapters from the reads
The CHO-K1 reference genome was extended to incorporate the transgene sequences so that the transcripts of the heterologous secretome can be quantified
Reads were then quasi-mapped to the extended CHO-K1 genome and quantified with Salmon
Assembly: CHO-K1
Supplementary files format and content: CSV (comma-separated values) file with gene counts for each Sample
Supplementary files format and content: CSV (comma-separated values) file with TPMs for each Sample
Supplementary files format and content: CSV (comma-separated values) file with transgene abundance for each Sample

value: expressing PGLYRP4


title: MBOO2_DMSO_bio_rep2

value: medulloblastoma cells


title: ATAC-seq TTC-549 DMSO rep1


title: SRF-KO OL replicate 1

value: brain


title: P6975_102

value: expressing FCER2


title: MBOO2_A485_6H_bio_rep1


title: P6975_101

value: expressing GNAS


title: CUT&RUN TTC-549 H3K27ac rep2


title: MBOO2_JQ1_6hr_bio_rep1


title: control OL replicate 4

value: lentivirus-GFP control


title: CUT&RUN TTC-549 H3K27ac rep1


title: control OL replicate 3


title: skin, non-irradiated, rep3

city: Qingdao

first: Chengwen

last: Dong

address: Jiangsu road 16

country: China

institute: affiliated hospital of Qingdao University

data_processing:
The basic reads were converted into sequence data by base calling. Low quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt or longer than 41 nt from the raw data were filtered, and the clean reads were obtained. For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and so on. These RNAs were aligned and then subjected to the Bowtie search against Rfam v.10.1. The known miRNAs were identified by aligning against miRBase v22 database, and the known miRNA expression patterns in different samples were analyzed. After that, unannotated reads were analyzed by mirdeep2 to predict novel miRNAs. Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence and miRNA mature sequence were also identified.
Assembly: miRBase v22
Supplementary files format and content: Excel file of raw counts
Supplementary files format and content: Excel file of TPM value

source_name: skin

growth_protocol: All the mice are under standard condition of 12 h light/dark cycle, room temperature, and standard humidity. All the mice had access to supplementation of abundant food and water freely.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol.
1 μg total RNA of each sample was used for the establishment of small RNA library using the TruSeq Small RNA Sample Prep Kits (Cat. No. RS-200-0012, Illumina, USA.)

value: skin

value: mouse skin


title: MBOO2_CCS1477_6hr_bio_rep1


title: CUT&RUN TTC-549 H3K4me3 rep2


title: control OL replicate 2

value: primary mouse OPC culture allowed to differentiate fro 3 days


title: SRF-KO OL replicate 3

value: SRF-floxed/floxed mice


title: skin, non-irradiated, rep2


title: P6975_104

value: expressing CCL14


title: skin, non-irradiated, rep1


title: control OL replicate 1


title: CM5_50_REP2

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 Riverside Pkwy

department: Cell Biology and Genetics

institute: Texas A&M University Health Science Center

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Reads per kilobase of exon per million reads mapped (RPKM) were calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM content for CM25 vs CM25_50 and CM5 vs CM5_50 sample sets

growth_protocol: The human cardiomyocyte (CM) cell line AC16 was maintained in DMEM containing 10% fetal bovine serum , 100 U/mL penicillin and 100 mg/mL streptomycin and cultured with either 5 mM or 25 mM D-glucose in a humidified incubator at 37°C with 5% CO2 for at least 3-passages prior to them being used for experiments.

extract_protocol:
Total RNAs from the AC16CMs cultures were extracted with TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells derived from respective cultures maintained with specific glucose concentrationswere trypsinized, passaged and cultured supplemented with either 5 mM or 25 mM glucose for 24 h followed by increasing the concentration of glucose supplementation to 50 mM in both sets of cultures (5 → 50 and 25 → 50) for the next 24 h afterward. Briefly, an additional amount of D-Glucose was added to supplement for the additional 45 mM glucose or the additional 25 mM glucose in the two culture systems in parallel, to represent a hyperglycemic-induced stress condition consisting of 50 mM glucose in total, for 24 h.

value: human cardiomyocyte

value: cultured in hyperglycemic conditions of 5–50 mM glucose


title: SRF-KO OPC replicate 3

value: primary mouse OPC culture

value: AAV-CRE


title: skin, UVA irradiated, rep3

value: UVA


title: CM5_50_REP1


title: CUT&RUN A204 IgG for H3K27ac rep1

value: rhabdoid tumor cell line

value: No treatment


title: CUT&RUN A204 IgG for H3K27ac rep2


title: CUT&RUN A204 H3K27ac rep2


title: CM5_REP3

value: cultured in 5 mM glucose


title: SRF-KO OPC replicate 2

value: brain


title: skin, UVA irradiated, rep1


title: SRF-KO OPC replicate 1


title: CM5_REP1


title: control OPC replicate 4

value: AAV-deleted CRE


title: AC_25_2

city: 杭州市

first: Mingyue

last: Guo

state: 浙江省

address: 浙江大学紫金港校区

institute: 浙江大学

data_processing:
Briefly, nuclei were extracted and purified from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads (Beckman, A63881) and library quality was assessed with Qubit (Thermo Fisher, Q32854). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform at Metware Biotechnology (Wuhan, China) and 150 bp paired-end reads were generated.
Assembly: Reference genome and gene model annotation files were downloaded from tomato genome website (https://solgenomics.net/) directly.
Supplementary files format and content: bigWig

organism: Solanum lycopersicum

source_name: leaves

extract_protocol:
Samples were prepared using sucrose sedimentation as previously reported but with slight modifications.
Briefly, the young leaves of AC and LA1777 were collected under normal conditions or under cold stress for 6 h, respectively, and then ground to fine powder in liquid nitrogen. For each sample, 0.2 g of the frozen tissue powder was homogenized in prechilled 1 ml lysis buffer (15 mM Tris-HCl pH7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 5 mM 2-ME, 0.2% TritonX-100), and the nuclear fraction was purified as described47. The nuclei pellet was resuspended in 1 ml cold lysis buffer. For ATAC-seq and ATAC-qPCR, a nuclei aliquot (25 µl) was stained with DAPI (10 µl of 1 µg ml-1) and counted using a haemocytometer. Approximately 50000 nuclei were used for each ATAC-seq or ATAC-qPCR reaction.

value: leaves

value: normal


title: CM25_50_REP3

value: cultured in hyperglycemic conditions of 25–50 mM glucose


title: CUT&RUN A204 IgG for H3K4me3 rep2


title: CUT&RUN TTC-549 H3K4me3 rep1


title: AC_25_1


title: control OPC replicate 3


title: MBOO2_DMSO_bio_rep1

value: medulloblastoma cells


title: CM25_50_REP2


title: CUT&RUN A204 IgG for H3K4me3 rep1


title: CUT&RUN A204 H3K4me3 rep2


title: control OPC replicate 2


title: CM25_REP3

value: cultured in 25 mM glucose


title: CM25_REP1


title: AC_4_2

value: cold


title: control OPC replicate 1

value: SRF-floxed/floxed mice


title: AC_4_1


title: skin, UVA irradiated, rep2

value: skin

value: mouse skin


title: CUT&RUN A204 H3K4me3 rep1


title: CUT&RUN A204 H3K27ac rep1


title: YLG136, mock, RPA ChIP, 4h, rep2

status: Public on Feb 22 2024

city: Planegg-Martinsried

first: Martina

last: Peritore

state: Bayern

address: Am Klopferspitz 18

institute: MPIB

data_processing:
Sequecing reads were mapped to the Saccharomyces cerevisiae genome using Bowtie2 (v2.4.2) with the parameters --no-discordant --no-mixed --local
SAMtools (v1.9) was used to filter out multiple mapping reads and select reads with alignment quality higher than 30 (MAPQ > 30)
Forward and reverse reads were separated using SAMtools
bedtools (v2.30.0) was used to generate coverage files (bedgraph format)
Assembly: LYZE00000000.1 (HML and HMR loci were removed from the sequence)
Supplementary files format and content: bedgraph files contain reads coverage

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YP-media supplemented with 2% raffinose at 30°C. Exponentially growing cells (OD600 0.5-0.7) were synchronized in M phase with 5 μg/ml nocodazole or in G1 phase with 0.5 µg/ml of alpha-factor for 2-3 hours. Cell cycle arrest was assessed via microscopy and DNA content measured by flow cytometry.

extract_protocol:
Cells were mechanically lysed and chromatin was sheared by sonication to fragments of 200-500 bp. 40% of the chromatin extract was used for immunoprecipitation, the purified complexes were treated with proteinase K and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Strand-specific ChIP-seq libraries were prepared starting from 1 ng of DNA using Accel-NGS® 1S Plus Library Kit, following manufacturer instructions. 12-14 cycles were used for library amplification. Clean-up steps were performed using SPRIselect beads.

treatment_protocol: DSB induction (pGAL-HO system) or synthetic expression of DDK (pGAL-DDK), were achieved by adding 2% galactose in the cultures. Cells were crosslinked at the indicated time points after DSB induction with 1% formaldehyde for 16 minutes at room temperature and the reaction quenched with glycine (final concentration 400 mM). Cells were harvested by centrifugation (3500xg at 4°C), washed with cold PBS and the pellet flash frozen in liquid nitrogen.

tag: material

value: Cells

tag: treament

value: mock

tag: chip antibody

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: YLG136, IAA, RPA ChIP, 0h, rep2

value: IAA


title: YLG136, mock, RPA ChIP, 0h, rep2


title: YLG136, IAA, RPA ChIP, 2h, rep2


title: YLG136, IAA, RPA ChIP, 4h, rep2


title: YLG135, mock, RPA ChIP, 4h, rep2


title: YLG136, mock, RPA ChIP, 2h, rep2


title: YLG135, IAA, RPA ChIP, 4h, rep2


title: YLG135, IAA, RPA ChIP, 0h, rep2


title: YLG135, mock, RPA ChIP, 2h, rep2


title: YLG135, mock, RPA ChIP, 0h, rep2


title: YLG136, IAA, input, 4h, rep2


title: YLG136, IAA, input, 2h, rep2


title: YLG136, IAA, input, 0h, rep2


title: YLG136, mock, input, 0h, rep2


title: YLG136, mock, input, 4h, rep2


title: YLG136, mock, input, 2h, rep2


title: YLG135, IAA, input, 0h, rep2


title: YLG135, IAA, input, 2h, rep2


title: YLG135, IAA, input, 4h, rep2


title: YLG135, mock, input, 2h, rep2


title: R6_CD45pos_NrasG12VPtenKO

city: Amsterdam

first: Masami

last: Ando-Kuri

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

description:
6293_24_2096690_TCGACGTC-TCTCTCCG_S24
Read_Counts_perGene_CD45pos.txt

data_processing:
The reads that are of low complexity or repetitive sequences were filtered.
Paired-end sequencing reads were trimmed with seqpurge and aligned with Hisat2 using as reference GRCm38 (mm10) (--min-intronlen 20 --max-intronlen 500000 -k 5 --minins 0 --maxins 500 --fr --new-summary --threads 16).
The read counts were generated using the function gensum (https://github.com/NKI-GCF/gensum) with gtf (v. 100) annotation.
Assembly: mm10
Supplementary files format and content: Read_Counts_perGene_Bulktumor.txt: tab-separated gene counts and gene annotation for all samples
Supplementary files format and content: Read_Counts_perGene_CD45pos.txt: tab-separated gene counts and gene annotation for all samples
Supplementary files format and content: Read_Counts_perGene_CancerCellLines.txt: tab-separated gene counts and gene annotation for all samples

extract_protocol:
Tissue samples were homogenized in 600ul of buffer RLT (79216, Qiagen) with the addition of 1% B-mercaptoethanol using the TissueLyserII (85300, Qiagen) for 6 minutes  with frequency setting 30 (1/s) in combination with 5mm stainless steel beads (69989, Qiagen). The total RNA was isolated  using the RNeasy Mini Kit (74106, Qiagen), including an on column DNase digestion (79254, Qiagen),  according to the manufactures instructions,.  Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA).  Total RNA samples having RIN>8 were subjected to library generation. CD45+ sorted cells (30.000-75.000 cells) from somatic HCC mouse model were homogenized in RLT buffer (79216, Qiagen), total RNA was isolated using the RNeasy Micro Kit (74004, Qiagen), including an on column DNase digestion (79254, Qiagen), according to the manufacturer’s instructions. Quality and quantity of the total RNA was assessed on the 2100 Bioanalyzer instrument following manufacturer’s instructions “Agilent RNA 6000 Pico” (G2938-90046, Agilent Technologies). In general RNA yields of 0.5-45 ng total RNA and RNA integrity numbers (RIN) above 7 were obtained, with only 1 sample had a RIN value of 5.7. RNA samples were concentrated with Agencourt RNAClean XP beads (A63987), according to manufacturer’s instructions (Protocol 001298v001, Agencourt) with modifications.
The library preparation for bulk tumors and cell lines was generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Document # 1000000040498 v00). The libraries were sequenced with  paired-end reads on a NovaSeq-6000 using a Reagent Kit v1.5 (Illumina Inc., San Diego). For CD45+ RNA-seq, the libraries were generated using Smart-Seq2 RNA (Illumina) according to the manufacturer’s instructions and paired-end sequenced using the Nextseq-550 High Output Kit v2.5 (150 Cycles).

value: CD45+ cells

value: NrasG12V overexpression Pten knockout

tag: time

value: End-stage

tag: disease state

value: cancer


title: R4_CD45pos_NrasG12VPtenKO

description:
6293_22_2053616_CGATCAGT-CTAAGCCT_S22
Read_Counts_perGene_CD45pos.txt


title: YLG135, mock, input, 4h, rep2


title: R2_CD45pos_NrasG12VPtenKO

description:
6293_20_2053613_ACTGAGCG-ACTGCATA_S15
Read_Counts_perGene_CD45pos.txt

value: Intermediate-stage


title: R5_CD45pos_NrasG12VPtenKO

description:
6293_23_2053619_TGCAGCTA-CGTCTAAT_S23
Read_Counts_perGene_CD45pos.txt


title: YLG135, IAA, RPA ChIP, 2h, rep2


title: R7_CD45pos_NrasG12VPtenKO

description:
6293_25_2096693_TAAGGCGA-TCGACTAG_S25
Read_Counts_perGene_CD45pos.txt


title: R5_CD45pos_NrasG12DPtenKO

description:
6293_14_2053584_GGAGCTAC-AAGGCTAT_S3
Read_Counts_perGene_CD45pos.txt

value: NrasG12D overexpression Pten knockout


title: R3_CD45pos_NrasG12DPtenKO

description:
6293_18_2053600_ATGCGCAG-TATCCTCT_S10
Read_Counts_perGene_CD45pos.txt


title: R2_CD45pos_NrasG12DPtenKO

description:
6293_17_2053599_TACGCTGC-CTCTCTAT_S19
Read_Counts_perGene_CD45pos.txt


title: R3_CD45pos_ MycOEPtenKO

description:
6293_8_2096688_CGAGGCTG-TCTCTCCG_S14
Read_Counts_perGene_CD45pos.txt

value: Myc overexpression Pten knockout


title: R4_CD45pos_NrasG12DPtenKO

description:
6293_12_2053579_ATCTCAGG-GCGTAAGA_S17
Read_Counts_perGene_CD45pos.txt


title: R6_CD45pos_NrasG12DPtenKO

description:
6293_15_2053593_GCGTAGTA-GAGCCTTA_S16
Read_Counts_perGene_CD45pos.txt


title: R3_CD45pos_NrasG12VPtenKO

description:
6293_21_2053614_CCTAAGAC-AAGGAGTA_S21
Read_Counts_perGene_CD45pos.txt


title: R3_CD45pos_ MycOETrp53KO

description:
6293_11_2096687_GCTCATGA-CCTAGAGT_S18
Read_Counts_perGene_CD45pos.txt

value: Myc overexpression Trp53 knockout


title: R1_CD45pos_NrasG12DPtenKO

description:
6293_13_2053581_ACTCGCTA-CTATTAAG_S1
Read_Counts_perGene_CD45pos.txt


title: R2_CD45pos_ MycOEPtenKO

description:
6293_7_2087575_CTCTCTAC-CGTCTAAT_S12
Read_Counts_perGene_CD45pos.txt


title: R1_CD45pos_ MycOEPtenKO

description:
6293_6_2087574_TAGGCATG-CTAAGCCT_S7
Read_Counts_perGene_CD45pos.txt


title: R2_CD45pos_ MycOETrp53KO

description:
6293_10_2089387_GTAGAGGA-TTCTAGCT_S11
Read_Counts_perGene_CD45pos.txt


title: R3_CD45pos_Control

description:
6293_3_2089377_AGGCAGAA-GTAAGGAG_S4
Read_Counts_perGene_CD45pos.txt

value: WT

value: 4 weeks

value: normal


title: R1_CD45pos_ MycOETrp53KO

description:
6293_9_2089374_AAGAGGCA-TCGACTAG_S13
Read_Counts_perGene_CD45pos.txt


title: R4_CD45pos_Control

description:
6293_4_2089378_TCCTGAGC-ACTGCATA_S8
Read_Counts_perGene_CD45pos.txt


title: R5_CD45pos_Control

description:
6293_5_2089379_GGACTCCT-AAGGAGTA_S9
Read_Counts_perGene_CD45pos.txt


title: YLG135, mock, input, 0h, rep2


title: R1_CD45pos_Control

description:
6293_1_2089375_TAAGGCGA-CTCTCTAT_S2
Read_Counts_perGene_CD45pos.txt


title: R2_CD45pos_Control

description:
6293_2_2089376_CGTACTAG-TATCCTCT_S5
Read_Counts_perGene_CD45pos.txt


title: R1_CD45pos_NrasG12VPtenKO

description:
6293_19_2053618_TAGCGCTC-GTAAGGAG_S20
Read_Counts_perGene_CD45pos.txt


title: R7_CD45pos_NrasG12DPtenKO

description:
6293_16_2053594_CGGAGCCT-TTATGCGA_S6
Read_Counts_perGene_CD45pos.txt


title: YSB517, RPA ChIP, 4h, rep2


title: YSB802, RPA ChIP, 4h, rep2


title: YSB802, RPA ChIP, 0h, rep2


title: YLG142, RPA ChIP, 4h, rep2

value: GAL_DDK sae2-S267E


title: YSB517, RPA ChIP, 0h, rep2


title: YSB517, RPA ChIP, 2h, rep2


title: YLG142, RPA ChIP, 2h, rep2


title: YLG137, RPA ChIP, 4h, rep2


title: YLG142, RPA ChIP, 0h, rep2


title: YLG137, RPA ChIP, 2h, rep2


title: YLG137, RPA ChIP, 0h, rep2


title: YSB802, input, 0h, rep2


title: YSB517, input, 2h, rep2


title: YSB802, input, 2h, rep2


title: YSB802, input, 4h, rep2


title: YSB517, input, 4h, rep2


title: YLG142, input, 0h, rep2


title: YSB517, input, 0h, rep2


title: YLG142, input, 4h, rep2


title: YSB802, RPA ChIP, 2h, rep2


title: YLG142, input, 2h, rep2


title: YLG137, input, 4h, rep2


title: YLG137, input, 2h, rep2


title: YSB802, RPA ChIP, 2h, rep1


title: YSB802, RPA ChIP, 4h, rep1


title: YSB517, RPA ChIP, 4h, rep1


title: YSB802, RPA ChIP, 0h, rep1


title: YSB517, RPA ChIP, 2h, rep1


title: YLG142, RPA ChIP, 4h, rep1


title: YSB517, RPA ChIP, 0h, rep1


title: YLG142, RPA ChIP, 0h, rep1


title: YLG142, RPA ChIP, 2h, rep1


title: YLG137, RPA ChIP, 0h, rep1


title: YSB802, input, 4h, rep1


title: YSB802, input, 2h, rep1


title: YLG137, RPA ChIP, 2h, rep1


title: YSB517, input, 2h, rep1


title: YSB517, input, 4h, rep1


title: YSB802, input, 0h, rep1


title: YSB517, input, 0h, rep1


title: YLG137, input, 0h, rep2


title: YLG142, input, 4h, rep1


title: YLG142, input, 0h, rep1


title: YLG137, input, 0h, rep1


title: YLG137, input, 2h, rep1


title: YLG142, input, 2h, rep1


title: YLG136, IAA, RPA ChIP, 4h, rep1


title: YLG137, input, 4h, rep1


title: YLG136, mock, RPA ChIP, 2h, rep1


title: YLG136, IAA, RPA ChIP, 0h, rep1


title: YLG136, IAA, RPA ChIP, 2h, rep1


title: YLG136, IAA, input, 2h, rep1


title: YLG136, IAA, input, 4h, rep1


title: YLG136, mock, RPA ChIP, 0h, rep1


title: YLG136, IAA, input, 0h, rep1


title: YLG137, RPA ChIP, 4h, rep1


title: YLG136, mock, input, 2h, rep1


title: YLG136, mock, input, 4h, rep1


title: YLG135, IAA, RPA ChIP, 4h, rep1


title: YLG135, IAA, RPA ChIP, 0h, rep1


title: YLG136, mock, input, 0h, rep1


title: YLG135, IAA, RPA ChIP, 2h, rep1


title: YLG135, mock, RPA ChIP, 0h, rep1


title: YLG135, mock, RPA ChIP, 2h, rep1


title: YLG135, IAA, input, 2h, rep1


title: YLG135, IAA, input, 4h, rep1


title: YLG135, mock, RPA ChIP, 4h, rep1


title: YLG135, mock, input, 4h, rep1


title: YLG136, mock, RPA ChIP, 4h, rep1


title: YLG135, mock, input, 2h, rep1


title: YLG135, IAA, input, 0h, rep1


title: ce_smallRNA_longTC_N2_47h

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Assembly: ce10
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

organism: Caenorhabditis elegans

growth_protocol: Synchronized L1's of N2 were plated on 10 cm plates (2000 worms/plate) and kept at 25°C for the time-course. Every hour samples were collected from 5 h to 48h

extract_protocol:
We harvested worms from 5h to 48h in hourly interval. Worms were collected from plates and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using conventional phenol extraction, as described previously (Hendriks et al., 2014). Total RNA was DNAse treated
Sequencing libraries were generated using Illumina TruSeq Small RNA Library Prep Kit according to the manufacturer’s instructions. Subsequently, library was sequenced on Illumina HiSeq2500, as 51 cycles single-end reads.

treatment_protocol: no treatment

tag: time (h)


title: ce_smallRNA_longTC_N2_45h


title: ce_smallRNA_longTC_N2_48h


title: ce_smallRNA_longTC_N2_44h


title: ce_smallRNA_longTC_N2_41h


title: ce_smallRNA_longTC_N2_42h


title: ce_smallRNA_longTC_N2_40h


title: ce_smallRNA_longTC_N2_43h


title: ce_smallRNA_longTC_N2_39h


title: ce_smallRNA_longTC_N2_38h


title: ce_smallRNA_longTC_N2_37h


title: ce_smallRNA_longTC_N2_33h


title: ce_smallRNA_longTC_N2_34h


title: ce_smallRNA_longTC_N2_32h


title: ce_smallRNA_longTC_N2_35h


title: ce_smallRNA_longTC_N2_29h


title: ce_smallRNA_longTC_N2_31h


title: ce_smallRNA_longTC_N2_30h


title: ce_smallRNA_longTC_N2_28h


title: ce_smallRNA_longTC_N2_26h


title: ce_smallRNA_longTC_N2_24h


title: ce_smallRNA_longTC_N2_23h


title: ce_smallRNA_longTC_N2_22h


title: ce_smallRNA_longTC_N2_21h


title: ce_smallRNA_longTC_N2_25h


title: ce_smallRNA_longTC_N2_46h


title: ce_smallRNA_longTC_N2_19h


title: ce_smallRNA_longTC_N2_18h


title: ce_smallRNA_longTC_N2_16h


title: YLG135, mock, input, 0h, rep1


title: ce_smallRNA_longTC_N2_20h


title: ce_smallRNA_longTC_N2_15h


title: ce_smallRNA_longTC_N2_13h


title: ce_smallRNA_longTC_N2_14h


title: ce_smallRNA_longTC_N2_11h


title: ce_smallRNA_longTC_N2_36h


title: ce_smallRNA_longTC_N2_10h


title: ce_smallRNA_longTC_N2_9h


title: ce_smallRNA_longTC_N2_7h


title: ce_smallRNA_longTC_N2_8h


title: ce_smallRNA_longTC_N2_6h


title: ce_smallRNA_longTC_N2_27h


title: ce_smallRNA_longTC_N2_5h


title: ce_smallRNA_lin28_TC_mut_23h

description: instrument model 2 for re-sequencing: NextSeq 500

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

growth_protocol: Synchronized L1's of HW1993 (xeSi312[eft-3p::luc::gfp::unc-54 3'UTR, unc-119(+)] IV)  and HW2706 (lin-28(xe192) I; xeSi312 [Peft-3::luc::gfp::unc-54 3’UTR, unc-119(+)] IV) were cultured in liquid culture (S-Basal supplemented with OP50, OD600=2.7, 1000 animals/mL) in a temperature controlled incubator at 25°C, shaking at 180 rpm.  Every hour samples were collected from 0 h to 23h

extract_protocol:
We harvested worms from 0h to 23h in hourly interval. Worms were collected from liquid culture and washed 3 times and resuspended in Tri Reagent (MRC, TR118) and RNA was extracted using Direct-zol™ RNA MicroPrep kit (Zymo Research; R2062) as per manufacturere's instructions. Total RNA was treated with DNAse on column.
There were three sequencing reactions done for this library. First, sequencing libraries were generated using Illumina TruSeq Small RNA Library Prep Kit according to the manufacturer’s instructions. The library was sequenced on Illumina HiSeq2500, as 51 cycles single-end reads. since we did not get enough reads, the libraries were reprocessed using CleanTag Small RNA library preparation kit (Trilink Biotechnology) according to manufacturer's instructions. The library pool was size selected on a gel (140-160 bp) to enrich for the small RNA fraction. Subsequently, library was sequenced on NextSeq 500 as 76 cycle single-end reads, and then resequenced on NextSeq 500 as 51 cycle single-end reads as to detect let-7 passenger strand.


title: ce_smallRNA_lin28_TC_mut_22h


title: ce_smallRNA_lin28_TC_mut_20h


title: ce_smallRNA_lin28_TC_mut_21h


title: ce_smallRNA_lin28_TC_mut_19h


title: ce_smallRNA_lin28_TC_mut_16h


title: ce_smallRNA_lin28_TC_mut_18h


title: ce_smallRNA_longTC_N2_17h


title: ce_smallRNA_lin28_TC_mut_15h


title: ce_smallRNA_lin28_TC_mut_17h


title: ce_smallRNA_lin28_TC_mut_14h


title: ce_smallRNA_longTC_N2_12h


title: ce_smallRNA_lin28_TC_mut_13h


title: ce_smallRNA_lin28_TC_mut_10h


title: ce_smallRNA_lin28_TC_mut_8h


title: ce_smallRNA_lin28_TC_mut_12h


title: ce_smallRNA_lin28_TC_mut_5h


title: ce_smallRNA_lin28_TC_mut_6h


title: ce_smallRNA_lin28_TC_mut_3h


title: ce_smallRNA_lin28_TC_mut_9h


title: ce_smallRNA_lin28_TC_mut_4h


title: ce_smallRNA_lin28_TC_mut_2h


title: ce_smallRNA_lin28_TC_mut_0h


title: ce_smallRNA_lin28_TC_mut_1h


title: ce_smallRNA_lin28_TC_WT_22h


title: ce_smallRNA_lin28_TC_WT_23h


title: ce_smallRNA_lin28_TC_WT_20h


title: ce_smallRNA_lin28_TC_WT_21h


title: ce_smallRNA_lin28_TC_mut_11h


title: ce_smallRNA_lin28_TC_WT_19h


title: ce_smallRNA_lin28_TC_WT_18h


title: ce_smallRNA_lin28_TC_WT_16h


title: ce_smallRNA_lin28_TC_mut_7h


title: ce_smallRNA_lin28_TC_WT_17h


title: ce_smallRNA_lin28_TC_WT_14h


title: ce_smallRNA_lin28_TC_WT_12h


title: ce_smallRNA_lin28_TC_WT_13h


title: ce_smallRNA_lin28_TC_WT_11h


title: ce_smallRNA_lin28_TC_WT_5h


title: ce_smallRNA_lin28_TC_WT_9h


title: ce_smallRNA_lin28_TC_WT_3h


title: ce_smallRNA_lin28_TC_WT_8h


title: ce_smallRNA_lin28_TC_WT_7h


title: ce_smallRNA_lin28_TC_WT_4h


title: ce_smallRNA_lin28_TC_WT_0h


title: ce_smallRNA_lin28_TC_WT_1h


title: ce_smallRNA_lin28_TC_WT_2h


title: ce_smallRNA_lin28_TC_WT_15h


title: ce_smallRNA_lin28_TC_WT_10h


title: 451Lu-R corin Input R2

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

department: Dermatology

institute: Boston University

data_processing:
FASTQ files were aligned using Bowtie 2.5.0 to the reference genomes (hg38, Genome Reference Consortium Human Build 38)
Peak calling was performed using Model-based Analysis of ChIP-seq (MACS) 1.4.2 (69) with ‘--nomodel’ and ‘--nolambda’ options.
In order to summarize the ChIP signal enrichment over input, the background subtracted bedGraph files with log-likelihood ratios were made using MACS2 version 2.1.1 with ‘bdgcmp -m logLR’ command.
Unique and overlapping peaks were defined using ‘intersect’ command in BEDTools suite
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Melanoma

growth_protocol: grown to 80% confluency in 150 cm² plates

extract_protocol:
Qiagen Dneasy Kit
Completed by Azenta

treatment_protocol: 2.5 uM corin or DMSO for 24 h

tag: tissue

value: Melanoma

value: cell line

tag: antibody

value: Corin


title: 451Lu-R DMSO H3K9ac R2

tag: cell type

value: DMSO


title: 451Lu-R DMSO Input R2

tag: treatment


title: 451Lu-R corin H3K4me2 R2

tag: cell line


title: 451Lu-R corin H3K27ac R1


title: 451Lu-R corin H3K27ac R2


title: 451Lu-R DMSO H3K27ac R2


title: ce_smallRNA_lin28_TC_WT_6h

tag: genotype


title: 451Lu-R DMSO H3K9ac R1


title: 451Lu-R corin Input R1


title: 451Lu-R DMSO H3K4me2 R1


title: 451Lu-R DMSO Input R1


title: 451Lu-R DMSO H3K27ac R1


title: 1205Lu-R corin H3K27ac R2


title: 1205Lu-R corin H3K4me2 R2


title: 451Lu-R corin H3K9ac R2


title: 1205Lu-R corin H3K9ac R2


title: 1205Lu-R corin Input R2


title: 1205Lu-R DMSO H3K27ac R2


title: 1205Lu-R corin H3K27ac R1


title: 1205Lu-R corin H3K4me2 R1


title: 1205Lu-R DMSO H3K9ac R2


title: 1205Lu-R DMSO H3K4me2 R2


title: 1205Lu-R corin H3K9ac R1


title: 451Lu-R corin H3K4me2 R1


title: 451Lu-R corin H3K9ac R1


title: 1205Lu-R DMSO H3K27ac R1


title: 1205Lu-R DMSO H3K4me2 R1


title: 1205Lu-R DMSO Input R1


title: HGSOC Patient EOC1005, post-chemotherapy

city: Helsinki

first: Anna

last: Perkiö

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Reads originating from poor-quality cells were excluded (quality control steps done and explained by Zhang et al., 2022, doi:10.1126/sciadv.abm1831 )
STAR 2.7.8a was used to perform alignment. Genome indices were generated based on the GRCh38.d1.vd1 reference genome and GENCODE v25 annotation. A maximum of two mismatches per read was allowed.
For the L1 expression matrix only: Reads mapping more than 1 percent or more to exons were excluded. In addition, reads mapping 90 percent or more to repeats were excluded. The annotations were derived from RepeatMasker (<http://www.repeatmasker.org>). The described steps were performed with Intersect from Pybedtools (v0.8.1), a wrapper of Bedtools
For the L1 expression matrix only: To extract reads aligned in 1kb downstream windows of L1s, Intersect was again used to only retain reads with a minimum overlap of 60 percent with the reference regions. The 1kb reference windows were based on the list from Deininger et al. (2017, doi:10.1093/nar/gkw1067), consisting of L1 loci with potentially functional promoters.
For the L1 expression matrix only: To exclude reads that mapped ambiguously to polyA regions, Pysam 0.16.0.1, a python wrapper of SAMtools, was used to exclude reads for which the A or T base composition was 60 percent or higher.
The expression of both L1s and the rest of the genome was quantified with UMI-tools 1.1.1. Before the alignment, cell barcodes and UMIs were extracted from the reads. Subsequently, the unfiltered reads were assigned straight to the genome (featureCounts from Subread v2.0.1), and the filtered reads were assigned to the L1 1kb downstream windows. Only reads that mapped uniquely and to the same strand as the reference were considered, deduplicated and counted per feature per cell.
For the gene expression matrix only: The genes with a total of less than 95 UMIs (from all samples combined) were excluded.
Assembly: GRCh38.d1.vd1, GENCODE v25
Supplementary files format and content: comma-separated files for gene expression (tumor samples) and L1 expression (all samples)

source_name: High-grade serous ovarian cancer

extract_protocol:
The samples were incubated overnight in a mixture of collagenase and hyaluronidase to obtain single cell suspensions.
Standard Chromium Single Cell 3′ Reagent Kit v. 2.0 (10x Genomics)

value: High-grade serous ovarian cancer

value: clinical patient sample

value: tumor + microenvironment

value: neoadjuvant chemotherapy


title: HGSOC Patient EOC733, post-chemotherapy


title: 1205Lu-R DMSO H3K9ac R1


title: HGSOC Patient EOC87, post-chemotherapy


title: HGSOC Patient EOC153, pre-chemotherapy

value: no treatment


title: HGSOC Patient EOC3, pre-chemotherapy


title: HGSOC Patient EOC3, post-chemotherapy


title: HGSOC Patient EOC136, post-chemotherapy


title: 1205Lu-R corin Input R1


title: HGSOC Patient EOC733, pre-chemotherapy


title: 1205Lu-R DMSO Input R2


title: HGSOC Patient EOC540, post-chemotherapy


title: MNC SF3B1 MUT rep21

city: Paris

first: David

last: Rombaut

address: 22 rue Méchain

country: France

institute: Institut Cochin

description:
B134T61
Re-analysis of GSM3893632

data_processing:
FASTQ files were mapped using STAR (v2.7.9) to align the reads against the human reference genome GRCh37 (UCSC version hg19). Read count normalizations and groups comparisons were performed using DESeq2 (v1.30.1), using the Wald test for significance testing. Genes with low counts were filtered, if at least half the samples have less than 20 normalized reads.
For differential expression study, the results obtained after DESeq2 comparison were selected for further analysis and filtered at Benjamini-Hochberg (BH)- adjusted P-value < 0.05 and log2(FC) > |1|.
To identify differentially expressed splicing events, we used KisSplice (v2.6.2), KisSplice2refgenome (v2.0.7) and KissDE (v1.15.3), and filtered results at BH adjusted P-value < 0.05 and ΔPSI > |0.10|.
Assembly: GRCh37
Supplementary files format and content: rawCOUNT_RNAseq_CMN.txt : raw count table (tabulated txt file). event_k2ref_CMN.tsv.gz : kissplice2refgenome output (splicing raw count, txt file), input_order_kissplice (txt file, order necessary to run splicing differential analysis with kissDE).

source_name: Bone marrow

extract_protocol:
Bone marrow mononuclear cells were purified on Ficoll gradient and processed for nucleic acid extraction using the DNA/RNA Kit (Qiagen). cDNA synthesis was conducted with MuLV Reverse Transcriptase (Invitrogen), with quality controls conducted on an Agilent 2100 Bioanalyzer (Agilent).
Libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) and sequenced on an Illumina HiSeq 2500 platform using a 100-bp paired-end sequencing strategy.

value: Bone marrow

value: mononuclear cells

value: SF3B1 MUT


title: HGSOC Patient EOC153, post-chemotherapy


title: HGSOC Patient EOC136, pre-chemotherapy


title: MNC SF3B1 MUT rep20

description:
B134T59
Re-analysis of GSM3893631


title: HGSOC Patient EOC1005, pre-chemo


title: HGSOC Patient EOC87, pre-chemotherapy


title: MNC SF3B1 MUT rep17

description:
B134T51
Re-analysis of GSM3893626


title: MNC SF3B1 MUT rep16

description:
B134T49
Re-analysis of GSM3893625


title: MNC SF3B1 MUT rep18

description:
B134T53
Re-analysis of GSM3893627


title: MNC SF3B1 MUT rep14

description:
B133_B136T43
Re-analysis of GSM3893622


title: MNC SF3B1 MUT rep15

description:
B133_B136T47
Re-analysis of GSM3893624


title: MNC SF3B1 WT rep6

description:
B134T54
Re-analysis of GSM3893628

value: SF3B1 WT


title: MNC SF3B1 WT rep5

description:
B133_B136T45
Re-analysis of GSM3893623


title: MNC SF3B1 MUT rep13

description:
B133_B136T41
Re-analysis of GSM3893621


title: MNC SF3B1 MUT rep11

description:
B133_B136T36
Re-analysis of GSM3893618


title: MNC SF3B1 MUT rep12

description:
B133_B136T38
Re-analysis of GSM3893619


title: MNC SF3B1 MUT rep9

description:
B132T29
Re-analysis of GSM3893615


title: MNC SF3B1 MUT rep7

description:
B132T23
Re-analysis of GSM3893613


title: MNC SF3B1 MUT rep6

description:
B132T20
Re-analysis of GSM3893612


title: MNC SF3B1 MUT rep8

description:
B132T26
Re-analysis of GSM3893614


title: MNC SF3B1 WT rep4

description:
B132T17
Re-analysis of GSM3893611


title: MNC SF3B1 MUT rep4

description:
B131T4
Re-analysis of GSM3893607


title: MNC SF3B1 WT rep3

description:
B131T7
Re-analysis of GSM3893608


title: MNC SF3B1 MUT rep19

description:
B134T57
Re-analysis of GSM3893630


title: MNC SF3B1 MUT rep5

description:
B131T9
Re-analysis of GSM3893610


title: MNC SF3B1 MUT rep3

description:
B131T16
Re-analysis of GSM3893605


title: MNC SF3B1 MUT rep1

description:
B130T66
Re-analysis of GSM3893602


title: MNC SF3B1 WT rep1

description:
B131T14
Re-analysis of GSM3893604


title: MNC SF3B1 WT rep2

description:
B131T1
Re-analysis of GSM3893606


title: 451Lu-R DMSO H3K4me2 R2


title: P32_7100

city: Bethesda

first: Jayakumar

middle: R

last: Nair

state: MD

address: 10 center drive

department: Women malignancies Branch

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing
CPM-TMM values are presented as a soft text file.
The mapped sequencing depth coverage over target (after alignment and marking duplicates) was between 141x to 395x. The mean insert size for these samples was between 185 and 262 bases. More than 95% of the target region have the coverage above 20x.
Assembly: HG38
Supplementary files format and content: Soft text files were generated using excel.  The unprocessed raw files are provided as gzipped FASTQ files.

source_name: Tumor biopsies

growth_protocol: Tumor needle biopsies were frozen in OCT compound at -80 Celsius.  Sections were used for total RNA isolation

extract_protocol: Qiagen micro RNA isolation kit

value: Ovarian

value: tumor

value: Prexasertib

tag: overall survival

value: Less than 6 months


title: P31_3800

value: Greater/equal to 6 months


title: CON_3

city: Shanghai

first: Qiu

last: Yushu

state: Yangpu

address: Kongjiang Road, No. 1665

institute: Xihua Hospital

data_processing:
The quality of the raw sequencing data was evaluated using Fastp (v0.36). After assembling the metagenome using Megahit (v1.2.9) and metaSPAdes (v3.13), the openness of the assembly results was predicted using Prodigal (v2.60). Reading frame (ORF) and CD-HIT (v2.60) software were used to remove redundant predicted genes.DIAMOND (v0.8.20) was used to compare the gene set with databases, such as KEGG and GO, to obtain the species and functional annotation information of the genes. GraPhlAn was used to construct a taxonomic tree of intestinal microbiota. The association of metadata with the gut microbiota and metabolomic parameters was analyzed using Spearman's rank correlation test.
Assembly: Metagenome Assembly
Supplementary files format and content: tab-delimited file includes the number of genes and the abundance information of each sample in each taxonomy hierarchy

organism: feces metagenome

source_name: feces

extract_protocol:
Briefly, after collecting 120-dpf adult zebrafish feces, metagenomic DNA was extracted using the Qiagen PowerFecal kit (Qiagen).
The Nextera DNA Flex library preparation kit (Illumina, California, USA) was used to create metagenomic libraries and metagenomic sequencing was performed using an Illumina Hiseq X Ten (Illumina) sequencer.

value: feces


title: CON_2


title: SMZ_5000_2


title: SMZ_5000_1


title: SMZ_5000_3


title: P30_3600


title: P29_4600


title: MNC SF3B1 MUT rep10

description:
B133_B136T33
Re-analysis of GSM3893617


title: P25_4200


title: P26_4300


title: P24_4150


title: P23_4000


title: P22_2050


title: P21_1600


title: P20_1550


title: MNC SF3B1 MUT rep2

description:
B131T13
Re-analysis of GSM3893603


title: P17_550


title: P18_517


title: Patient Normal_6, Non-cancerous fallopian tube/fimbria

source_name: fallopian tube/fimbriae

value: fallopian tube/fimbriae

value: fallopian tube/fimbriae + microenvironment


title: P16_428


title: Patient Normal_4, Non-cancerous fallopian tube/fimbria


title: P19_604


title: Patient Normal_7, Non-cancerous fallopian tube/fimbria


title: CON_1


title: HGSOC Patient EOC443, post-chemotherapy

value: High-grade serous ovarian cancer


title: HGSOC Patient EOC443, pre-chemotherapy

value: clinical patient sample


title: HGSOC Patient EOC372, pre-chemotherapy

value: tumor + microenvironment


title: HGSOC Patient EOC372, post-chemotherapy

value: neoadjuvant chemotherapy


title: ChIP-seq in immortalized MEFs in hypoxia

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

institute: IBiS, Universidad de Sevilla-CSIC

description: ChIP-seq

data_processing:
Reads were aligned using Bowtie
Peaks were called using MACS2 software with  q<0.01
Supplementary_files_format_and_content: Called peaks in narrowPeak format
Supplementary_files_format_and_content: ChIP-seq signal in binary bigWig format

source_name: immortalized MEFs

growth_protocol: Culture medium used was DMEM supplemented with 10% fetal bovine serum (FBS; Life Technologies), penicillin 40 μg/ml, and streptomycin 40 μg/ml (Merck).

extract_protocol:
24x106 MEFs were fixed using a final concentration of 1% paraformaldehyde (PFA) in 200 mM phosphate buffer added to the culture medium and incubated during 10 minutes at 37ºC. Crosslinking reaction was stopped adding 125 mM glycine and incubating during 10 minutes at room temperature. After this, cells were collected from the culture dish with cold PBS with protease inhibitors cocktail (PIC) (Merck) and phenylmethylsulfonyl fluoride (PMFS) (Merck).  Nuclei were extracted and lysed, and chromatin sonicated in a Covaris M220 sonicator to an average of 300bp fragments. Sonicated chromatin was divided in 4 aliquots and incubated overnight at 4ºC with 2µg of antibody (anti-Tfcp2l1, Novus Biologicals; AF5726) per aliquiot. Immunoprecipitated chromatin was then incubated with magnetic beads, washed, TAGmented with Tn5 transposase (Schmidl et al., 2015) and eluted from beads. Then, chromatin was decrosslinked and DNA was purified using Minelute kit (Qiagen)
Preparation of ChIPmentation libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

treatment_protocol: MEFs were cultured under normoxic (20% O2) or hypoxic (3% O2) atmospheres with 5% CO2 at 37ºC. Hypoxia was achieved and maintained by flushing hypoxic gas mixture in CO2 incubators.

value: MEFs

value: Hypoxia 3% oxygen

value: Immortalized

value: anti-Tfcp2l1 Novus Biologicals AF5726


title: ChIP-seq in senescent MEFs in normoxia

description: ChIP-seq

source_name: senescent MEFs

value: Normoxia 20% oxygen

value: Senescent


title: Oesophagus, replicate1, scRNAseq

city: Stockholm

first: Michael

last: Hagemann-Jensen

address: Solnavägen 9

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

data_processing:
The data was sequenced paired-end 100bp on a MGI DNBSEQ-G400 sequencer and output of MGI sequencing runs are a read1.fastq and read2.fastq file and the cellular barcodes (combined dual indexes) can be retrieved from the last 20 bp in the read2.fastq file (position 101-120). To run zUMIs, the expected barcodes from our sequencing runs are added as processed data files 'Oesophagus_expected_barcodes_run1.txt' and 'Oesophagus_expected_barcodes_run2.txt'.
zUMI version 2.9.7 was used to process raw FASTQ files. UMI-containing reads were identified and low-quality barcodes and UMIs applied to filter reads. Reads were mapped using STAR version 2.7.3a and the Gencode GRCm39 vM29 annotation was used to calculate readcounts and umicounts, respectively. The resulting BAM files were filtered using the stand-alone script pyTSOfilter (https://github.com/cziegenhain/pyTSOfilter).
Since our two sequencing runs contain overlapping barcodes we renamed the original barcodes (found in the supplemented annotation file in column 'BC_preprocess') and appended 'X1' to barcodes from sequencing run1 and 'X2' to barcodes from sequencing run 2 using the 'Sequencing_run' column in the supplemental annotation file. The resulting barcodes were stored in column 'BCX' in the supplemental annotation file.
We selected cells that fulfilled our QC criteria (labelled "pass" in column 'QC' in the supplemented annotation file to create a seurat object. Within seurat we integrated our dataset based on performed runs according to colum 'Exp_batch' in our supplemented annotation file and used clustering obtained with resolution parameter = 0.8 for subsequent analysis. Our original clustering was stored in column 'seurat_clusters' in the supplemental annotation file.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab-delimited .txt files and matrix files

source_name: Oesophagus

extract_protocol:
C57Bl/6 mice were i.p injected with 100 𝜇L pentobarbital and perfused with at least 50 mL ice-cold DPBS. The oesophagus was dissected and the muscularis externa mechanically removed. The oesophagus was longitudinally opened using spring-scissors with a ball tip and incubated in 0.5 mg/mL Thermolysin for 15 min at 37°C. Subsequently, stroma and epithelium were separated using forceps under a dissection microscope and cut into 3 equally sized tissue pieces. Afterwards, tissue samples were thoroughly minced and incubated in 0.25 mg/mL Liberase™ and 0.25 mg/mL DNase I in HBSS at 37°C for 30 min or 60 min for stroma and epithelium, respectively. Samples were thoroughly pipetted up and down every 15 min using a 200 𝜇L pipette tip. In addition, epithelial samples were run on a gentleMACS™ Dissociator. Cells ere washed twice in 1% FBS/PBS and kept on ice until sorting using a BD FACSMelody™ instrument.
Library preparation was performed according to Hagemann-Jensen, Michael, et al. "Single-cell RNA counting at allele and isoform resolution using Smart-seq3." Nature Biotechnology 38.6 (2020): 708-714. In short, cells were sorted and lysed in 384- well plates. Afterwards, 10 cycles of reverse transcription, 22 cycles of cDNA amplification, cDNA purification, normalisation and dilution to 100 pg/ml was performed. Subsequently, tagmentation and 12 cycles of index PCR using Nextera Index primers were done. Subsequently, cDNA libraries were pooled and purified. To prepare sequencing on an MGI platform, circular ssDNA libraries were created and adapter conversion PCR run for 5 cycles followed by circularisation. DNA nanoballs were created and 100 bp paired-end sequencing was run.

value: Oesophagus

tag: Sex

value: pooled male and female

value: epithelial and stromal

value: 10 - 14 weeks


title: Oesophagus, replicate 2 and 3, scRNAseq

tag: strain