title: Triad1 shRNA + Gcn1 shRNA polysomal RNA rep 3

description: Library name: HW-25


title: VCaP16, siFOXA1_1

status: Public on Jan 01 2025

type: SRA

city: Boston

first: Steven

middle: P

last: Balk

state: MA

address: 3 Blackfan Circle

department: Hematology/Oncology

country: USA

institute: Harvard Medical School

description:
Cuff_Gene_Counts_VCaP16siFOXA1_siNTC.csv
VCaP16siFOXA1_vs_siNTC.deseq.csv

library_source: transcriptomic

data_processing:
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters
cufflinks v2.2.1 was used to generate FPKM values
Assembly: hg19
Supplementary files format and content: comma-separated values file includes FPKM vaues for each sample
Supplementary files format and content: comma-separated values file includes differential gene expressions (log2(Fold Change) and statistical values)

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

growth_protocol: VCaP cells (ATCC, Manassas, VA) were maintained in DMEM with 10% fetal bovine serum (FBS), VCaP16 cells (enzalutamide-resistant VCaP) were maintained in DMEM with 10% fetal bovine serum (FBS) with 16uM enzalutamide.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
Transcriptome library construction (with Novogene)

treatment_protocol: VCaP cells in DMSO (VCaP_DMSO), VCaP treated with 10uM enzalutamide for 96 hrs (VCaP-E), enzalutamide-resistant VCaP16 cells in 16uM enzalutamide (VCaP16). VCaP16 in DMSO and treated with AR degrader (ARD) - 500nM ARCC-32 for 36 or 24hrs. VCaP16 cells treated with AR variant 7 siRNA (siV7), with AR Exon1 siRNA (siEx1), with AR Exon7 siRNA (siEx7), with FOXA1 siRNA (siFOXA1), with NFIB and NFIX siRNA (siNFIBX) and with non-targeted control siRNA (siNTC_AR, siNTC_FOXA1, siNTC_NFIBX).

tag: tissue

value: Prostate

tag: cell line

value: ENZ-resistant VCaP

tag: cell type

value: prostate cancer

tag: genotype

value: WT

tag: treatment

value: 16uM enzalutamide + FOXA1 siRNA


title: 10n dTag Cut&Run rep1

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

country: China

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
The raw reads with sequencing adaptors or low-quality ends from reads were trimmed by trim_galore.
The cleaned reads were aligned to mouse mm10 genome via bowtie2.
The bam files were sorted by samtools. Duplicates were marked and removed by Picard, and then, MACS2 was used to call significant peaks with parameters “-f BAMPE --keep-dup all -g mm -q 0.05 --broad --max-gap 200”.
For IGV visualization of the signals, the read coverage was normalized by reads per kilobase per million (RPKM) via bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Run

molecule: genomic DNA

organism: Mus musculus

source_name: 2i+LIF ESC

extract_protocol:
Cells were treated homemade pAG-MNase and antibody, then digested DNA was enriched.
NEBNext Ultra II DNA Library Prep Kit for llumina was used for library contrucation following manufacture’s protocol.

tag: strain

value: 2i+LIF ESC

value: mESC

value: Brg1 dTag knock in

value: 24h, 10n mol/L  dTag


title: 3n dTag Cut&Run rep2

value: 24h, 3n mol/L  dTag


title: Anopheles-Olfactory, 6am, Read 1, rep 1

city: PUNE

first: Tanwee

last: Das De

state: MAHARASHTRA

address: Dr. Homi Bhaba Road, Pashan

department: Department of Biology

country: India

institute: Indian Institute of Science Education and Research

data_processing:
The raw reads were demultiplexed and converted to FASTQ format using bcl2fastq software
Sequence reads were trimmed for adaptor sequence and low quality sequence using FastQC tool using default parameter
After quality checking and adaptor trimming the sample specific reads were aligned to the reference genome of An. culicifacies (VectorBase-54-AculicifaciesA-37-Genome) and Ae. aegypti (VectorBase-54-AaegyptiLVP-AGWG-Genome) respectively by using STAR-alignment tool
The transcriptome data of An. culicifacies showed 70-80% alignment rate whereas, Ae. aegypti data showed ~90% alignment
Read counts are calculated by htseq count tool
Assembly: AaegL5.0 &   AculA1.7
Supplementary files format and content: Tab delimited text file includes raw counts of Aedes samples
Supplementary files format and content: Tab delimited text file includes raw counts of Anopheles samples

organism: Anopheles culicifacies

source_name: Olfactory

growth_protocol: Both Aedes and Anopheles mosquitoes were maintained at 80% relative humidity and 27 ± 2°C temperature under 12hr/12hr LD cycle

extract_protocol:
Total RNA was extracted from the clean olfactory and brain tissues by standard trizol method
cDNA library were prepared using NEBNext® UltraII RNA library preparation kit (Cat No. E7775S) by following the manufacturer protocol.
For multiplexing of the samples NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (Cat No. E6440S) were used.

treatment_protocol: To understand the molecular rhythm of the olfactory and the brain system, complete olfactory tissue including antennae, maxillary palp, proboscis and labium, and the brain were dissected from 5-6-day old adult females’ mosquitoes (same cohort) at four different zeitgeber times 6am, 12pm, 6pm and 12am.

value: Olfactory

value: Circadian Cycle


title: Triad1 shRNA + Gcn1 shRNA polysomal RNA rep 2

city: Chicago

first: Marcelo

middle: G.

last: Bonini

state: IL

address: 303 E. Superior St. Suite 7-123

department: Feinberg School of Medicine

institute: Northwestern University

description: Library name: HW-24

library_source: other

data_processing:
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt (Martin, 2011).  Trimmed reads were aligned to the Human genome (hg38) using STAR (Dobin et al, 2013).  Read counts for each gene were calculated using htseq-count (Anders et al, 2015) in conjunction with a gene annotation file for hg38 obtained from Ensembl
Assembly: hg38
Supplementary files format and content: htseq count files

molecule: other

extract_protocol:
Total RNA was harvested using Trizol kit (Ambion).  250 ng of total RNA was used for the construction of sequencing libraries. Polysomal RNA was harvested using AllPrep RNA/Protein kit (Qiagen). 1000 ng polysomal RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA-Seq Library Prep kit.

treatment_protocol: Briefly, the cells need to be treated with 10 ug/ml cyclohexamide for 20 mins before collection, then cells were treated with hypotonic lysis buffer containing cyclohexamide.  Polysomal fractionation was performed using 10-50% sucrose gradients and polysomal fractions were pooled and RNA was extracted. Total RNA was extracted, in parallel, from the same cells that did not go through a polysome isolation process.

value: myeloid lineage cells

value: Triad1 and GCN1 double knockdown


title: Anopheles-Brain, 12am rep 3

source_name: Bain

value: Bain


title: VCaP16, siNTC_2, FOXA1

value: 16uM enzalutamide + non-targeted siRNA


title: Triad1 shRNA polysomal RNA rep 3

description: Library name: HW-19

value: Triad1 knockdown


title: 3n dTag Cut&Run rep1


title: OGDH KO3

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

data_processing:
Using subread to extract read count
Assembly: hg38
Supplementary files format and content: expr.txt

extract_protocol:
Collected by trizol
Send RNA to sangon for library construction

value: melanoma


title: 1n dTag Cut&Run rep1

value: 24h, 1n mol/L  dTag


title: Anopheles-Brain, 12pm rep 3


title: OGDH KO2


title: Anopheles-Brain, 6am, rep 3


title: Control vector polysomal RNA rep 5

description: Library name: HW-26


title: OGDH KO1


title: VCaP16, siNTC_1, FOXA1

value: Prostate

value: ENZ-resistant VCaP

value: prostate cancer


title: 0.3n dTag Cut&Run rep2

value: 2i+LIF ESC

value: 24h, 0.3n mol/L  dTag


title: Control vector polysomal RNA rep 4

description: Library name: HW-21

value: WT


title: Anopheles-Brain, 12am rep 2


title: Ctrl;-Glucose3


title: Ctrl;-Glucose2


title: Control vector polysomal RNA rep 3

description: Library name: HW-18


title: 0.3n dTag Cut&Run rep1

value: mESC

value: Brg1 dTag knock in


title: Ctrl;-Glucose1


title: Anopheles-Brain, 6pm rep 2


title: Triad1 shRNA + Gcn1 shRNA polysomal RNA rep 1

description: Library name: HW-23


title: Control Cut&Run rep2


title: Anopheles-Brain, 6pm rep 3


title: 1n dTag Cut&Run rep2


title: Ctrl3


title: WT.unt.none.r2

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description: WT cells, harvested 0h after no treatment, replicate 2

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.12.0 (https://doi.org/10.5281/zenodo.7998767) with the STAR (Dobin et al, 2012) /RSEM (Li et al 2011) option against human genome assembly GRCh38 and Ensembl release 110 transcript annotations.  The “--additional_fasta” parameter was used to simultaneously quantify reads against synthetic ERCC spike-ins.  All other options were left as default.
Counts Per Million mapped reads (CPM) scaled BigWig files were generated from BAM files using Deeptools v3.5.1’s bamCoverage function for each strand in turn using the options “--normalizeUsing CPM –binSize 1 --filterRNAstrand” (Ramirez et al., 2014).
Assembly: GRCh38
Supplementary files format and content: Counts-per-million scaled, strand-specific, bigwig files.
Supplementary files format and content: Comma separated, integer raw gene counts for each sample in a matrix format.

molecule: polyA RNA

growth_protocol: Cells were grown in DMEM at 37°C with 5% CO2

extract_protocol:
RNA was extracted according to the Qiagen Rneasy extraction kit's protocol
RNA-seq libraries were prepared using NEBNext Ultra II Directional PolyA mRNA according to the manufacturers' instructions.

treatment_protocol: Cells were treated with or without UV and with and without ATRi dissolved in DMSO

tag: timepoint

tag: replicate


title: Ctrl2


title: Anopheles-Brain, 12am rep 1


title: Control Cut&Run rep1


title: WT.unt.none.r1

description: WT cells, harvested 0h after no treatment, replicate 1


title: Anopheles-Brain, 6pm rep 1


title: WT.3h.none.r3

description: WT cells, harvested 3h after no treatment, replicate 3


title: 100n dTag ATAC rep2

data_processing:
The raw reads with sequencing adaptors or low-quality ends from reads were trimmed by trim_galore.
The clean reads were aligned to mm10 via bowtiew2 with parameter “-q -X 2000”
Then Picard was used to remove duplicates and MACS was used to call significant peaks with parameters “-f BAMPE --keep-dup all -g mm -B -q 0.05”.
For IGV visualization of the signals, the read coverage was normalized by reads per kilobase per million (RPKM) via bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
DNA was extract using homemade Tn5.
Cells were treated with homemade Tn5 and fragmented DNA was enriched by PCR using Nebnext High-Fidelity 2X PCR Master Mix

value: 24h, 100n mol/L  dTag


title: OGDH KO; -Glucose3


title: Ctrl1


title: 10n dTag ATAC rep2

value: 24h, 10n mol/L  dTag


title: OGDH KO; -Glucose2


title: Anopheles-Brain, 12pm rep 1

value: Circadian Cycle


title: Anopheles-Brain, 6am, rep 1


title: 10n dTag ATAC rep1


title: WT.3h.none.r1

description: WT cells, harvested 3h after no treatment, replicate 1


title: WT.4h.DMSO.r3

description: WT cells, harvested 4h after DMSO treatment, replicate 3

value: DMSO


title: WT.unt.none.r3

description: WT cells, harvested 0h after no treatment, replicate 3


title: exp 2 set29 mutant promastigotes/H2O2-treated/biological replicate 2

city: New Delhi

first: Swati

last: Saha

state: Delhi

address: Benito Juarez Road

department: Department of Microbiology

institute: University of Delhi South Campus

data_processing:
TrimGalore (v0.6.10)
Raw reads were pre-processed by trimming the adapter sequences with TrimGalore (v0.6.10), using the arguments: “--quality 20 --paired --length 25”
STAR (v2.7.10b) was used to align the paired end reads to the genome sequence and gene annotation for Leishmania donovani LdBPK282A1 obtained from the TriTrypDB portal. The reads mapping to genomic features were counted in the alignment step using the “–quantMode GeneCounts” option.
Genes with total count less than 200 across all samples of an experimental set were filtered out, and the differentially expressed genes within the sample sets were identified using the DESeq2
The data was visualised using ggplot2
Assembly: Leishmania donovaniBPK282A1; genome version ID: GCA_000227135.2
Supplementary files format and content: csv formatted text file includes raw count for each sample

organism: Leishmania donovani

source_name: promastigotes

growth_protocol: The cells were maintained in Medium199 supplemented with 10% FBS, 100 μM Adenine and 5 μg/ml Hemin and mainatined at 26ºC.

extract_protocol:
The RNA was isolated RNA was isolated following manufacturer's instructions for PureLink RNA isolation kit (Invitrogen, USA). On-column DNase I treatment was performed during the isolation to eliminate genomic DNA contamination in the isolated RNA, as per manufacturer’s instructions.
RNA-seq library was prepared using the Illumina Stranded mRNA Prep kit.

treatment_protocol: The cultures were initiated at 1x106 cells/ml from stationary phase cultures. After 48 hours, the culture was divided into two. One half of the culture was treated with 100 µM H2O2 for 5h followed by transfer of cells into fresh medium without H2O2 for 3 hours after which RNA was isolated. Two biological replicates were set for each sample.

value: promastigotes

value: Treated with 100 µM H2O2 for 5h followed by transfer of cells into fresh medium without H2O2 for 3 hours


title: OGDH KO; -Glucose1


title: Anopheles-Brain, 12pm rep 2

value: Bain


title: WT.4h.DMSO.r2

description: WT cells, harvested 4h after DMSO treatment, replicate 2


title: 3n dTag ATAC rep1

value: 24h, 3n mol/L  dTag


title: MSC, siSLC29A2,sample3

city: Hangzhou

first: Mingyang

last: Chen

address: Yuhangtang 866

institute: Zhejiang University

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the (http://mascotton.njau.edu.cn/info/1054/1118.htm) TM-1 reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Assembly: TM-1
Supplementary files format and content: txt include FPKM values for each Sample

source_name: MSC

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

value: MSC

value: Mesenchymal stromal cell

value: SLC29A2 KD


title: exp 2 set29 mutant promastigotes/untreated/biological replicate 2

value: Untreated


title: WT.4h.DMSO.r1

description: WT cells, harvested 4h after DMSO treatment, replicate 1


title: MSC, siSLC29A2,sample1


title: exp 2 set29 mutant promastigotes/H2O2-treated/biological replicate 1


title: MSC, siSLC29A2,sample2


title: 1n dTag ATAC rep1

value: 2i+LIF ESC

value: 24h, 1n mol/L  dTag


title: exp 2 set29 mutant promastigotes/untreated/biological replicate 1


title: 100n dTag ATAC rep1


title: 1n dTag ATAC rep2


title: WT.20h.DMSO.r3

description: WT cells, harvested 20h after DMSO treatment, replicate 3

value: WT


title: WT.20h.DMSO.r2

description: WT cells, harvested 20h after DMSO treatment, replicate 2


title: MSC, siSLC29A1,sample3

value: SLC29A1 KD


title: 0.3n dTag ATAC rep2

value: mESC

value: Brg1 dTag knock in

value: 24h, 0.3n mol/L  dTag


title: WT.3h.none.r2

description: WT cells, harvested 3h after no treatment, replicate 2


title: exp 2 Leishmania donovani 1S promastigotes/untreated/biological replicate 2

value: wild type


title: MSC, siSLC29A1,sample2


title: exp 2 Leishmania donovani 1S promastigotes/untreated/biological replicate 1


title: MSC, siSLC29A1,sample1


title: WT.20h.DMSO.r1

description: WT cells, harvested 20h after DMSO treatment, replicate 1

value: DMSO


title: WT.4h.ATRi.r3

description: WT cells, harvested 4h after ATRi treatment, replicate 3

value: ATRi


title: MSC,Negtive control, sample3


title: exp1 set7 null promastigotes/H2O2-treated/biological replicate 2

growth_protocol: The cells were maintained in Medium199 supplemented with 10% FBS, 100 μM Adenine and 5 μg/ml Hemin and mainatined at 26ºC. If required drugs were added in the culture

extract_protocol:
The RNA was isolated following manufacturer's instructions for PureLink RNA isolation kit (Invitrogen, USA). On-column DNase I treatment was performed during the isolation to eliminate genomic DNA contamination in the isolated RNA, as per manufacturer’s instructions.
RNA-seq library for the first experimental set was prepared using the TruSeq RNA Library Prep Kit v2.

value: promastigotes

value: Treated with 100 µM H2O2 for 5h followed by transfer of cells into fresh medium without H2O2 for 3 hours


title: Control ATAC rep2


title: 0.3n dTag ATAC rep1


title: Control ATAC rep1


title: exp1 set7 null promastigotes/untreated/biological replicate 2


title: WT.4h.ATRi.r2

description: WT cells, harvested 4h after ATRi treatment, replicate 2


title: 3n dTag ATAC rep2

value: 24h, 3n mol/L  dTag


title: MSC,Negtive control, sample2

value: MSC


title: WT.4h.ATRi.r1

description: WT cells, harvested 4h after ATRi treatment, replicate 1


title: exp1 set7 null promastigotes/H2O2-treated/biological replicate 1


title: WT ATAC rep2


title: exp1 set7 null promastigotes/untreated/biological replicate 1


title: WT.20h.ATRi.r3

description: WT cells, harvested 20h after ATRi treatment, replicate 3


title: exp1 Leishmania donovani 1S promastigotes/H2O2-treated/biological replicate 2


title: WT.20h.ATRi.r2

description: WT cells, harvested 20h after ATRi treatment, replicate 2


title: MSC,Negtive control, sample1

value: Mesenchymal stromal cell


title: 100n dTag RNA-seq rep2

data_processing:
The raw reads with sequencing adaptors or low-quality ends from reads were trimmed by trim_galore.
The clean reads were aligned to mouse genome using hisat2
To quantify gene expression, featureCounts was used to count the sequencing reads within each gene
Assembly: mm10
Supplementary files format and content: Table-delimited text file includes raw counts for each gene

extract_protocol:
RNA was extracted using Trizol. 500 ng of total RNA was used for library contruction
RNA-seq libraries were preparing using SMART-Seq Stranded Kit following manufacture's protocol

treatment_protocol: mESC was treated in fresh medium containing dTag13 chemical for 24h

value: 24h, 100n mol/L  dTag


title: WT ATAC rep1


title: 100n dTag RNA-seq rep1


title: exp1 Leishmania donovani 1S promastigotes/H2O2-treated/biological replicate 1


title: AC16 cells, siSLC29A2,sample2

value: cardiomyocyte

value: SLC29A2 KD


title: exp1 Leishmania donovani 1S promastigotes/untreated/biological replicate 2

value: Untreated


title: AC16 cells, siSLC29A2,sample1


title: WT.20h.ATRi.r1

description: WT cells, harvested 20h after ATRi treatment, replicate 1

value: WT


title: exp1 Leishmania donovani 1S promastigotes/untreated/biological replicate 1


title: 10n dTag RNA-seq rep2

value: 2i+LIF ESC

value: 24h, 10n mol/L  dTag


title: STK19_KO2.unt.none.r2

description: STK19 KO2 cells, harvested 0h after no treatment, replicate 2


title: AC16 cells, siSLC29A1,sample3

value: SLC29A1 KD


title: 10n dTag RNA-seq rep1

value: mESC

value: Brg1 dTag knock in


title: STK19_KO2.unt.none.r1

description: STK19 KO2 cells, harvested 0h after no treatment, replicate 1


title: AC16 cells, siSLC29A1,sample2


title: NET, scRNA-seq

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

country: Russia

institute: Moscow Center for Advanced Studies

description:
5' 10X Genomics
Instrument model: SurfSeq 5000

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0. Quality control included removal of cells with inappropriate gene-umi relationship using gene.vs.molecule.cell.filter (pagoda2 package), high mitochondrial (> 20 %) or ribosomal (> 20 %) RNA content. Droplets, containing multiplets were removed using Scrublet package. Expression profile was corrected for ambient RNA using DecontX from celda package. Next, cells containing > 3000 UMIs and > 1000 unique genes were remained.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix file

source_name: neuroendocrine tumor

extract_protocol:
Fresh tumor tissues were mechanically chopped with scalpels on a plate and enzymatically digested with collagenase type IV (Servicebio) and DNAse I (Magen). Following digestion, the cell suspension was subjected to erythrocyte removal using the red blood cell lysis buffer (QuantoBio). Cell suspension was filtered through a 70 μm strainer (MACS), and dissociated cells were pelleted and re-suspended in phosphate buffer saline (PBS) with 0.04% BSA (bovine serum albumin).
The Chromium Next GEM Single Cell 5' v2 Kit (10× Genomics, USA) and the Chromium Single Cell Controller Instrument were used to generate a 10× single-cell library according to the manufacturer’s instructions.

value: neuroendocrine tumor

tag: age

tag: Sex

value: female


title: 3n dTag RNA-seq rep2


title: STK19_KO2.3h.none.r3

description: STK19 KO2 cells, harvested 3h after no treatment, replicate 3


title: AC16 cells, siSLC29A1,sample1


title: AC16 cells, siSLC29A2,sample3


title: MEF,KO2

city: 武汉

first: zixuan

last: wang

state: 湖北省

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 4

data_processing:
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fastp (version 0.19.7) was used to perform basic statistics on the quality of the raw reads.
The clean reads were then mapped to the mouse genome using HISAT.
Assembly: GRCm39
Supplementary files format and content: file folder includes raw counts for each Sample
Supplementary files format and content: excel file includes FPKM values for each Sample

source_name: MEF

growth_protocol: cells were cultured in Dulbeccos’ modified Eagle's medium (DMEM) (VivaCell) supplemented with 10% fetal bovine serum (FBS) (VivaCell).

extract_protocol:
Whole RNA of mef cells infected with VSV were purified using RNeasy Mini Kit (QIAGEN NO. 74104).
Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) accordingly to the manufacturer’s protocol, and index codes were added to assign sequences to each sample.

value: MEF

value: Mouse Embryonic Fibroblast

value: SMYD3 KO

value: VSV


title: 3n dTag RNA-seq rep1

value: 24h, 3n mol/L  dTag


title: AC16 cells,Negtive control,sample3


title: STK19_KO2.3h.none.r2

description: STK19 KO2 cells, harvested 3h after no treatment, replicate 2


title: STK19_KO2.3h.none.r1

description: STK19 KO2 cells, harvested 3h after no treatment, replicate 1


title: MEF,WT2

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 2


title: STK19_KO2.4h.DMSO.r3

description: STK19 KO2 cells, harvested 4h after DMSO treatment, replicate 3

value: DMSO


title: 1n dTag RNA-seq rep2

value: 24h, 1n mol/L  dTag


title: STK19_KO2.4h.DMSO.r2

description: STK19 KO2 cells, harvested 4h after DMSO treatment, replicate 2


title: MEF,WT1

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 1


title: PESTEM [WES]

city: Seoul

first: Hyuk-Jin

last: Cha

address: 215-20 Gwan-ak ro Gwan-ak gu

country: South Korea

institute: Seoul National University

description: Whole Exome Sequencing

data_processing:
The Illumina platform generates raw images and base calling with an integrated primary analysis software called RTA. The base calling files which are expressed in binary are converted into FASTQ by Illumina package bcl2fastq v2.20.0. The demultiplexing option (—barcode-mismatches) is set as value : 0. ‘FastQC’ is then used to check the sequencing quality. Paired-end sequences produced by NovaSeq Instrument are firstly mapped to the human reference genome using the mapping program ‘BWA’. (BWA-MEM is used out of the three algorithms provided by BWA) The mapping result file is generated in BAM format, without unordered sequences and alternate haplotypes. PCR duplicates are removed using MarkDuplicates.jar from ‘Picard-tools’ package, which requires reads to be sorted. Reads with identical starting positions are considered as duplicates and reduced into a single read. BAM files are then recalibrated with Base Quality Score Recalibration (BQSR). BQSR is a process which uses machine learning to model the sequencing errors empirically and adjust the quality scores accordingly. Based on the BAM file previously generated, variant genotyping for each sample is performed with Haplotype Caller of GATK. In this stage SNP and short indels candidates are detected at nucleotide resolution. We filter variants with VariantFiltration of GATK Tool. This tool is designed for hard-filtering variant calls based on certain criteria. Records are hard-filtered by changing the value in the FILTER field to something else other than PASS. Filtered records will be preserved in the output unless their removal is requested in the command line. Filtered variants are annotated with another program called SnpEff and filtered with dbSNP and SNPs from the 1000 genome project. The format of the final product is in vcf. Then, in-house program and SnpEff are used to annotate with additional databases, including ESP6500, ClinVar, dbNSFP, ACMG information.
Assembly: hg38 from UCSC (original GRCh38 from NCBI, Dec. 2013).
Supplementary files format and content: Excel file (.xlsx) for each sample.

growth_protocol: H9 cells were maintained in stemMACS (Milteni Biotec.) media with 0.1% gentamicin.

extract_protocol:
gDNA of each sample was harvested by using Wizard® Genomic DNA Purification Kit (Promega).
Target Enrichment and Sequencing A gDNA library was prepared from 50ng of input gDNA using the Twist Library Preparation EF Kit (96 samples, PN 101058) with full-length combinatorial dual index TruSeq-compatible Y-adapters (Illumina) according to the Twist Bioscience Library Protocol. The DNA quantity and quality is measured by PicoGreen and agarose gel electrophoresis, respectively. We use 50ng of each gDNA diluted with EB Buffer and sheared to a target peak size of 200bp with the fragmentation enzyme. Fragmentation is followed by end-repair and the addition of ‘A’ tail. Twist CD index adapters are then ligated to the fragments. After assessing the efficiency of ligation, the adapter ligated product is PCR amplified.
The final purified product is quantified by TapeStation DNA screentape D1000 (Agilent) and PicoGreen. For exome capture, each hybridization reaction requires a total of 1500 ng of indexed libraries, made by pooling equal amounts from 8 individual libraries. And mixed with Fast hybridization mix, Twist exome probe, Blocker solution, and Universal Blocker, according to the Twist library preparation protocol. The captured DNA is washed and amplified. The final purified product is quantified by qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantification kits for Illumina Sequencing platforms) and qualified by the TapeStation DNA screentape D1000 (Agilent).

value: PESTEM


title: 1n dTag RNA-seq rep1


title: 0.3n dTag RNA-seq rep2

value: 24h, 0.3n mol/L  dTag


title: STK19_KO2.4h.DMSO.r1

description: STK19 KO2 cells, harvested 4h after DMSO treatment, replicate 1


title: D14 scRNA-seq of gene-edited mouse lung

city: Guilin

first: Honghao

last: Yu

state: Guangxi

address: Guilin Medical College, Lingui District, Guilin City, Guangxi

institute: Guilin Medical University

description:
Library name: D14_lung
PE150

data_processing:
Raw data was quality controlled using fastp to remove low-quality reads, adapters, and poly-A tails. Clean reads were aligned to the GRCm38 (mm10) mouse reference genome using STAR, generating a gene expression matrix for further bioinformatic analysis. Single-cell transcriptomics analysis was then performed using the Seurat package to identify differentially expressed genes and cell types.
Assembly: All sequencing data were aligned to the GRCm38 (mm10) mouse reference genome.
Supplementary files format and content: a gene expression matrix (CSV), metadata (CSV), and UMI counts (CSV)

source_name: lung

extract_protocol:
The entire lung tissues were harvested from euthanized mice, immediately placed in pre-chilled RPMI 1640 medium for initial washing to remove blood residues. The tissues were washed twice with PBS, cut into 1-2mm³ pieces, and enzymatically digested using SeekGene Tissue Dissociation Reagent A, Collagenase IV (0.1 mg/ml), and DNase I (0.01 mg/ml) in a 37°C water bath for 30 minutes to dissociate lung tissues into single-cell suspensions.
Single-cell RNA libraries were prepared using the SeekOne® Digital Droplet Single Cell Library Preparation Kit (SeekGene K00202). Cells were mixed with reverse transcription reagents and loaded into SeekOne® chips, followed by the addition of barcoded hydrogel beads and separation oil. After droplet generation, reverse transcription was performed at 42°C for 90 minutes, and PCR amplification was carried out to prepare the sequencing library.

treatment_protocol: Trav4 gene-edited mice were used in the experiments. All mice were euthanized before sample collection, and lung tissues were immediately dissected for further analysis.

value: lung

value: Trav4 gene-edited


title: PE [WES]

description: Whole Exome Sequencing

value: PE


title: Control RNA-seq rep2

value: 2i+LIF ESC


title: raw264.7,Tppu-3

city: DaLian

first: YiDing

last: Liu

address: wwde

institute: Dalian Medical University

description:
Library name: M1-TPPU-3
Column name in count.annot.xlsx:sh-LIS1-3

data_processing:
FASTQ
Remove adapter sequences from the reads
If the number of 'N' bases in a read exceeds 10% of the total read length, remove these paired reads
If the number of low-quality bases (Q ≤ 20) in a read exceeds 50% of the total read length, remove these paired reads
Assembly: mm10
Supplementary files format and content: fpkm.txt
Supplementary files format and content: txt files include fpkm values for each Sample

extract_protocol:
To extract RNA from samples, the Trizol method was used. After successful extraction, the RNA was dissolved in 50 µL of DEPC-treated water. Then, the total RNA was identified and quantified using a Qubit fluorometer and a Qsep400 high-throughput fragment analyzer.
Library construction involves enriching polyA-tailed mRNA using Oligo(dT) beads, fragmenting the mRNA, and synthesizing first strand cDNA with random hexamer primers. The second strand is synthesized with dUTP for strand specificity. After ligating adapters, the library is amplified via PCR and purified. Finally, concentration is measured with Qubit, fragment size analyzed with Qsep400, and effective concentration quantified by qPCR.

value: Macrophages cells

value: Tppu

tag: batch


title: STK19_KO2.20h.DMSO.r3

description: STK19 KO2 cells, harvested 20h after DMSO treatment, replicate 3


title: BESTEM [WES]

description: Whole Exome Sequencing

value: BESTEM


title: MEF,KO1

address: 湖北省武汉市东湖南路7号

institute: 中国科学院水生生物研究所

description: Library name: sample 3


title: Control RNA-seq rep1

value: mESC

value: Brg1 dTag knock in


title: raw264.7,Tppu-2

description:
Library name: M1-TPPU-2
Column name in count.annot.xlsx:sh-LIS1-2


title: BE [WES]

description: Whole Exome Sequencing

value: BE


title: STK19_KO2.20h.DMSO.r2

description: STK19 KO2 cells, harvested 20h after DMSO treatment, replicate 2


title: AC16 cells,Negtive control,sample2

value: cardiomyocyte

value: WT


title: raw264.7,Tppu-1

description:
Library name: M1-TPPU-1
Column name in count.annot.xlsx:sh-LIS1-1


title: STK19_KO2.20h.DMSO.r1

description: STK19 KO2 cells, harvested 20h after DMSO treatment, replicate 1


title: EP [WES]

description: Whole Exome Sequencing

value: Electroporation only


title: AC16 cells,Negtive control,sample1


title: A. fumigatus DsodB, MSB treated 2

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A. fumigatus A1163 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: genome: https://fungidb.org/common/downloads/Current_Release/AfumigatusA1163/fasta/data/FungiDB-56_AfumigatusA1163_Genome.fasta; gff3: https://fungidb.org/common/downloads/Current_Release/AfumigatusA1163/gff/data/FungiDB-56_AfumigatusA1163.gff
Supplementary files format and content: excel file includes count and RPKM values for each Sample

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: Submerged cultivation: 500 ml Erlenmeyer flasks containing 100 ml of modified Barratt’s minimal nitrate broth were inoculated with 5×107 conidia and incubated at 37° C and at 3.7 Hz shaking frequency for 20 h. The modified Barratt’s minimal broth contained 20 g/L glucose (instead of 1 g/L) and 0.92 g/L diammonium-tartrate (instead of 6 g/L NaNO3).

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq (single read, 75 bp)  were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: 6 mM menadione sodium bisulfite (MSB) treated and untreated

value: mycelium

value: delta_sodB mutant

value: MSB treated


title: A. fumigatus DsodB, MSB treated 3


title: STK19_KO2.4h.ATRi.r3

description: STK19 KO2 cells, harvested 4h after ATRi treatment, replicate 3

value: ATRi


title: raw264.7,NC-3

description:
Library name: M1-3
Column name in count.annot.xlsx:control-3

value: Control


title: NHA_CROPseq_Lib8_guidePCR

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: UNSW Sydney, High Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description:
10X Genomics Chromium V3
FinalCells_Metadata.csv

data_processing:
Data demultiplexing, barcode assignment, and gene quantification were performed using CellRanger v6.0.2 (10X Genomics)
Cells were called using the EmptyDrops algorithm (Lun, 2019).
Cells were excluded if annotated as damaged by DropletQC (Muskovic, 2021), or had a mitochondrial, MALAT1, or ribosomal transcriptome percentage > 20.
Assembly: hg38
Supplementary files format and content: The Counts, GeneNames, and Barcodes files are tab-separated values for the final set of called cells from all 7 libraries. Counts are in a sparse matrix format, with rows and columns given by GeneNames and Barcodes, respectively
Supplementary files format and content: The Metadata file is of comma-separated values for the final set of called cells from all 7 libraries. Rows correspond to Barcodes (and therefore columns in Counts)

source_name: Normal Human Astrocytes (Lonza, #CC-2565)

growth_protocol: NHA were grown in DMEM media supplemented with 10% foetal bovine serum and 1% streptomycin/penicillin at 37°C, 5% CO2

extract_protocol:
On Day7, a single cell suspension was prepared by detaching cells with trypsin and neutralising with DMEM. Cells were passed through a cell strainer, and pelleted by centrifugation at 300 x g for 5 min. The supernatant was removed, and cells were resuspended in 1 mL 1X PBS with 0.04% BSA. Cells were again centrifuged at 300 x g for 5 min, and then resuspended in 200µL 1x PBS with 0.04% BSA to a final concentration of 1050 cell/µL
Library construction was performed according to manufacturer's instructions (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 10X Genomics). For each library, a subset of the cDNA was also PCR amplified to enrich for the guide RNA expression, per Hill et al. (doi: 10.1038/nmeth.4604)

treatment_protocol: NHA were transduced with the negative control, positive control, and enhancer guide libraries at MOIs of 5, 0.2, and 5, respectively. Media was replaced after 24h, and after 48h selection was performed using 3 µg/mL of puromycin. Cells were pooled at day 4.

value: Transduction with library of 3028 guide RNAs in the CROP-seq-opti vector


title: 0.3n dTag RNA-seq rep1

value: 24h, 0.3n mol/L  dTag


title: A. fumigatus DsodB, MSB treated 1


title: raw264.7,NC-2

description:
Library name: M1-2
Column name in count.annot.xlsx:control-2


title: STK19_KO2.4h.ATRi.r2

description: STK19 KO2 cells, harvested 4h after ATRi treatment, replicate 2


title: A94 scRNA-seq of gene-edited mouse lung

description:
Library name: A94_lung
PE150

value: lung

value: Trav4 gene-edited


title: A. fumigatus DsodB, untreated 3

value: untreated


title: NHA_CROPseq_Lib7_guidePCR

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: raw264.7,NC-1

description:
Library name: M1-1
Column name in count.annot.xlsx:control-1

value: Macrophages cells


title: NHA_CROPseq_Lib5_guidePCR


title: A. fumigatus DsodB, untreated 2


title: STK19_KO2.4h.ATRi.r1

description: STK19 KO2 cells, harvested 4h after ATRi treatment, replicate 1


title: NHA_CROPseq_Lib4_guidePCR


title: eWAT, wild-type C57BL/6J mice，rep3

city: Shanghai

first: Suzhen

state: -- None --

address: 600 Yishan Road, Shanghai, China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 6
Column name in raw counts All Samples.txt: WT

data_processing:
xls files include FPKM values for each Sample
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was extracted from mouse adipose tissues or adipocytes using TRIzol reagent (Thermo Fisher Scientiﬁc, 15596).
RNA sequencing libraries were prepared from 4 μg of total RNA using the mRNA-seq V2 Library Prep Kit for Illumina (Vazyme, NR601) following the manufacturer’s instructions.

value: epididymal white adipose tissue

value: high-fat diet


title: STK19_KO2.20h.ATRi.r3

description: STK19 KO2 cells, harvested 20h after ATRi treatment, replicate 3


title: A. fumigatus DsodB, untreated 1


title: eWAT, wild-type C57BL/6J mice，rep2

description:
Library name: Sample 5
Column name in raw counts All Samples.txt: WT


title: NHA_CROPseq_Lib3_guidePCR


title: A. fumigatus akuBku80, MSB treated 3

value: reference strain


title: STK19_KO2.20h.ATRi.r2

description: STK19 KO2 cells, harvested 20h after ATRi treatment, replicate 2


title: eWAT, wild-type C57BL/6J mice，rep1

description:
Library name: Sample 4
Column name in raw counts All Samples.txt: WT

value: WT


title: NHA_CROPseq_Lib2_guidePCR


title: STK19_KO2.20h.ATRi.r1

description: STK19 KO2 cells, harvested 20h after ATRi treatment, replicate 1


title: A. fumigatus akuBku80, MSB treated 2


title: eWAT, EKO C57BL/6J mice，rep3

description:
Library name: Sample 3
Column name in raw counts All Samples.txt: EKO

value: Eepd1 knockout


title: STK19_KO1.unt.none.r3

description: STK19 KO1 cells, harvested 0h after no treatment, replicate 3


title: NHA_CROPseq_Lib1_guidePCR


title: A. fumigatus akuBku80, MSB treated 1

value: mycelium


title: eWAT, EKO C57BL/6J mice，rep2

description:
Library name: Sample 2
Column name in raw counts All Samples.txt: EKO


title: STK19_KO1.unt.none.r2

description: STK19 KO1 cells, harvested 0h after no treatment, replicate 2


title: NHA_CROPseq_Lib8

description:
10X Genomics Chromium V3
FinalCells_Counts.mtx
FinalCells_GeneNames.tsv
FinalCells_Barcodes.tsv
FinalCells_Metadata.csv


title: eWAT, EKO C57BL/6J mice，rep1

description:
Library name: Sample 1
Column name in raw counts All Samples.txt: EKO


title: STK19_KO1.unt.none.r1

description: STK19 KO1 cells, harvested 0h after no treatment, replicate 1


title: A. fumigatus akuBku80, untreated 3


title: A. fumigatus akuBku80, untreated 2


title: NHA_CROPseq_Lib7


title: C80 scRNA-seq of WT mouse lung

description:
Library name: C80_lung
PE150

treatment_protocol: Galt gene-edited mice (GAL mice) and wild-type (WT) mice were used in the experiments. All mice were euthanized before sample collection, and lung tissues were immediately dissected for further analysis.

value: Wild-type (WT)


title: NHA_CROPseq_Lib5


title: STK19_KO1.3h.none.r3

description: STK19 KO1 cells, harvested 3h after no treatment, replicate 3


title: A. fumigatus akuBku80, untreated 1


title: T21 CA IFN 2

city: Boulder

first: Meaghan

last: Courvan

state: CO

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

data_processing:
Raw files were mapped separately to both human (hg38) and drosophila (dm6) genomes using the NascentFlow pipeline (https://github.com/Dowell-Lab/Nascent-Flow). Gene body reads from mapped .bam files were counted using featureCounts (Liao et al. Bioinformatics 2014).
Bidirectional reads for the human genome were identified using the BidirectionalFlow pipeline (https://github.com/Dowell-Lab/Bidirectional-Flow). A master "annotation" file of every bidirectional site in every sample was created from this output, and was used to count bidirectional reads in each sample using featureCounts.
Bidirectional reads from BidirectionalFlow and mapped .bam files from NascentFlow were input into Transcription Factor Enrichment Analysis (https://github.com/Dowell-Lab/TFEA) to characterize relative transcription factor activity
Assembly: hg38
Assembly: dm6
Supplementary files format and content: All *.rcc.tdf files were generated as part of NascentFlow pipeline using hg38
Supplementary files format and content: featurecounts_hg38_5ptrunc.txt file is the output of featureCounts for reads mapping to hg38 gene bodies. This was counted using an annotation file in which the 5' end of genes was truncated to eliminate the effects of disproportionately high transcription observed across 5' ends
Supplementary files format and content: featurecounts_hg38_bidir.txt file is the output of featureCounts for bidirectional transcription reads, generated from the output of BidirectionalFlow
Supplementary files format and content: featurecounts_dm6_diff53prime.txt file is the output of featureCounts for reads mapping to dm6 gene bodies.

source_name: Immortalized cells

growth_protocol: Lymphoblastoid suspension cells were grown in RPMI medium supplemented with 20% fetal bovine serum, pennicilin/strep, and L-glutamine in incubators set to 37C and 5% CO2

extract_protocol:
45 minutes after vehicle or IFNγ treatment, cells were collected, spun down, washed once in PBS,  then nuclei were isolated using a lysis buffer containing 10 mM Tris pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1 uL/10 mL SUPERase-In, and protease/phosphatase inhibitor cocktail. Nuclei were snap-frozen in freezing buffer consisting of 50 mM Tris pH 8.3, 5 mM MgCl2, 40% glycerol. 0.1 mM EDTA, and SUPERase-In until library preparation
10 million human nuclei/replicate were mixed with 100,000 Drosophila melanogaster nuceli per replicate. Nuclear run-ons were performed in the presence of biotinylated CTP and nascent RNA was isolated using strepdavidin beads. Library preparation was performed as described in Fant et al. Mol Cell 2021 (PMID 32229306)
PRO-seq

treatment_protocol: Cells were split and plated on T75 flasks, allowed to recover for 24 hours, then media containing either vehicle (final concentration 0.01% DMSO) or Cortistatin A (100 nM) was added to each flask. After 30 minutes, media containing either vehicle (final concentration 40 μM Tris pH 7.4) or 10 ng/mL recombinant IFNγ (Gibco, PHC4031)

value: Immortalized cells

value: Lymphoblastoid

value: B cells

value: 100 nM Cortistatin A + 10 ng/mL IFNg


title: E27 scRNA-seq of GAL mouse lung

description:
Library name: E27_lung
PE150

value: Galt gene-edited (GAL)


title: NHA_CROPseq_Lib3

value: Transduction with library of 3028 guide RNAs in the CROP-seq-opti vector


title: STK19_KO1.3h.none.r1

description: STK19 KO1 cells, harvested 3h after no treatment, replicate 1


title: E19 scRNA-seq of GAL mouse lung

description:
Library name: E19_lung
PE150

value: lung


title: STK19_KO1.3h.none.r2

description: STK19 KO1 cells, harvested 3h after no treatment, replicate 2


title: T21 IFN 2

value: 0.01% DMSO + 10 ng/mL IFNg


title: T21 CA IFN 1


title: NHA_CROPseq_Lib2

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: STK19_KO1.4h.DMSO.r3

description: STK19 KO1 cells, harvested 4h after DMSO treatment, replicate 3

value: DMSO


title: STK19_KO1.4h.DMSO.r2

description: STK19 KO1 cells, harvested 4h after DMSO treatment, replicate 2


title: NHA_CROPseq_Lib1


title: T21 IFN 1


title: prefrontal cortex, hGFAP-Cre_Egfr-cko_biol rep 3

first: Guoping

address: 138 Yi Xue Yuan Road

institute: Fudan University

description:
Library name: RNA sample2 _biol rep 3
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls

data_processing:
scRNA-seq: High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
bulk RNA-seq: Remove the adapter sequences contained in the reads. Remove bases with a quality score (Q) lower than 20 at the 3' end, which corresponds to a base error rate of less than 0.01, where Q = -10log(error_ratio). Remove reads with a length of less than 25. Remove ribosome RNA reads belonging to the species in question.
bulk RNA-seq: Genome mapping using Hisat2 (Version: 2.0.4)
bulk RNA-seq: Default parameters
Assembly: mm10/GRCm38
Supplementary files format and content: scRNA-seq: Tab-separated value files and matrix files and Rdata
Supplementary files format and content: bulk RNA-seq: table

source_name: prefrontal cortex

extract_protocol:
scRNA-seq: FlashTag (CellTrace Yellow, Life Technologies, #C34567, 0.5 μl of 10 mM) was injected into the cortical lateral ventricle of control mice, hGFAP-Cre; Egfr-cko and hGFAP-Cre; MAP2k1/2-dcko mice at E18 and E16, respectively. P2 and E17 brains were harvested respectively and submerged in fresh ice-cold Hanks’ balanced salt solution (Gibco 14175-095). The dorsal cortices were cut into small pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufacturer’s instruction. The tdTomato+ (tdT+) cells were captured and harvested through fluorescence-activated cell sorting (FACS).
scRNA-seq: The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina Novaseq 6000.
bulk RNA-seq: The P50 PFC tissue was collected from hGFAP-Cre; Egfr-cko and same-litter homozygotes . Direct-zol RNA Miniprep kit (Zymo, catalog #R2050) was used to isolate total RNA following the manufacturer’s instructions.
bulk RNA-seq: The purified Total RNA is subjected to mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, 3’ end A addition, linker ligation, enrichment, and other processes

value: prefrontal cortex


title: prefrontal cortex, hGFAP-Cre_Egfr-cko_biol rep 2

description:
Library name: RNA sample2 _biol rep 2
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls


title: D21 CA IFN 2


title: STK19_KO1.20h.DMSO.r3

description: STK19 KO1 cells, harvested 20h after DMSO treatment, replicate 3


title: endoC-BH1 - exp216 - Non-Treated

city: Anderlecht

first: Florian

last: Szymczak

state: Brussels

address: Route de Lennik 808 - CP618

department: Faculty of Medicine

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
The raw RNA-seq data of EndoC-BH1 cells treated with IFNa, IL-1B, and TNFa [ 2 x 150-bp paired-end with a sequencing depth > 200 million reads (Eurofins Genomics, Germany)] were first subjected to a quality check using fastp to remove low quality reads and adaptor trimming. The passing reads were then subjected to quality control (QC) using FastQC (Babraham Bioinformatics, Cambridge, UK).
For comparison purposes, these five paired RNA-seq replicates were re-analyzed as described below. Gene expression was quantified using Salmon v1.457 with additional parameters “-seqBias -gcBias -validateMappings” and expressed in TPM (transcripts per million).
GENCODE v36 was used as the reference genome and indexed with default k-mer values. The genes differentially expressed after exposure to cytokines were identified by DESeq2 v1.30.158.
For each gene, a log2 fold change value was obtained based on the comparison performed (cytokine-treated condition versus non-treated condition). Each gene comparison has an associated Wald test statistic, p-value, and an adjusted p-value (Benjamini-Hochberg correction). Genes presenting an adjusted p-value < 0.05 were considered significantly differentially expressed.
Assembly: GENCODE v36
Supplementary files format and content: Tab Separated Values (TSV) file containing TPM values at the gene level

growth_protocol: The human insulin-secreting EndoC-BH1 cells were provided by Dr. R. Scharfmann (Institut Cochin, Université Paris Descartes, Paris, France). EndoC-BH1 cells were cultured in DMEM containing 5.6 mmol/L glucose (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), 2% BSA fraction V, fatty acid free (Roche, Basel, Switzerland), 50 μmol/L 2-mercaptoethanol (Sigma-Aldrich, St Louis, MO, USA), 10 mmol/L nicotinamide (Calbiochem, Darmstadt, Germany), 5.5 μg/mL transferrin (Sigma-Aldrich), 6.7 ng/mL selenite (Sigma-Aldrich), 100U/mL penicillin + 100 μg/mL streptomycin (Lonza, Leusden, Netherlands), in matrigel-fibronectin-coated plates, as previously described.

extract_protocol:
After treatment with the respective cytokines for 24h, total RNA was isolated from EndoC-BH1 cells using the RNeasy Plus Micro Kit (Qiagen, Venlo, Netherlands), according to the recommended protocol. For all the samples, a minimum of 500 ng of high-quality RNA with RNA integrity number (RIN) > 9 (determined using Agilent Bioanalyzer) was used for the library preparation.
RNA-sequencing (RNA-seq) was performed on NovaSeq 6000 (Eurofins Genomics Europe Sequencing GmbH, Konstanz, Germany).

treatment_protocol: EndoC-BH1 cells were exposed or not to IFNg (1000 U/mL, PeproTech Inc.), IL-1B (50 U/mL, R&D Systems, Minneapolis, MN, USA), and TNFa (1000 U/mL,  PeproTech Inc.) for 24h. After this period, the cells were washed with PBS and harvested for RNA and protein extraction.

value: pancreatic beta cells

value: NT


title: prefrontal cortex, hGFAP-Cre_Egfr-cko_biol rep 1

description:
Library name: RNA sample2 _biol rep 1
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls


title: prefrontal cortex, hGFAP-Cre_Egfr-cko

description:
Library name: RNA sample2
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls


title: D21 CA IFN 1


title: endoC-BH1 - exp216 - IL1B


title: C73 scRNA-seq of WT mouse lung

description:
Library name: C73_lung
PE150


title: STK19_KO1.20h.DMSO.r2

description: STK19 KO1 cells, harvested 20h after DMSO treatment, replicate 2

extract_protocol:
RNA was extracted according to the Qiagen Rneasy extraction kit's protocol
RNA-seq libraries were prepared using NEBNext Ultra II Directional PolyA mRNA according to the manufacturers' instructions.


title: NHA_CROPseq_Lib4


title: D21 CA 2

value: 100 nM Cortistatin A + 40 uM Tris pH 7.4


title: P50 prefrontal cortex RNA-seq_biol rep 3

description:
Library name: RNA sample1_biol rep 3
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls

value: CTR (same litters homozygote)


title: endoC-BH1 - exp214 - TNFa

value: TNFa


title: STK19_KO1.20h.DMSO.r1

description: STK19 KO1 cells, harvested 20h after DMSO treatment, replicate 1


title: D21 CA 1


title: STK19_KO1.4h.ATRi.r3

description: STK19 KO1 cells, harvested 4h after ATRi treatment, replicate 3

value: ATRi


title: endoC-BH1 - exp214 - IL1B


title: STK19_KO1.4h.ATRi.r2

description: STK19 KO1 cells, harvested 4h after ATRi treatment, replicate 2


title: STK19_KO1.4h.DMSO.r1

description: STK19 KO1 cells, harvested 4h after DMSO treatment, replicate 1


title: P50 prefrontal cortex RNA-seq_biol rep 1

description:
Library name: RNA sample1_biol rep 1
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls


title: P50 prefrontal cortex RNA-seq

description:
Library name: RNA sample1
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls


title: P50 prefrontal cortex RNA-seq_biol rep 2

description:
Library name: RNA sample1_biol rep 2
Bulk RNA-seq
P50_hGFAP-Cre Egfr_PFC.xls


title: endoC-BH1 - exp216 - TNFa


title: STK19_KO1.4h.ATRi.r1

description: STK19 KO1 cells, harvested 4h after ATRi treatment, replicate 1


title: D21 IFN 1

value: Immortalized cells


title: E17 cortex single cell RNA-seq

description:
Library name: scRNA sample4
10x Genomics
E16_FT_E17_hGFAP-Cre_mek12dcko.Rdata

source_name: cortex

value: cortex


title: endoC-BH1 - exp214 - Non-Treated


title: D21 V 2

value: Lymphoblastoid

value: B cells

value: 0.01% DMSO + 40 uM Tris pH 7.4


title: STK19_KO1.20h.ATRi.r3

description: STK19 KO1 cells, harvested 20h after ATRi treatment, replicate 3


title: D21 V 1


title: cortex, hGFAP-Cre_MAP2K1/2-dcko

description:
Library name: scRNA sample3
10x Genomics
E16_FT_E17_hGFAP-Cre_mek12dcko.Rdata


title: endoC-BH1 - exp213 - TNFa


title: 5.2102EP-YSTlike.R1

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
Raw sequencing data was processed using the 10X Genomics CellRanger software (v7.0). Raw BCL-files were demultipexed and processed to Fastq-files using the CellRanger mkfastq pipeline. Alignment of reads to the GRCh38 genome and UMI counting was performed via the CellRanger count pipieline to generate a gene-barcode matrix. All samples were aggregated and normalized for sequencing depth using the cellranger aggr pipeline.
Further analyses were carried out with the Seurat v4.1.1 R package. Initial quality control consisted of removal of cells with fewer than 200 detected genes as well as removal of genes expressed  in less than 3 cells. Furthermore, cells with a mapping rate of > 10 % to the mitochondrial genome have been removed, as they represent dead or damaged cells. Cell doublets have been removed from the dataset using DoubletFinder v2.0 [4]. Normalization has been carried out utilizing SCTransform. Dimensional reduction of the data set was achieved by Principal Component analysis (PCA) based on identified variable genes and subsequent UMAP embedding. The number of meaningful Principal Components (PC) was selected by ranking them according to the percentage of variance explained by each PC, plotting them in an “Elbow Plot” and manually determining the number of PCs that represent the majority of variance in the data set. Cells were clustered using the graph-based clustering approach implemented in Seurat.  Markers defining each cluster as well as differential gene expression between different clusters were calculated using a Wilcoxon Rank Sum test which is implemented in Seurat.
Assembly: Alignment of reads to the Homo sapiens (GRCh38) genome sequence.
Supplementary files format and content: CellRanger output

growth_protocol: NCCIT cells were cultured in RPMI 1640 (Thermo Fisher Scientific). 2102EP were cultured in DMEM-GlutaMaX with Pyruvat (Thermo Fisher Scientific). Both media were supplemented with 10% FBS (Thermo Fisher Scientific), 1% penicillin/streptomycin  and 200 mMl-glutamine. GCT27 cells were cultivated in DMEM-GlutaMaX including 10& FBS (Thermo Fisher Scientific), 0.5 % penicillin/streptomycin  and 200 mMl-glutamine.

extract_protocol:
Cells were washed with PBS. Next cells were treated with 0,05 % trypsin and incubated for 5 minutes, 37°C, 7,5% CO2. After detaching from cell culture dish, cells were resuspended in DMEM-GlutaMaXx containing 10% FBS, 1% L-Glutamin and 1 % Pen/Strep.
Single cells were generated on the 10X Chromium Controller system for single-cell droplet library generation utilizing the Chromium Single Cell 3’ NextGEM Reagent Kit v3.1 (10X Genomics) according to manufacturer’s instructions. Sequencing was carried out on a NextSeq2000 system (Illumina Inc) with a mean sequencing depth of ~50,000 reads/cell for gene expression libraries.

treatment_protocol: All three embryonal carcinoma cell lines (2102EP-, GCT27-,NCCIT-lenti-MPHv2) were differentiated via treatment with SOX17-lenti-SAMv2-lentiviruses to induce endogenous overexpression of transcription factor SOX17. Next day, viruses were washed away and follow up treatment with recombinant Activin-A (100 ng/ml), CHIRON (3 µM), recombinant FGF2 (25 ng/ml) and recombinant Heparin (1 µg/ml) was added. The treatment with the recombinant protein mixture was repeated every 48h for 8 days.

value: embryonal carcinoma, germ cell tumor

value: YST-like differentiation


title: endoC-BH1 - exp213 - Non-Treated


title: STK19_KO1.20h.ATRi.r1

description: STK19 KO1 cells, harvested 20h after ATRi treatment, replicate 1

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.12.0 (https://doi.org/10.5281/zenodo.7998767) with the STAR (Dobin et al, 2012) /RSEM (Li et al 2011) option against human genome assembly GRCh38 and Ensembl release 110 transcript annotations.  The “--additional_fasta” parameter was used to simultaneously quantify reads against synthetic ERCC spike-ins.  All other options were left as default.
Counts Per Million mapped reads (CPM) scaled BigWig files were generated from BAM files using Deeptools v3.5.1’s bamCoverage function for each strand in turn using the options “--normalizeUsing CPM –binSize 1 --filterRNAstrand” (Ramirez et al., 2014).
Assembly: GRCh38
Supplementary files format and content: Counts-per-million scaled, strand-specific, bigwig files.
Supplementary files format and content: Comma separated, integer raw gene counts for each sample in a matrix format.


title: endoC-BH1 - exp213 - IL1B


title: CSB_KO.unt.none.r3

description: CSB KO cells, harvested 0h after no treatment, replicate 3


title: D21 IFN 2

value: 0.01% DMSO + 10 ng/mL IFNg


title: endoC-BH1 - exp213 - IFNg

value: IFNg


title: P2 cortex single cell RNA-seq

description:
Library name: scRNA sample
10x Genomics


title: 1.NCCIT-YSTlike.R1

source_name: NCCIT

value: NCCIT


title: endoC-BH1 - exp214 - IFNg


title: ROSAE3_Cntrl_6

first: Carles

last: Gaston-Massuet

state: London

address: Charterhouse Sq

department: Endocrinology

institute: Queen Mary University  of London

description: Library name: ROSAE3

data_processing:
Reads were quality trimmed using trimgalore v0.6.5 and aligned to reference genome GRCm39 using STAR v2.7.9a. Reads were counted using featurecounts, and the ENSEMBL annotation gencode.vM33.primary_assembly.annotation.gtf. Downstream analysis was performed in DESeq2.
Assembly: GRCm39
Supplementary files format and content: FeatureCounts_APC_study.xlsx

source_name: Pituitary

extract_protocol:
FAC-sorted pituitary APC-mutant and wild-type cells were sorted into triazole and frozen at -80C. mRNA extraction was performed using PureLinkTM RNA Micro Kit (Ref  12183-016) according to the manufacturer protocol and only samples with a RIN of 9.5 where submitted to mRNA-seq. RNA-Seq analysis was performed using Novogene in-house protocol on the Illumina NovaSeq platform (HWI-ST1276) with paired-end 150bp sequencing strategy
RNA amplification (SMARTer kit). Data quality control,Illumina Sequencing PE150,RNA sample QC,mRNA library preparation (poly A enrichment)

value: Pituitary

value: wildtype


title: HPC-Int

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Subreads coming from PacBio Sequel II SMRTcells were processed via the SMRTLink’s IsoSeq3 pipeline (version 10.0.0) with default parameters.
This pipeline is composed of the following 6 steps: Circular Consensus Sequence (CCS) calling, primer removal/demultiplexing, refining, merging, clustering and polishing. Resulting FLNC reads were mapped with minimap2 (v2.22) against GRCh38 genome with the following parameters : -cx splice:hq -uf .
Assembly: GRCh38
Supplementary files format and content: BED
Library strategy: Iso-Seq

source_name: iPS-derived hepatic progenitor cells

extract_protocol:
Total RNA was extracted by RNeasy Mini (QIAGEN, Venlo, Netherlands).
Firstly, the first strand cDNA was synthesized from the polyA+ tail by NEBNext’s reverse transcriptase. Then the enzyme’s terminal transferase activity added a few extra nucleotides to the 3’ end of the cDNA. Subsequently template switching, extension and amplification were performed to generate double-stranded cDNA. The cDNA was ligated with universal hairpin adapters. After purification with magnetic beads , sequencing primer was annealed to the SMRTbell templates, followed by binding of the sequence polymerase to the annealed templates.

value: iPS-derived hepatic progenitor cells


title: ROSAE2_Cntrl_5

description: Library name: ROSAE2


title: endoC-BH1 - exp212 - TNFa

value: pancreatic beta cells


title: STK19_KO2.unt.none.r3

first: Richard

description: STK19 KO2 cells, harvested 0h after no treatment, replicate 3


title: CSB_KO.unt.none.r1

description: CSB KO cells, harvested 0h after no treatment, replicate 1


title: CSB_KO.unt.none.r2

description: CSB KO cells, harvested 0h after no treatment, replicate 2


title: endoC-BH1 - exp212 - IL1B


title: STK19_KO1.20h.ATRi.r2

description: STK19 KO1 cells, harvested 20h after ATRi treatment, replicate 2


title: CSB_KO.3h.none.r3

description: CSB KO cells, harvested 3h after no treatment, replicate 3


title: cortex, hGFAP-Cre_Egfr-cko

description:
Library name: scRNA sample2
10x Genomics


title: endoC-BH1 - exp212 - Non-Treated

value: NT


title: ROSAJC2_Cntrl_2

description: Library name: ROSAJC2


title: 3.GCT27-YSTlike.R1


title: CSB_KO.3h.none.r1

description: CSB KO cells, harvested 3h after no treatment, replicate 1


title: endoC-BH1 - exp211 - TNFa

value: TNFa


title: endoC-BH1 - exp211 - Non-Treated


title: Pj_AM_mRNA

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

description: Pj

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter(GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG) trimmed with fastx_clipper
mapped using bowtie -t -k 2 -v 2 -p 16 --sam --quiet  --solexa1.3-quals --chunkmbs 256 --sam-nohead --sam-nosq --best --strata
detecting different expression gene using edgeR
Genome_build: Final_unigene.fa (Parabronema skrjabini denovo transcriptome assembly)
Supplementary_files_format_and_content: expressed_gene_RPKM.txt reports abundance measurements

organism: Parabronema skrjabini

source_name: adult male

extract_protocol:
Total RNA was extracted from eggs, infective larvae, adult male and female using the TRIzol reagent. RQ1 DNase was added to remove the DNA templates. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smart spec plus. RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each stage, 5μg of total RNA was used for RNA-seq library preparation with the Balancer NGS Library Preparation Kit (Gnomegen). Dyna oligo (dT) beads (Ambion) were used to isolated poly(A) mRNA from the total RNA samples. Purified mRNAs were fragmented into short pieces in fragmentation buffer. RNA fragments were end-repaired and ligated with 5'adaptor. Then reverse transcription was performed using RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified. The PCR products corresponding to 300-500 bps were purified, quantified and stored at -80 ℃ until used for sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to Illumina Nextseq 500 system for 150nt and Hiseq 2000 system for 90nt paired-end sequencing by ABlife. Inc (Wuhan, China).

tag: developmental stage

value: A

tag: gender

value: M


title: Pj_egg_mRNA

description: Pj

source_name: egg

value: egg


title: Pj_AF_mRNA

description: Pj

source_name: adult female

value: F


title: ROSAJC1_Cntrl_1

description: Library name: ROSAJC1


title: CSB_KO.4h.DMSO.r3

address: 1 Midland Road

institute: The Francis Crick Institute

description: CSB KO cells, harvested 4h after DMSO treatment, replicate 3

value: DMSO


title: endoC-BH1 - exp211 - IL1B


title: ROSAJC4_Cntrl_4

description: Library name: ROSAJC4


title: HAP1 DNMT1 L1TD1 DKO rep3

city: Vienna

first: Christian

last: Seiser

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

data_processing:
RNA-Seq pipeline of IMP/IMBA Bioinfo core facility (ii-bioinfo@imp.ac.at)
Adapters are clipped with trimgalore (Martin, 2011). Abundant sequence fractions (rRNA) are removed using (bowtie2) (Langmead & Salzberg, 2012).
Mapped reads are assigned to corresponding genes using featureCounts
Analysis of differentially expressed genes is performed using DESeq2
Assembly: Cleaned raw reads are mapped against the reference genome (hg38,Homo_sapiens.GRCh38.107.gtf) with STAR.
Supplementary files format and content: genecounts.txt

source_name: chronic myelogenous leukemia (CML) cell line

growth_protocol: DNMT1 KO and DNMT1 L1TD1 DKO HAP1 cells were cultured in IMDM medium supplemented with 10% FBS and 1% pen/strep in 37C humidified incubator with 5% CO2

extract_protocol:
Total RNA isolation was done using TRIZOL and 1ug was taken for library preparation
Libraries were prepared following the protocol of QuantSeq 3' mRNA-seq Library Prep (FWD) Kit. Quality of the libraries was analysed by Bioanalyzer.

value: CML

value: DNMT1 L1TD1 DKO


title: CSB_KO.4h.DMSO.r2

city: London

last: Mitter

description: CSB KO cells, harvested 4h after DMSO treatment, replicate 2


title: endoC-BH1 - exp211 - IFNg


title: JS13_APC_Lef1_6

description: Library name: JS13

value: APC-mutant


title: HBV-KMT2B integrated HCC Iso-seq

data_processing:
Subreads coming from PacBio Sequel II SMRTcells were processed via the SMRTLink’s IsoSeq3 pipeline (version 9.0.0) with default parameters.
This pipeline is composed of the following 6 steps: Circular Consensus Sequence (CCS) calling, primer removal/demultiplexing, refining, merging, clustering and polishing. Resulting FLNC reads were mapped with minimap2 (v2.22) against GRCh38 genome with the following parameters : -cx splice:hq -uf .
Assembly: GRCh38
Supplementary files format and content: BED
Library strategy: Iso-Seq

source_name: Hepatocellular carcinoma

value: Hepatocellular carcinoma


title: HAP1 DNMT1 L1TD1 DKO rep2

value: chronic myelogenous leukemia (CML) cell line


title: ROSAJC3_Cntrl_3

description: Library name: ROSAJC3


title: CSB_KO.4h.DMSO.r1

description: CSB KO cells, harvested 4h after DMSO treatment, replicate 1


title: JS12_APC_Lef1_5

description: Library name: JS12


title: patient-derived cervical cancer cell group, β-estradiol stimulation, day1, Rep3

city: 湖北

first: Yiyi

last: Kang

address: Donghu road

institute: WuHan University

data_processing:
The index trimmed pair-end 150 base pair reads were aligned to the human reference genome (GRCh38) using Hisat2 (v2.1.0).
StringTie (v2.1.1) was used to assemble and quantitative full-length transcripts representing multiple splice variants for each gene locus.
Assembly: GRCh38
Supplementary files format and content: Processed data files include FPKM values and count values for each Sample

source_name: PDCC

extract_protocol:
Total RNA was extracted from uterine tissues or cells with the RNeasy Mini Kit (74104, Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared using the Ribo-Zero GoldrRNA Removal (Illumina) followed by sequencing on NovaSeq6000 (Illumina).

value: PDCC

value: Human uterine primary cells

value: WT

value: estradiol stimulation


title: CSB_KO.3h.none.r2

description: CSB KO cells, harvested 3h after no treatment, replicate 2


title: HAP1 DNMT1 L1TD1 DKO rep1


title: CSB_KO.20h.DMSO.r3

description: CSB KO cells, harvested 20h after DMSO treatment, replicate 3


title: patient-derived cervical cancer cell group, β-estradiol stimulation, day1, Rep2


title: HAP1 DNMT1 KO rep2

value: DNMT1 KO


title: patient-derived cervical cancer cell group, β-estradiol stimulation, day1, Rep1


title: JS2_APC_Lef1_1

description: Library name: JS2

value: Pituitary


title: JS11_APC_Lef1_4

description: Library name: JS11


title: HAP1 DNMT1 KO rep3


title: JS8_APC_Lef1_2

description: Library name: JS8


title: CSB_KO.20h.DMSO.r2

description: CSB KO cells, harvested 20h after DMSO treatment, replicate 2


title: patient-derived cervical cancer cell group, control, day1, Rep3

value: control


title: HAP1 DNMT1 KO rep1


title: LA1339

city: Stanford

first: Gabor

last: Boross

state: CA

address: 450 Serra Mall

institute: Stanford University

description: barcode region of lentiviral backbones from genomic DNA from bulk tumor-bearing lungs were PCR-amplified and high-throughput DNA sequenced

data_processing:
For genomic barcoded DNA, the sgIDs (specific for given guideRNA and so genotype of the tumor) and barcodes (specific to tumor) were identified from fastq files and tumor size (cell number) was calculated by normalizing the number of reads to  three benchmarks “spike-in” cell lines with custom R and python scripts.
Assembly: no genome build or mapping to genome was done
Supplementary files format and content: The dual_guide_tumor_sizes.csv file contains all tumor sizes (number of cells) for all tumors/expansions. The mouse genotype, sample title, guideRNA are shown in comma separated text table.
Library strategy: Amplicon-seq

growth_protocol: Autochthonous lung tumors were initiated in mice below with Lenti-U6BC-sgDbl/Cre lentiviral pool  and harvested after ~3 months.Mice genotypes used: KrasLSL-G12D;R26LSL-Tomato (KT); KT;H11_LSL-Cas9 and KT;H11LSL-Cas9.

extract_protocol:
Following homogenization and overnight protease K digestion, genomicDNA was extracted from the lung lysates using standard phenol-chloroform and ethanolprecipitation methods.
Tuba-seqUltra libraries were generated by isolating genomic DNA from bulk tumor- bearing lung tissue, followed by PCR amplification of the BC-sgRNA1-sgRNA2 region from 32 μg of bulk lung genomic DNA using Q5 Ultra II High-Fidelity 2× Master Mix (New England Biolabs, M0494X). Unique dual-indexed primers were used to amplify each sample followed by purification using Agencourt AMPure XP beads (Beckman Coulter, A63881). The libraries were pooled based on lung weights to ensure even read depth and sequenced (read length 2 × 150 bp) on the Illumina NextSeq 6000 platform.

value: lung


title: CSB_KO.20h.DMSO.r1

description: CSB KO cells, harvested 20h after DMSO treatment, replicate 1


title: patient-derived cervical cancer cell group, control, day1, Rep2


title: DNMT1 L1TD1 DKO IP-3

data_processing:
RNA-Seq pipeline of IMP/IMBA Bioinfo core facility (ii-bioinfo@imp.ac.at)
Adapters are clipped with trimgalore (Martin, 2011). Abundant sequence fractions (rRNA) are removed using (bowtie2) (Langmead & Salzberg, 2012).
Mapped reads are assigned to corresponding genes using featureCounts
Analysis of differentially expressed genes is performed using DESeq2
Assembly: Cleaned raw reads are mapped against the reference genome (hg38,Homo_sapiens.GRCh38.107.gtf) with STAR.

extract_protocol:
Total RNA isolation was done using TRIZOL and 1ug was taken for library preparation
Libraries were prepared following the protocol of SmartSeq V3. The quality of the libraries was analysed by Bioanalyzer.


title: CSB_KO.4h.ATRi.r2

description: CSB KO cells, harvested 4h after ATRi treatment, replicate 2

value: ATRi


title: CSB_KO.4h.ATRi.r3

description: CSB KO cells, harvested 4h after ATRi treatment, replicate 3


title: patient-derived cervical cancer cell group, control, day1, Rep1


title: DNMT1 L1TD1 DKO IP-2


title: CSB_KO.4h.ATRi.r1

description: CSB KO cells, harvested 4h after ATRi treatment, replicate 1


title: LA1332


title: cervical intraepithelial Neoplasia HPV18 cells group, β-estradiol stimulation, day1, Rep3


title: DNMT1 L1TD1 DKO IP-1


title: LA1330


title: CSB_KO.20h.ATRi.r3

description: CSB KO cells, harvested 20h after ATRi treatment, replicate 3


title: cervical intraepithelial Neoplasia HPV18 cells group, β-estradiol stimulation, day1, Rep2


title: LA1317


title: cervical intraepithelial Neoplasia HPV18 cells group, β-estradiol stimulation, day1, Rep1


title: CSB_KO.20h.ATRi.r2

description: CSB KO cells, harvested 20h after ATRi treatment, replicate 2


title: DNMT1 KO IP-3


title: cervical intraepithelial Neoplasia HPV18 cells group, control, day1, Rep3


title: DNMT1 KO IP-2


title: LA1309


title: LA1281


title: VCaP16, siNTC_AR_3

city: Boston

first: Steven

last: Balk

state: MA

address: 3 Blackfan Circle

institute: Harvard Medical School

description: Cuff_Gene_Counts_siEx1_siEx7_siV7_ARD.csv

data_processing:
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters
cufflinks v2.2.1 was used to generate FPKM values
Assembly: hg19
Supplementary files format and content: comma-separated values file includes FPKM vaues for each sample
Supplementary files format and content: comma-separated values file includes differential gene expressions (log2(Fold Change) and statistical values)

source_name: Prostate

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
Transcriptome library construction (with Novogene)

value: Prostate

value: ENZ-resistant VCaP

value: prostate cancer

value: 16uM enzalutamide + non-targeted siRNA


title: cervical intraepithelial Neoplasia HPV18 cells group, control, day1, Rep2


title: CSB_KO.20h.ATRi.r1

description: CSB KO cells, harvested 20h after ATRi treatment, replicate 1


title: LA1314

source_name: lung


title: DNMT1 L1TD1 DKO  10% input rep3

value: CML

value: DNMT1 L1TD1 DKO


title: LA1303


title: VCaP16, siNTC_AR_2


title: cervical intraepithelial Neoplasia HPV18 cells group, control, day1, Rep1


title: VCaP16, siNTC_AR_1


title: LA1302


title: LA1290


title: DNMT1 L1TD1 DKO  10% input rep1


title: normal cervical epithelial cells group, β-estradiol stimulation, day1, Rep2

source_name: NCEC

value: NCEC


title: VCaP16, siEx7_3

description:
Cuff_Gene_Counts_siEx1_siEx7_siV7_ARD.csv
VCaP16_siExon7AR_vs_siCntr.deseq.csv

value: 16uM enzalutamide + AR Exon7 siRNA


title: DNMT1 KO  10% input rep3

value: chronic myelogenous leukemia (CML) cell line


title: normal cervical epithelial cells group, β-estradiol stimulation, day1, Rep1

value: Human uterine primary cells


title: VCaP16, siEx7_2

value: WT


title: VCaP16, siEx7_1


title: DNMT1 KO  10% input rep2


title: DNMT1 KO IP-1


title: LA1279


title: DNMT1 KO  10% input rep1


title: VCaP16, siEx1_3

description:
Cuff_Gene_Counts_siEx1_siEx7_siV7_ARD.csv
VCaP16_siExon1AR_vs_siCntr.deseq.csv

value: 16uM enzalutamide + AR Exon1 siRNA


title: VCaP16, siEx1_2


title: normal cervical epithelial cells group, control, day1, Rep2


title: LA1277


title: normal cervical epithelial cells group, control, day1, Rep1


title: VCaP16 ARCC-32, ARv7, IP rep 2

description:
V16_12_ARD_ARv7.rep1_treat_pileup.bw
V16_12_ARD_ARv7.rep1_sorted_peaks.narrowPeak.bed

data_processing:
CHromatin enrIchment ProceSsor (CHIPS) an analysis pipelinewas used to analyze ChIP-seq reads. Fastq files were aligned to hg19 reference genome using bwa mem aligner (0.7.15-r1140) with default parameters
MACS2 (2.2.7.1) or HOMER (v3.12 ) was used to call peaks
MACS2 (2.2.7.1) and bedGraphToBigWig (v 4) were used to generate bigwig files
Assembly: hg19
Supplementary files format and content: bigwig files contain aweraged genome-wide signal data betweeen replicates, bed files contain intersected genomic regions between replicates, narrowPeak.bed files contain genomic regions for each sample,

growth_protocol: VCaP cells were cultured in DMEM (10% FBS), enzalutamide-resistant VCaP (VCaP16) cells were cultured in DMEM (10% FBS) with 16uM enzalutamide. LNCaP95 cells were cultured in RPMI (10% FBS).

extract_protocol:
Cells were crosslinked with fresh 1% methanol-free formaldehyde (FA) for 10 minutes. This step was carried out for immunoprecipitation (IP) of histone modification marks (H3K27Ac, H3K4me1), ARfl, FOXA1, BRD4, and p300. Double fixation: For IP of ARv7, cells were first crosslinked in 2 mM fresh disuccinimidyl glutarate for 35 minutes, followed by 1% FA for an additional 10 minutes. The samples were sonicated using the Covaris E220 in sarkosyl lysis buffer.
ChIP-seq libraries for ARv7, ARfl and H3K27Ac ChIP DNA were generated using the ThruPLEX DNA-seq Kit (Rubicon Genomics) according to the manufacturer’s instructions and standard 8 bp Illumina primers. Libraries were pooled and sequenced on the Illumina NextSeq 500 platform at the Molecular Biology Core Facility (DFCI). ChIP-seq libraries for H3K4me1, FOXA1 were prepared using Accel-NGS 2S Plus DNA Libraries Kit with Unique Dual Indexing (Swift Biosciences, cat# 29096/290384) according to the manufacturer’s instructions. ChIP-seq libraries for H3K27Ac, BRD4 and p300 were generated using SimpleChIP ChIP-seq Multiplex Oligos for Illumina with Dual Index Primers (Cell Signaling Technology, cat# 47538) according to the manufacturer’s instructions. Libraries were pooled and sequenced using a NovaSeq 6000 Sequencing System.

treatment_protocol: VCaP, VCaP16 or LNCaP95 cells were grown to 70-80% confluence.


title: DNMT1 L1TD1 DKO  10% input rep2


title: VCaP16 ARCC-32, ARv7, IP rep 1

description:
V16_11_ARD_ARv7.rep1_treat_pileup.bw
V16_11_ARD_ARv7.rep1_sorted_peaks.narrowPeak.bed


title: LA1276


title: VCaP16 DMSO, ARv7, IP rep 2

description:
V16_4_DMSO_ARv7L.rep1_treat_pileup.bw
V16_4_DMSO_ARv7L.rep1_sorted_peaks.narrowPeak.bed


title: normal cervical epithelial cells group, β-estradiol stimulation, day1, Rep3

value: estradiol stimulation


title: LA1268


title: VCaP16 DMSO, ARv7, IP rep 1

description:
V16_3_DMSO_ARv7.rep1_treat_pileup.bw
V16_3_DMSO_ARv7.rep1_sorted_peaks.narrowPeak.bed


title: VCaP16, siEx1_1


title: VCaP16, siV7_3

description:
Cuff_Gene_Counts_siEx1_siEx7_siV7_ARD.csv
VCaP16_siV7_vs_siCntr.deseq.csv

value: 16uM enzalutamide + AR variant 7 siRNA


title: Patient R4291 prot

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

country: France

institute: Assistance Publique des Hôpitaux de Paris

description:
Patient
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and aligned using GRCh38 genome assembly as reference data.
Further processing was done with Seurat v4.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Peripheric blood

extract_protocol:
NA
Library was prepared using Chromium Single Cell 3ʹ version CG000317 rev B protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ version CG000317 rev B protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA and the antibody-derived tagged cDNAs. For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ version CG000317 rev B protocol (10x Genomics).
Libraries were equimolar pooled to obtain at least 20,000 read pairs per cell and 5,000 read pairs for feature barcode part after sequencing on Illumina Novaseq 6000 (100 cycles cartridge).
OTHER : CITE-seq

value: Peripheric blood

value: PBMC

value: ADT derived cDNA

value: Haetopoietic stem cell transplant


title: Patient R4151 prot


title: LA1264 (LET)

description: barcode region of lentiviral backbones from genomic DNA from bulk tumor-bearing lungs were PCR-amplified and high-throughput DNA sequenced

value: lung


title: VCaP16, siV7_2

value: Prostate

value: ENZ-resistant VCaP

value: prostate cancer


title: Patient R4124 prot


title: LA1263


title: VCaP16, Input rep 1, H3K27Ac

value: Input gDNA


title: LA1278


title: normal cervical epithelial cells group, control, day1, Rep3

value: NCEC

value: control


title: LA1280


title: VCaP, Input rep 1, H3K27Ac

value: VCaP


title: LA1248


title: VCaP16, ARD_3

description:
Cuff_Gene_Counts_siEx1_siEx7_siV7_ARD.csv
VCaP16_ARDvsDMSO.deseq.csv

value: 16uM enzalutamide + 500nM ARCC-32 36hrs


title: VCaP16, H3K27Ac, IP rep 3

description:
VCaP16_H3K27Ac.wig.bw
R3V16K27.rep1_sorted_peaks.narrowPeak.bed

value: WT

value: H3K27Ac (Diagenode, C15410196)


title: Patient R4077 prot


title: LA1243


title: Patient R4064 prot


title: VCaP16, ARD_2


title: VCaP16, H3K27Ac, IP rep 2

description:
VCaP16_H3K27Ac.wig.bw
R2V16K27.rep1_sorted_peaks.narrowPeak.bed


title: LA1239


title: Patient R3986 prot


title: LA1238


title: VCaP16, H3K27Ac, IP rep 1

description:
VCaP16_H3K27Ac.wig.bw
R1V16K27.rep1_sorted_peaks.narrowPeak.bed


title: VCaP16, ARD_1


title: VCaP16, DMSO_3

value: 16uM enzalutamide + DMSO


title: Patient R3882 prot


title: Patient R3756 prot


title: LA1235


title: VCaP16, DMSO_2


title: VCaP, H3K27Ac, IP rep 2

description:
VCaP_H3K27Ac.wig.bw
R2VCK27.rep1_sorted_peaks.narrowPeak.bed


title: VCaP16, DMSO_1


title: Patient R4093 prot


title: VCaP16, siV7_1

value: 16uM enzalutamide + AR variant 7 siRNA


title: LA1227


title: 4 hr DHT VCaP16 Input rep 2 (ARv7)

description:
V7_DHT_VCaP16_input.wig.bw
v7_DHT_VCaP16.bed


title: Patient R3753 prot

value: Peripheric blood


title: VCaP16_3

description: diff_expression_VCaPdmso_VCaP-E_VCaP16.csv

value: 16uM enzalutamide


title: SL1135

value: KT


title: Patient R3733 prot

value: PBMC

value: ADT derived cDNA

value: Haetopoietic stem cell transplant


title: VCaP16_2

value: Prostate

value: ENZ-resistant VCaP


title: VCaP16_1

value: prostate cancer


title: Patient R3692 prot


title: Patient R3640 prot


title: 4 hr Enza VCaP16 Input rep 2 (ARv7)

description:
V7_Enza_VCaP16_input.wig.bw
v7_Enza_VCaP16.bed

value: Input gDNA


title: 4 hr DHT VCaP16 Input rep 1 (ARv7)


title: SL1133

value: lung


title: VCaP, ENZ_3

value: VCaP

value: 10uM enzalutamide 96hrs


title: SL1131


title: 4 hr Enza VCaP16 Input rep 1 (ARv7)

value: WT


title: VCaP, H3K27Ac, IP rep 3

description:
VCaP_H3K27Ac.wig.bw
R3VCK27.rep1_sorted_peaks.narrowPeak.bed

value: H3K27Ac (Diagenode, C15410196)


title: SL1132


title: VCaP, ENZ_2


title: Patient R3570 prot


title: Patient R3532 prot


title: LA1234


title: SL1124


title: 4 hr DHT VCaP Input rep 2 (ARv7)

description:
V7_DHT_VCaP_input.wig.bw
v7_DHT_VCaP.bed


title: 4 hr DHT VCaP Input rep 1 (ARv7)


title: Patient R3504 prot


title: VCaP, DMSO_3

value: DMSO


title: MT2268


title: Patient R3500 prot


title: Patient R3486 prot


title: 4 hr Enza VCaP Input rep 2 (ARv7)

description:
V7_Enza_VCaP_input.wig.bw
v7_Enza_VCaP.bed


title: MT2230


title: VCaP, DMSO_2


title: 4 hr Enza VCaP Input rep 1 (ARv7)


title: MT2229


title: Patient R3429 prot


title: Patient R3435 prot


title: 4 hr DHT VCaP16 Input rep 1 (ARfl)


title: MT2228


title: MT2217


title: HC2594


title: 4 hr DHT VCaP16 Input rep 2 (ARfl)


title: Patient R3388 prot


title: VCaP, DMSO_1


title: HC2583


title: Patient R3358 prot


title: 4 hr Enza VCaP16 Input rep 1 (ARfl)


title: 4 hr DHT VCaP Input rep 2 (ARfl)


title: VCaP, ENZ_1


title: 4 hr Enza VCaP16 Input rep 2 (ARfl)


title: HC2581


title: Patient R3338 prot


title: 4 hr DHT VCaP Input rep 1 (ARfl)


title: 4 hr Enza VCaP Input rep 2 (ARfl)


title: Patient R3325 prot


title: HC2576


title: 4 hr Enza VCaP Input rep 1 (ARfl)


title: Patient R3291 prot


title: Patient R3242 prot


title: HC2572


title: 4 hr DHT VCaP16 ARv7 IP rep 2

description:
V7_DHT_VCaP16.wig.bw
v7_DHT_VCaP16.bed

value: ARv7 (RevMAb Biosciences USA Inc., 31-1109-00)


title: HC2571


title: Patient R3222 prot

value: Peripheric blood


title: 4 hr DHT VCaP16 ARv7 IP rep 1

description:
V7_DHT_VCaP16.wig.bw
v7_DHT_VCaP16.bed


title: Patient R3182 prot


title: Patient R3195 prot


title: 4 hr Enza VCaP16 ARv7 IP rep 2

description:
V7_Enza_VCaP16.wig.bw
v7_Enza_VCaP16.bed


title: 4 hr DHT VCaP ARv7 IP rep 1

description:
V7_DHT_VCaP.wig.bw
v7_DHT_VCaP.bed


title: HC2566


title: 4 hr Enza VCaP16 ARv7 IP rep 1


title: Patient R3353 prot


title: Patient R3086 prot


title: 4 hr Enza VCaP ARv7 IP rep 1

description:
V7_Enza_VCaP.wig.bw
v7_Enza_VCaP.bed


title: 4 hr DHT VCaP ARv7 IP rep 2

description:
V7_DHT_VCaP.wig.bw
v7_DHT_VCaP.bed


title: 4 hr Enza VCaP ARv7 IP rep 2

description:
V7_Enza_VCaP.wig.bw
v7_Enza_VCaP.bed


title: Patient R3052 prot


title: HC2556


title: HC2565


title: Patient R3017 prot


title: HC2577


title: Patient R3008 prot


title: Patient R3075 prot


title: 4 hr DHT VCaP16 ARfl IP rep 1

description:
FL_DHT_VCaP16.wig.bw
fl_DHT_VCaP16.bed

value: ARfl (Spring Bioscience, clone SP242)


title: CM3536


title: HC2552


title: 4 hr DHT VCaP16 ARfl IP rep 2

description:
FL_DHT_VCaP16.wig.bw
fl_DHT_VCaP16.bed


title: HC2570


title: Patient R2813 prot


title: HC2562


title: 4 hr Enza VCaP16 ARfl IP rep 2

description:
FL_Enza_VCaP16.wig.bw
fl_Enza_VCaP16.bed


title: Patient R2807 prot


title: HC2557


title: CM3531


title: 4 hr Enza VCaP16 ARfl IP rep 1


title: Patient R2904 prot


title: Patient R2794 prot


title: LA944


title: HC2553


title: CM3534


title: 4 hr DHT VCaP ARfl IP rep 2

description:
FL_DHT_VCaP.wig.bw
fl_DHT_VCaP.bed


title: Patient R2759 prot


title: VCaP, H3K27Ac, IP rep 1

description:
VCaP_H3K27Ac.wig.bw
R1VCK27.rep1_sorted_peaks.narrowPeak.bed


title: 4 hr DHT VCaP ARfl IP rep 1

description:
FL_DHT_VCaP.wig.bw
fl_DHT_VCaP.bed


title: CM3532


title: Patient R2718 prot


title: 4 hr Enza VCaP ARfl IP rep 1

description:
FL_Enza_VCaP.wig.bw
fl_Enza_VCaP.bed


title: LA866


title: 4 hr Enza VCaP ARfl IP rep 2

description:
FL_Enza_VCaP.wig.bw
fl_Enza_VCaP.bed


title: Patient R2684 prot


title: LA865


title: Patient R2700 prot


title: VCaP16

description: 10X Genomics

library_source: genomic single cell

data_processing:
The raw FASTQ files underwent preprocessing using the Cell Ranger ATAC pipeline, version 1.2.0, provided by 10X Genomics (https://support.10xgenomics.com/single-cell-atac/software). The data was aligned to hg19
Assembly: hg19
Supplementary files format and content: comma-separated values files, tab-separated values files, matrix files

extract_protocol:
For single cell ATAC-seq, approximately 7000 cells were targeted for each sample and processed according to the 10X Genomics scATAC-seq sample preparation protocol (Chromium Single Cell ATAC Library & Gel Bead Kit, 10Å~ Genomics)
Chromium Single Cell ATAC Library & Gel Bead Kit, 10Å~ Genomics

treatment_protocol: VCaP cells in DMSO (VCaP_DMSO), VCaP treated with 10uM enzalutamide for 96 hrs (VCaP-E), enzalutamide-resistant VCaP16 cells in 16uM enzalutamide (VCaP16).

value: 16uM ENZ


title: Patient R2643 prot

value: PBMC


title: CM3535


title: LA910


title: VCaP, ENZ

description: 10X Genomics

value: 10uM ENZ 96hrs


title: LA917


title: VCaP16_3

growth_protocol: VCaP cells were cultured in DMEM (10% FBS), enzalutamide-resistant VCaP (VCaP16) cells were cultured  in DMEM (10% FBS) with 16uM enzalutamide.

extract_protocol:
For bulk ATAC-seq cells were crosslinked with fresh 1% formaldehyde for 10 minutes, then quenched with glycine and frozen. Cells were thawed in cold ATAC-seq buffer (ASB, 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) and centrifuged. Cells were lysed by resuspension in .05 mL of lysis buffer (ASB with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin), followed by addition of 1 mL ASB with 0.1% Tween-20 and centrifugation. Nuclei were resuspended in 50 μL tagmentation reaction containing 25 mL tagmentation buffer (Illumina 15027866), 16.5 mL PBS, 0.5 mL Tween-20, 0.5 mL 1:1 water diluted digitonin, 2.5 mL Tn5 transposase (Illumina 15027865), and 5 mL water, and incubated at 37°C for 30 minutes. Transposed DNA was purified using Qiagen columns.
~ 7000 cells were targeted for each sample and processed according to the 10X Genomics scATAC-seq sample preparation protocol (Chromium Single Cell ATAC Library & Gel Bead Kit, 10Å~ Genomics).


title: Patient R2521 prot

value: ADT derived cDNA

value: Haetopoietic stem cell transplant


title: VCaP, DMSO

description: 10X Genomics

value: Prostate


title: Patient R2632 prot


title: Patient R2508 prot


title: LA907


title: LA870


title: VCaP16_1

value: ENZ-resistant VCaP

value: prostate cancer


title: Patient R2475 prot


title: CM3533

value: lung


title: LA909


title: Patient R2315 prot


title: VCaP, ENZ_3

value: VCaP


title: LA991


title: Patient R2412 prot


title: Patient R2268 prot


title: Patient R2122 prot


title: VCaP, DMSO_3


title: LA867


title: VCaP, ENZ_2


title: VCaP, ENZ_1


title: LA869


title: VCaP, DMSO_2


title: LA868


title: Patient R2029 prot


title: VCaP, DMSO_1


title: LA912


title: VCaP16_2


title: Patient R1896 prot


title: Healthy donor number 6 HD6 prot

description:
Healthy donor number 6
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: LA860

value: KT


title: HCT116_siPRDX3_3

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

institute: Ewha Womans University

data_processing:
Sequence reads were mapped with the bowtie2 software tool, which yielded bam files.
Read counts mapped to a mature miRNA sequence were extracted from the alignment file using bedtools v2.25.0 and Bioconductor , which use the R statistical programming language. Read counts were used to determine the expression level of miRNAs.
The CPM+TMM normalization method was used for between-sample comparison.
Assembly: hsa mirBase
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

source_name: colon

extract_protocol:
Exosomal RNA was isolated using the TRIzol LS reagent. RNA quality was assessed by an Agilent 2100 bioanalyzer using the RNA 6000 Pico Chip, and RNA quantification was performed using a NanoDrop 2000 Spectrophotometer system
library construction was performed with a NEBNext Multiplex Small RNA Library Prep kit according to the manufacturer’s instructions.

value: colon

value: carcinorma cell


title: HCT116_siPRDX3_2


title: Healthy donor number 5 HD5 prot

description:
Healthy donor number 5
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: HCT116_siPRDX3_1


title: LA859

description: barcode region of lentiviral backbones from genomic DNA from bulk tumor-bearing lungs were PCR-amplified and high-throughput DNA sequenced


title: HCT116_siCTL_2


title: LA969


title: Healthy donor number 4 HD4 prot

description:
Healthy donor number 4
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: Healthy donor number 3 HD3 prot

description:
Healthy donor number 3
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: HCT116_siCTL_3


title: Healthy donor number 2 HD2 prot

description:
Healthy donor number 2
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: Patient R2043 prot

description:
Patient
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: LA861


title: Healthy donor number 1 HD1 prot

description:
Healthy donor number 1
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: Patient R4291 geneexp

value: mRNA derived cDNA


title: HPC-HT H3K4me3

data_processing:
DNA libraries were quantified and sequenced on Illumina’s NextSeq 550 (8 million reads, 38 paired end).
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed and only reads that mapped uniquely (mapping quality >= 1) and as matched pairs were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Assembly: GRCh38
Supplementary files format and content: BW
Library strategy: CUT&Tag

growth_protocol: HPC medium [1:1 mixture of DEME/F12 and hepatic colony-forming units in culture (H-CFU-C) medium supplemented with 40 ng/ml recombinant human hepatocyte growth factor (HGF), 20ng/ml recombinant human epidermal growth factor (EGF), 0.25 mM A83-01, 10 mM Y-27632, and 10% FBS]. H-CFU-C medium consisted of DMEM/F12 supplemented with 2 × non-essential amino acids, 2 × insulin-transferrin-selenium, 5 mM HEPES, 2 × 10-7 M dexamethasone, and 2 × antibiotic-antimycotic mixed solution.

extract_protocol:
Cells were prepared by removing MEF using a Feeder Removal Microbeads mouse (Miltenyi Biotec).
Cells were incubated overnight with Concanavalin A beads and 1.3 µl of the primary anti-H3K4me3 antibody per reaction (Active Motif, catalog number 39159). After incubation with the secondary antibody (1:100), cells were washed and tagmentation was performed at 37℃ using protein-A-Tn5. Tagmentation was halted by the addition of EDTA, SDS, and proteinase K at 55℃, after which DNA extraction and ethanol purification was performed, followed by PCR amplification and barcoding

value: HBV-KMT2B integrated HPCs

value: iPS-derived hepatic progenitor cells

tag: antibody

value: H3K4me3 antibody (Active Motif, catalog number 39159)


title: HPC-Int H3K4me3

value: KMT2B heterozygous knockout HPCs

value: H3K4me3 antibody(Active Motif, catalog number 39159)


title: DFGC_3_ATAC,snMultiome

city: Duarte

first: Zhao

last: Wang

address: 1500 E Duarte Rd

department: Diabetes and Cancer Metabolism

institute: City of Hope

data_processing:
CellRanger arc v2.0.2 count and aggr functions to aggreate RNA and ATAC output from nine samples into a single set of output: filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz, which are used for following Seurat and Signac analysis
Assembly: mm10
Supplementary files format and content: CellRanger arc aggr output:  filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz

source_name: frozen heart

extract_protocol:
The nuclei isolated by different methods were put into sterile PCR tubes containing reagents as per the 10x user guide. GEMs were generated using the 10x Genomics Chromium Controller with Next GEM Chip J single cell kit (10x Genomics Inc., Pleasanton, CA, USA).
After pre-amplification PCR, all libraries are divided into two parts, one part is used to perform snRNA-seq library, while the other is used to perform snATAC-seq library according to CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevA.

value: frozen heart

value: cardiomyocyte,macrophage, endothelial cell, epicardial cell, fibroblast, et al