title: rVSMC，sg-U6-3

city: shanghai

first: yue

last: lou

address: No. 393 HuaxiaCentral Road

institute: Shanghai Jiao Tong University

description: Library name: sg-U6-3

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to rat genome (Rnor6.0) using the Hisat2. We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis, P-value and FDR analysis  were subjected to the following criteria: i) Fold Change>1.5 or < 0.667; ii) ,P-value<0.05,FDR<0.05.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: vessel

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C.
The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction. The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

treatment_protocol: rVSMCs traeted with CRISPR-dCas9 system to overexperss lncRNA MIAT, a negtive control sgRNA was designed as "sg-U6" for control groups.

value: vessel

value: Vascular smooth muscle cells


title: Rpb1_MOT1AA uninduced_with Rapamycin_Replicate 2

status: Public on Sep 25 2025

type: SRA

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 49 Convent Drive Bldg49/Rm 6A30

country: USA

institute: NIH, NICHD

description:
Library name: PM162_116
Biological replicate 2

library_source: genomic

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of TBP, Rpb1, Gcn4, and TFIIB were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Assembly: SacCer3
Supplementary files format and content: Bigwig files

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Whole yeast cells

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.3 to 0.4) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), cells were treated with rapamycin  at 1µg/ml for 90 min before adding SM at 1µg/ml or no SMsulfometuron (SM) for 25 min to induce Gcn4.

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-TBP (from Joseph Reese's lab), anti-Rpb1 (Biolegend, Cat#664906), anti-Gcn4 (in-house),and anti-TFIIB (from Stephen Buratowski's lab). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

treatment_protocol: Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)

tag: cell type

value: Whole yeast cells

tag: strain

tag: chip antibody

value: anti-Rpb1 (Biolegend, Cat#664906)

tag: genotype

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4

tag: treatment

value: Formaldehyde-fixed and sonicated


title: PBMCs_CHB_rep5

type: RNA

city: Chongqing

first: Li

last: Zhou

state: Chongqing

address: 61 Middle University Road，Huxi Street

department: College of Public Health

country: China

institute: Chongqing Medical University

description: PBMCs at 5, CHB group

hyb_protocol: 5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 25× Fragmentation Buffer and 10× Gene Expression Blocking following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Gex Hybridization buffer was added to the fragmentation mixture and hybridized to Sino Human ceRNA array V3.0 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G5761A) using one color scan setting for 1x44k array slides.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The Processed_data.txt contains fold-change data.

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs from the CHB patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using RNA 6000 Nano Assay Kit (RNA Series II Kit, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The peripheral blood mononuclear cells (PBMCs)

extract_protocol: Total RNA was isolated using RNeasy Total RNA Isolation Kit (Qiagen,  GmBH, Germany) according to the manufacturer’s instructions.

tag: tissue

value: PBMCs

tag: gender

value: female

tag: age

tag: subject status

value: patient with chronic hepatitis B


title: Rpb1_MOT1AA uninduced_with Rapamycin_Replicate 3

description:
Library name: PM162_117
Biological replicate 3


title: Monocyte, LPS stimulated, high inflammation risk, patient4

city: Wuhan

first: Jiyu

last: Zhang

state: Hubei

address: 1277 Jiefang Road, Jianghan District, Wuhan 430022, Hubei, China

institute: Huazhong University of Science and Technology

description: Library name: H4L

library_source: transcriptomic

data_processing:
Raw sequencing data were first filtered by Trimmomatic (version 0.39). Low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed using fastp (version 0.23.1).
Clean reads were mapped back to the human genome Homo_sapiens. GRCh38 using STAR software (version 2.5.3a).
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then FPKMs were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: polyA RNA

source_name: blood

growth_protocol: Monocytes were cultured in 96-well flat plates with RPMI 1640 basic  at 37°C and 5% CO2. 10% fetal bovine serum and 10 μg/mL gentamicin were added to the culture.

extract_protocol:
Total RNA was extracted from cell pellets using TRIzol Reagent (Invitrogen, 15596026) according to the manufacturer's instructions. A total of 1 μg RNA per sample was used for stranded RNA-sequencing library construction.
RNA-sequencing library using the KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog no. DR08402) following the manufacturer’s instructions.

treatment_protocol: After purification with magnetic cell sorting, monocytes were either processed immediately as fresh samples or stimulated with LPS (10 ng/mL) for 6 hours before processing.

value: blood

value: monocyte

value: After isolating with magnetic cell sorting, monocytes were stimulated with 10 ng/ml LPS for 6 hours


title: Rpb1_MOT1AA SM_induced_with Rapamycin_Replicate 1

description:
Library name: AGH151_7
Biological replicate 1


title: rVSMC，sg-U6-2

description: Library name: sg-U6-2

organism: Rattus norvegicus

value: WT

value: rVSMCs traeted with CRISPR-dCas9 system to overexperss lncRNA MIAT, a negtive control sgRNA was designed as "sg-U6" for control groups.


title: LS174T_3

city: Hangzhou

first: Qingqing

last: Wang

state: Zhejiang

address: 866 Yu Hang Tang Road

department: Institute of Immunology

institute: Zhejiang University

description: Library name: WT3

data_processing:
Raw RNA sequencing fastq format data were processed through in-house perl scripts and clean data were obtained by removing reads containing adapter or poly-N and low-quality reads from raw data. Reads were then mapped to mm10 RefSeq genes downloaded from the UCSC Table Browser using Hisat2(v2.0.5). FeatureCounts(v1.5.0-p3) was used to count the reads numbers mapped to each gene. And FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length and reads count mapped to the gene.
Assembly: mm10
Supplementary files format and content: csv file inculde raw counts for each sample

source_name: Colon

extract_protocol:
Approximately 2000000 cells per sample were pelleted and lysed in TRIzol reagent and cryopreserved at -80 °C, followed by RNA extraction.
RNA libraries for Rna-seq were prepared uding NEBNext UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations.

value: Colon

tag: cell line

value: Human Colorectal Adenocarcinoma cells;goblet-like cell


title: Monocyte, LPS stimulated, high inflammation risk, patient3

description: Library name: H3L


title: rVSMC，sg-U6-1

description: Library name: sg-U6-1


title: Rpb1_MOT1AA uninduced_with Rapamycin_Replicate 1

description:
Library name: PM162_115
Biological replicate 1


title: Monocyte, LPS stimulated, high inflammation risk, patient2

description: Library name: H2L


title: Rpb1_WTAA SM_induced_with Rapamycin_Replicate 1

description:
Library name: AGH151_4
Biological replicate 1

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: Rpb1_WTAA DA_induced_with Rapamycin_Replicate 4

description:
Library name: PM162_114
Biological replicate 4


title: rVSMC，sg-MIAT-3

description: Library name: sg-MIAT-3

value: vessel

value: MIAT overexpression


title: Rpb1_WTAA uninduced_with Rapamycin_Replicate 3

description:
Library name: AGH151_3
Biological replicate 3

value: Whole yeast cells


title: Monocyte, LPS stimulated, high inflammation risk, patient1

description: Library name: H1L


title: Rpb1_WTAA DA_induced_with Rapamycin_Replicate 2

description:
Library name: PM162_112
Biological replicate 2

value: anti-Rpb1 (Biolegend, Cat#664906)


title: Rpb1_WTAA uninduced_with Rapamycin_Replicate 2

description:
Library name: AGH151_2
Biological replicate 2


title: rVSMC，sg-MIAT-1

description: Library name: sg-MIAT-1

value: Vascular smooth muscle cells


title: Rpb1_WTAA SM_induced_with Rapamycin_Replicate 3

description:
Library name: AGH151_6
Biological replicate 3

value: Formaldehyde-fixed and sonicated


title: Monocyte, LPS stimulated, low inflammation risk, patient5

description: Library name: L5L


title: Rpb1_WTAA DA_induced_with Rapamycin_Replicate 1

description:
Library name: PM162_111
Biological replicate 1


title: Monocyte, LPS stimulated, low inflammation risk, patient4

description: Library name: L4L


title: Rpb1_WTAA DA_induced_with Rapamycin_Replicate 3

description:
Library name: PM162_113
Biological replicate 3


title: Monocyte, LPS stimulated, low inflammation risk, patient6

description: Library name: L6L


title: Rpb1_WTAA DA_uninduced_with Rapamycin_Replicate 3

description:
Library name: PM162_110
Biological replicate 3


title: rVSMC，sg-MIAT-2

description: Library name: sg-MIAT-2


title: TBP_MOT1AA SM_induced_with Rapamycin_Replicate 2

description:
Library name: AGH150_8
Biological replicate 2

value: TBP ( J.C. Reese)

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4


title: Monocyte, LPS stimulated, low inflammation risk, patient3

description: Library name: L3L


title: TBP_MOT1AA SM_induced_with Rapamycin_Replicate 3

description:
Library name: AGH150_9
Biological replicate 3


title: Rpb1_WTAA uninduced_with Rapamycin_Replicate 1

description:
Library name: AGH151_1
Biological replicate 1


title: Rpb1_WTAA DA_uninduced_with Rapamycin_Replicate 2

description:
Library name: PM162_108
Biological replicate 2


title: 8 pooled human AP gastruloids at 120 hrs derived from hPSCs

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Library name: AP_gastruloids_120h

library_source: transcriptomic single cell

data_processing:
Single-cell transcriptome data (10X) were processed using Cell Ranger 8.0.0 with default settings, followed by filtering of low-quality cells based on UMI counts, detected genes, and doublet detection. Additional quality control included filtering cells based on mitochondrial and ribosomal read percentages.
Assembly: GRCh38
Supplementary files format and content: The gene-by-cell matrix (sparse matrix; MTX), cell and gene metadata (TSV)

source_name: Human AP gastruloids

extract_protocol:
For cell collection, human AP gastruloids (n=8) were harvested from the 96-well plate at 120 hours and pooled into a 15 ml centrifuge tube, washed with DPBS twice, and dissociated with 1ml 0.05% trypsin-EDTA (Thermo Fisher, 25300054) for 8 mins at 37 °C and quenched with 200 μL FBS. Gastruloids were dissociated into single cells by pipetting, pelleted by centrifuging at 300 rcf for 3 mins, resuspended in StemCell Banker (Amsbio, 11924), and stored at -80 °C.
Single-cell RNA-seq (scRNA-seq) libraries were created using 10x Genomics Chromium platform, GEM-X Universal 3' Gene Expression v4 reagents kit following manufacturer specifications and guidelines. In brief, dissociated and frozen single cell suspension were thawed in Essential 6 medium containing 10% FBS, washed with PBS with 0.04% BSA, counted and diluted to 1500 cell/uL to target an optimal recovery of 20,000 cells/lane. The generated scRNA-seq libraries were visualized and quantified by TapeStation (Agilent), and sequenced on NextSeq 2000 (Illumina) with the following read structure: Read 1: 28 cycles; i7 Index: 10 cycles; i5 Index: 10 cycles; Read 2: 90 cycles.

value: Human AP gastruloids

value: iPS11-mScarlet, RUES2-GLR

value: human pluripotent stem cells


title: Rpb1_WTAA SM_induced_with Rapamycin_Replicate 2

description:
Library name: AGH151_5
Biological replicate 2


title: TBP_MOT1AA SM_induced_with Rapamycin_Replicate 1

description:
Library name: AGH150_7
Biological replicate 1


title: HUVEC, aKGM, 24 hours, replicate 2

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe Universität Frankfurt am Main

description: Library name: aKGM_24h_N2

data_processing:
Sequencing reads were aligned against the hg38 genome assembly using STAR (v2.7.10, RRID:SCR_004463), with the parameter – quantMode set to “GeneCounts”.
Differential gene expression analysis was performed using DESeq2 (v1.32.0; RRID:SCR_015687) in R (v4.1.1; R Project for Statistical Computing (RRID:SCR_001905).
Differentially expressed genes were taken as those with a false discovery rate-adjusted p-value of less than 0.05. Gene set enrichment analysis was performed using the gprofiler2 (v0.2.3, RRID:SCR_018190) package for R, using the WikiPathways (RRID:SCR_002134) source.
Assembly: hg38
Supplementary files format and content: XLSX, DESeq2 differential gene expression analysis and normalized gene counts

source_name: HUVEC

growth_protocol: Pooled human umbilical vein endothelial cells (HUVEC) were purchased from PromoCell (#C12203, Heidelberg, Germany) and cultured in endothelial growth medium (EGM), consisting of endothelial basal medium (EBM) supplemented with 8 % fetal calf serum, 0.5 % penicillin/ streptomycin (50 µg/mL), growth factors (EGF, bFGF, IGF, VEGF, #PB-C-MH-100-2199, PeloBiotech, Germany), heparin, L-glutamine but without hydrocortisone. For each experiment, at least three different batches of HUVEC at highest passage number 4 were used. Human embryonic kidney 293 cells (HEK 293) (ATCC, Manassas, USA) and Lenti-X 293 T cells (Takara, 632180, Japan) were cultured in Dulbecco’s Modified Eagle Medium High Glucose (Gibco) supplemented with 8% FCS, penicillin/ streptomycin (50 μg/mL of each) (#15140‐122, Gibco/ Lifetechnologies, USA). All cells were cultured in a humidified atmosphere (5% CO2, 37 oC).

extract_protocol:
Total RNA isolation was performed with the RNA Mini Kit (Bio&Sell) according to the manufacturers protocol
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). Sequencing was performed on NextSeq2000 instrument (Illumina) with 1 x 72 bp single end setup. The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (RRID:SCR_014583).

treatment_protocol: HUVEC were treated with αKGM (300 µM) for 4 or 24 h.

value: HUVEC

value: aKGM 24h


title: HUVEC, aKGM, 24 hours, replicate 1

description: Library name: aKGM_24h_N1


title: Monocyte, LPS stimulated, low inflammation risk, patient2

description: Library name: L2L

value: blood

value: monocyte

value: After isolating with magnetic cell sorting, monocytes were stimulated with 10 ng/ml LPS for 6 hours


title: Monocyte, LPS stimulated, low inflammation risk, patient1

description: Library name: L1L


title: Rpb1_WTAA DA_uninduced_with Rapamycin_Replicate 1

description:
Library name: PM162_107
Biological replicate 1

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: HUVEC, CTL, 24 hours, replicate 3

description: Library name: CTL_24h_N3

value: CTL 24h


title: Monocyte, unstimulated, high inflammation risk, patient6

description: Library name: H6

value: Freshly isolated with magnetic cell sorting


title: TBP_WTAA SM_induced_with Rapamycin_Replicate 2

description:
Library name: AGH150_5
Biological replicate 2

value: Whole yeast cells


title: TBP_MOT1AA DA_induced_with Rapamycin_Replicate 2

description:
Library name: PM161_121
Biological replicate 2


title: Monocyte, unstimulated, high inflammation risk, patient5

description: Library name: H5


title: HUVEC, aKGM, 24 hours, replicate 3

description: Library name: aKGM_24h_N3


title: TBP_MOT1AA DA_induced_with Rapamycin_Replicate 1

description:
Library name: PM161_120
Biological replicate 1


title: Monocyte, unstimulated, high inflammation risk, patient4

description: Library name: H4


title: HUVEC, CTL, 24 hours, replicate 1

description: Library name: CTL_24h_N1


title: TBP_WTAA SM_induced_with Rapamycin_Replicate 1

description:
Library name: AGH150_4
Biological replicate 1


title: TBP_MOT1AA uninduced_with Rapamycin_Replicate 4

description:
Library name: PM161_118
Biological replicate 4


title: TBP_WTAA uninduced_with Rapamycin_Replicate 3

description:
Library name: AGH150_3
Biological replicate 3


title: TBP_WTAA uninduced_with Rapamycin_Replicate 2

description:
Library name: AGH150_2
Biological replicate 2


title: Monocyte, unstimulated, high inflammation risk, patient3

description: Library name: H3


title: TBP_MOT1AA uninduced_with Rapamycin_Replicate 3

description:
Library name: PM161_117
Biological replicate 3


title: HUVEC, aKGM, 4 hours, replicate 2

description: Library name: aKGM_4h_N2

value: aKGM 4h


title: Monocyte, unstimulated, high inflammation risk, patient2

description: Library name: H2


title: TBP_MOT1AA uninduced_with Rapamycin_Replicate 2

description:
Library name: PM161_116
Biological replicate 2


title: HUVEC, aKGM, 4 hours, replicate 3

description: Library name: aKGM_4h_N3


title: TBP_WTAA uninduced_with Rapamycin_Replicate 1

description:
Library name: AGH150_1
Biological replicate 1


title: Monocyte, unstimulated, high inflammation risk, patient1

description: Library name: H1


title: TBP_MOT1AA DA_induced_with Rapamycin_Replicate 3

description:
Library name: PM161_122
Biological replicate 3


title: TBP_WTAA SM_induced_with Rapamycin_Replicate 3

description:
Library name: AGH150_6
Biological replicate 3


title: TBP_MOT1AA uninduced_with Rapamycin_Replicate 1

description:
Library name: PM161_115
Biological replicate 1


title: HUVEC, CTL, 4 hours, replicate 3

description: Library name: CTL_4h_N3

value: CTL 4h


title: HUVEC, CTL, 24 hours, replicate 2

description: Library name: CTL_24h_N2


title: Mouselungs_Bleo_NVP-BHG712_3

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

description: 10X Genomics

data_processing:
The demultiplexing, gene counting and alignment processes were performed using CellRanger software (v 7.0).
Doublets were removed for each sample. Normalization was performed with help of Seurat (v4.4.1) R package and integration of all sequenced samples was performed using Harmony (v0.1) R package.
Each cell cluster identified was annotated by canonical cell surface markers.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

organism: Mus musculus

source_name: Lungs

extract_protocol:
Nuclei were isolated from frozen mouse lungs (n=12, weighing approximately 50 mg) by physical dissociation using a glass dounce homogenizer and were sorted using fluorescence-activated cell sorting (FACS) based on DAPI-positive fluorescence to obtain a single nuclei population. Nuclei concentration was manually determined using DAPI staining and hemocytometer and adjusted to 1000 nuclei/uL.
Single nuclei RNA sequencing libraries were generated using the 10X Genomics Chromium Instrument andChromium Next GEM Single Cell 3’ Reagent Kits (v3.1) from approximately 4000 nuclei.Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).

treatment_protocol: Lungs were extracted with mice instilled with PBS or bleo treated with/without EphB4 Inhibitor (NVP-BHG712) and stored in liquid nitrogen until use. Total 12 mouse lungs (n=3 PBS+vehicle, n=3 PBS+ NVP-BHG712, n=3 bleomycin+vehicle and n=3 bleomycin+NVP-BHG712) were subjected to single nuclei RNA sequencing.

value: Lungs

tag: run number


title: Monocyte, unstimulated, low inflammation risk, patient6

description: Library name: L6


title: HUVEC, CTL, 4 hours, replicate 2

description: Library name: CTL_4h_N2


title: Monocyte, unstimulated, low inflammation risk, patient5

description: Library name: L5


title: TBP_WTAA DA_induced_with Rapamycin_Replicate 3

description:
Library name: PM161_114
Biological replicate 3

value: TBP ( J.C. Reese)

value: Formaldehyde-fixed and sonicated


title: Mouselungs_Bleo_NVP-BHG712_1

description: 10X Genomics


title: TBP_WTAA DA_induced_with Rapamycin_Replicate 2

description:
Library name: PM161_113
Biological replicate 2


title: HUVEC, CTL, 4 hours, replicate 1

description: Library name: CTL_4h_N1


title: Mouselungs_PBS_NVP-BHG712_3

description: 10X Genomics


title: Mouselungs_Bleo_NVP-BHG712_2

description: 10X Genomics


title: HUVEC, NIT2-GLS1-KO, replicate 4

description: Library name: NIT2-GLS1-KO_N4

treatment_protocol: Guide RNAs targeting coding sequences for NIT2 and GLS1 were designed using the publicly available CRISPR algorithm (www.benchling.com). gRNAs targeting the regulatory element within the NIT2 gene were designed using CRISPOR (http://crispor.tefor.net).48 gRNAs were cloned into a lentiviral CRISPR/Cas9 v2 (LCV2) plasmid using the “Golden Gate” cloning protocol.49 gRNAs were cloned into plasmids containing either puromycin resistance (gift from Feng Zhang, Addgene plasmid #52961; http://n2t.net/addgene:52961; RRID:Addgene_52961) or hygromycin resistance (kindly provided by Frank Schnütgen, Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Frankfurt, Germany). Lentivirus were produced in Lenti-X 293 T cells (Takara, #632180) using Polyethylenamine, psPAX2 and pVSVG (pMD2.G). pMD2.G was a gift from Didier Trono (Addgene plasmid #12259; http://n2t.net/addgene: 12259; RRID:Addgene_12259). psPAX2 was a gift from Didier Trono (Addgene plasmid #12260; http://n2t.net/addge ne:12260; RRID:Addgene_12260). LentiCRISPRv2-produced virus was transduced for 24 hours in HEK 293 cells or HUVEC (at passage 1) with polybrene transfection reagent (MerckMillipore, #TR-1003-G) and selection was performed with puromycin (1 μg/mL) or hygromycin (100 µg/mL) for 6 days.


title: Mouselungs_PBS_NVP-BHG712_2

description: 10X Genomics


title: HUVEC, NIT2-GLS1-KO, replicate 3

description: Library name: NIT2-GLS1-KO_N3


title: Monocyte, unstimulated, low inflammation risk, patient4

description: Library name: L4


title: Monocyte, unstimulated, low inflammation risk, patient2

description: Library name: L2


title: TBP_WTAA DA_induced_with Rapamycin_Replicate 1

description:
Library name: PM161_111
Biological replicate 1


title: TBP_WTAA DA_uninduced_with Rapamycin_Replicate 3

description:
Library name: PM161_109
Biological replicate 3


title: Monocyte, unstimulated, low inflammation risk, patient3

description: Library name: L3


title: TBP_WTAA DA_uninduced_with Rapamycin_Replicate 2

description:
Library name: PM161_108
Biological replicate 2


title: HUVEC, NIT2-GLS1-KO, replicate 2

description: Library name: NIT2-GLS1-KO_N2


title: Monocyte, unstimulated, low inflammation risk, patient1

description: Library name: L1


title: HUVEC, aKGM, 4 hours, replicate 1

description: Library name: aKGM_4h_N1


title: Mouselungs_PBS_NVP-BHG712_1

description: 10X Genomics


title: TBP_WTAA DA_uninduced_with Rapamycin_Replicate 1

description:
Library name: PM161_107
Biological replicate 1


title: Mouselungs_PBS_Vehicle_3

description: 10X Genomics


title: HUVEC, NIT2-GLS1-KO, replicate 1

description: Library name: NIT2-GLS1-KO_N1


title: HUVEC, GLS1-KO, replicate 4

description: Library name: GLS1-KO_N4


title: Mouselungs_PBS_Vehicle_2

description: 10X Genomics


title: TFIIB_MOT1AA SM_induced_with Rapamycin_Replicate 3

description:
Library name: PM159_106
Biological replicate 3

value: TFIIB (S. Buratowski)

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4


title: 1d7_homo rep3

city: Saint Louis

first: Elliott

last: Klotz

state: MO

address: 1Brookings Dr

institute: Washington University

description: Library name: 1d7_homo-3

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting
Assembly: GRCh38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: iPSC

extract_protocol:
Total RNA was isolated from iPSC-derived neurons (14 days differentiation). Cells were lysed with Trizol (Zymo Research, Irvine, CA), and total RNA was purified using the Direct-Zol RNA kit (Zymo Research, Irvine, CA) following the manufacturer's protocol. RNA concentration was determined by NanoDrop spectrophotometer.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was blocked using FastSelect reagents (Qiagen) during cDNA synthesis. RNA was fragmented in reverse transcriptase buffer with FastSelect reagent and heating to 94 degrees for 5 minutes, 75 degrees for 2 minutes, 70 degrees for 2 minutes, 65 degrees for 2 minutes, 60 degrees for 2 minutes, 55 degrees for 2 minutes, 37 degrees for 5 minutes, 25 degrees for 5 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags.

value: iPSC

value: CTBP1 homozygous mutant


title: 1d7_homo rep2

description: Library name: 1d7_homo-2


title: Mouselungs_PBS_Vehicle_1

description: 10X Genomics


title: TFIIB_MOT1AA SM_induced_with Rapamycin_Replicate 2

description:
Library name: PM159_104
Biological replicate 2


title: HUVEC, GLS1-KO, replicate 3

description: Library name: GLS1-KO_N3

value: HUVEC


title: 1d7_homo rep1

description: Library name: 1d7_homo-1


title: 4C1194F

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample.
Cutadapt (v1.18) is used to maintain minimum read length of 25 bp post trimming of adapters as well as trimming of N’s.
Splice-aware alignment of reads using a Hierarchical Graph FM index (HGFM) method is performed using HISAT2 software (v2.1.0) with parameters (--rna-strandness RF –dta) against mouse reference genome (vGRCm38).
To obtain the abundance of each of these transcripts based only on the known reference genome and transcriptome, StringTie was run again using different parameters (-e -B -G referencetranscripts.gtf) to generate output of Ballgown software as compatible table files.
A script named ‘prepDE.py’ by StringTie software was used to extract the read count information.
Assembly: GRCm38
Supplementary files format and content: 1 tab-delimited text file includes raw count values for each Sample.

source_name: Lung

growth_protocol: Ephb4f/f; Col1a2-CreERT2 mice are treated with 4-hydroxytamoxifen to knockdown Ephb4 expression or corn oil (control) at 4 weeks of age and bleomycin (or PBS control) at 6 weeks of age to induce lung fibrosis. At 14-day post-bleomycin follow-up, fibroblasts are harvested from mouse lungs and cultured in 10% FBS complete DMEM until 80% confluency is attained. Cells are passaged a single time to enrich fibroblast population and RNA is collected.

extract_protocol:
Total RNA is extracted from P1 lung fibroblasts attained from mice with EphB4 Col1a2-driven deletion or control, and then bleomycin treatment or control by standard Trizol method and quantified using the Qubit RNA BR assay (Denovix). Quality of RNA is assessed using the Agilent RNA Nano chips on a Bioanalyzer instrument. For all the samples, RNA integrity number (RIN) was >9.
Total RNA libraries are prepared from 200 ηg total RNA using the TruSeq Stranded total RNA library preparation kit (Illumina Cat# 20020596) as per manufacturer’s recommendations.  Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
For sequencing, samples from each group are divided into two groups of 8 and 9 samples each. Libraries prepared for sequencing (volumetrically pooled, diluted and denatured): 75 paired end read-cycles on an Illumina NextSeq 550 sequencer.

treatment_protocol: No in vitro treatment is applied.

value: Lung

value: primary fibroblasts

tag: ephb4 ko status

value: PBS

tag: Sex

value: female


title: TFIIB_MOT1AA SM_induced_with Rapamycin_Replicate 1

description:
Library name: PM159_103
Biological replicate 1


title: HUVEC, GLS1-KO, replicate 2

description: Library name: GLS1-KO_N2


title: 1e11_het rep3

description: Library name: 1e11_het-3

value: CTBP1 heterozygous mutant


title: 4C1172F


title: HUVEC, GLS1-KO, replicate 1

description: Library name: GLS1-KO_N1


title: 1e11_het rep2

description: Library name: 1e11_het-2


title: TFIIB_MOT1AA uninduced_with Rapamycin_Replicate 2

description:
Library name: PM159_100
Biological replicate 2


title: HUVEC, NIT2-KO, replicate 4

description: Library name: NIT2-KO_N4


title: 4C1165M

value: male


title: TFIIB_MOT1AA uninduced_with Rapamycin_Replicate 4

description:
Library name: PM159_102
Biological replicate 4

value: Whole yeast cells


title: bjff.6_wt rep3

description: Library name: bjff.6_wt-3

value: WT


title: TFIIB_MOT1AA uninduced_with Rapamycin_Replicate 3

description:
Library name: PM159_101
Biological replicate 3


title: 4C1242M


title: HUVEC, NIT2-KO, replicate 3

description: Library name: NIT2-KO_N3


title: 4C1231M


title: HUVEC, NIT2-KO, replicate 2

description: Library name: NIT2-KO_N2


title: bjff.6_wt rep2

description: Library name: bjff.6_wt-2


title: TFIIB_MOT1AA uninduced_with Rapamycin_Replicate 1

description:
Library name: PM159_99
Biological replicate 1


title: HUVEC, NIT2-KO, replicate 1

description: Library name: NIT2-KO_N1


title: TFIIB_WTAA SM_induced_with Rapamycin_Replicate 3

description:
Library name: PM159_98
Biological replicate 3

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: 4C1164M

value: bleomycin


title: bjff.6_wt rep1

description: Library name: bjff.6_wt-1


title: HUVEC, NTC, replicate 4

description: Library name: NTC_N4

value: NTC


title: 4C1241F


title: ID45v0, SCI, Acute

city: Manhasset

first: Ona

last: Bloom

state: New York

address: 350 Community Dr

department: Molecular Medicine

institute: Feinstein Institute

description: Library name: ID45v0

data_processing:
Partek Genomics Flow software
trimmed reads aligned to hg38 genome assembly using STAR
filtered for expression >50
normalized using the Trimmed Mean of M-values (TMM) method using the edgeR package
log2 transformed
Assembly: hg38
Supplementary files format and content: Normalized Morrison 2025 processed data.txt

source_name: Whole blood

extract_protocol:
Total RNA was isolated using the PAXgene total RNA kit and the Qiagen QIAcube, acccording to manufacturer's protocol
RNA seq libraries were prepared using Illumina TruSeq Stranded Total RNA according to manufacturer's instructions.

value: Whole blood

tag: group

value: SCI

value: Acute

value: Male

tag: ais

value: D

tag: nli


title: HUVEC, NTC, replicate 3

description: Library name: NTC_N3

value: HUVEC


title: 4C1243M

value: Lung


title: TFIIB_WTAA SM_induced_with Rapamycin_Replicate 1

description:
Library name: PM159_96
Biological replicate 1

value: TFIIB (S. Buratowski)

value: Formaldehyde-fixed and sonicated


title: 1e11_het rep1

description: Library name: 1e11_het-1

value: iPSC


title: ID44v0, SCI, Acute

description: Library name: ID44v0

value: Female

value: C


title: HUVEC, NTC, replicate 2

description: Library name: NTC_N2


title: TFIIB_WTAA SM_induced_with Rapamycin_Replicate 4

description:
Library name: PM159_94
Biological replicate 4

value: Whole yeast cells


title: ID43v0, SCI, Acute

description: Library name: ID43v0

value: B


title: TFIIB_WTAA uninduced_with Rapamycin_Replicate 3

description:
Library name: PM159_93
Biological replicate 3

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: HUVEC, NTC, replicate 1

description: Library name: NTC_N1


title: 4C1181F

value: primary fibroblasts

value: Ephb4f/f; Col1a2-CreERT2 (corn oil)

value: PBS

value: female


title: TFIIB_WTAA uninduced_with Rapamycin_Replicate 2

description:
Library name: PM159_92
Biological replicate 2


title: CUT&RUN CHD1L in Mutant Line 2 hNPC

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

description: Library name: NDLH16

data_processing:
Reads were trimmed using cutadapt v1.18 with option: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -m 5 -e 0.1. Paired-end reads were mapped to Homo Sapiens genome (assembly hg38) using Bowtie2 (release 2.3.4.3, parameter: -N 1 -X 1000). Reads overlapping with ENCODE hg38 blacklisted region V2 were removed using Bedtools. Reads were size selected to <120 bp for NDLH5 (CHD1L) sample. Bigwig tracks were generated using bamCoverage from deepTools v3.5.1. Tracks were normalized with RPKM method.
Assembly: hg38
Supplementary files format and content: bigwig, with fragment size selection <120bpn (*_120.bw), or without size selection (*blfilter.bw)
Library strategy: CUT&RUN

source_name: 2D culture

growth_protocol: Human induced pluripotent stem cells (iPSCs 8330), derived from adult fibroblasts, were kindly provided by Prof. M. Talkowski (MIT); the cells were maintained on Matrigel-coated dish (Corning) with mTESR™ (StemCell) and incubated at 37 °C in a humidified atmosphere with 5% CO2. CHD1L KO hiPSC were generated by CRISPR-Cas9 and main Off-Target were screnned for isogenic CHD1L KO hiPSC validation. We used the control line and two mutants line (Line 1 and Line 2) of hiPSC for our experiments.

extract_protocol:
P3406
Protocol was adapted from Hainer and Fazzio (2019) and Skene and Henikoff (2019).
P3010 : CUT&RUN samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). CUT&RUN libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (10 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: The differentiation into NPCs was achieved by performing the Neural Precursor Cells (NPCs) differentiation procedure described in the StemXVivo Neural Progenitor Differentiation Kit (R&D systems) manual.

value: 2D culture

value: hiPSC-derived control

value: Neural Progenitor Cells

value: Mutant Line 2 CHD1L-/-

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit

tag: antibody


title: 4C1177F

value: Lung

tag: cell type


title: ID41v0, SCI, Acute

description: Library name: ID41v0

value: Whole blood

value: SCI

value: Acute

value: Male


title: 4C1154F


title: CUT&RUN CHD1L in Mutant Line 1 hNPC

description: Library name: NDLH15

value: Mutant Line 1 CHD1L-/-


title: TFIIB_WTAA uninduced_with Rapamycin_Replicate 1

description:
Library name: PM159_91
Biological replicate 1

value: Whole yeast cells

tag: strain

value: TFIIB (S. Buratowski)

value: Formaldehyde-fixed and sonicated


title: 4C1195F

value: primary fibroblasts

value: bleomycin


title: TFIIB_WTAA SM_induced_with Rapamycin_Replicate 2

description:
Library name: PM159_97
Biological replicate 2

tag: chip antibody

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: Ovarian cancer, Patient8

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description:
Library name: Patient_8
FFPE spatial transcriptome sequencing

data_processing:
The Visium sequencing data were processed by Space Ranger.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducial.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: ovarian cancer

extract_protocol:
FFPE tissues of HGSOC (5μm) was mounted into each capture area of Visium FFPE slides (6.5mm × 6.5mm).
Library construction was performed according to the standard Visium for the FFPE workflow.

value: ovarian cancer

tag: age at_sample_colletion

tag: Stage

value: Stage IVB

tag: treatment before_sample_collection

value: TC + Bev ×6 → TC ×7

tag: timing of_sample_collection

value: Interval debulking surgery

tag: sample

value: Ovary

tag: treatment before_olaparib_treatment

value: DC ×4 +Bev ×3 → Bev maintenance ×11 → Surgery → DC ×3

tag: response to_prior_platinum_regimen

value: PR


title: 4C1241M

tag: tissue

value: Lung

value: Ephb4f/f; Col1a2-CreERT2 (corn oil)

tag: treatment

value: PBS

value: male


title: MOT1AA SM_induced_with Rapamycin_Replicate 3

description: Library name: PM9460-9 (Rep. 9)

data_processing:
The RNA-sequencing reads were aligned to the S. cerevisiae reference genome S288C (assembly version: SacCer3) using STAR aligner PCR duplicates were removed using samtools. The total number of reads obtained from ERCC alignment was used to calculate the size factor for each sample, and reads corresponding to yeast genes were normalized by the size factors.
To identify the differentially expressed genes DeSeq2 analysis was performed using 3 biological replicates of each strain
Assembly: SacCer3
Supplementary files format and content: Bigwig files

extract_protocol:
Total RNA isolation was carried out using Hot-Phenol Method followed by DNAse1 digestion and RNA clean up using  RNA clean up using RNA Clean and Concentrator kit . Prior to library preparation For spike in normalization of the RNA, an equal amount (2.4 µl of 1:100 fold dilution) of ERCC spike-in mix (Thermo Fisher #4456740) was added to 1.2 ug of RNA samples of each strain.
RNA-sequencing libraries preparation was performed by NHLBI-genome sequencing core using the Illumina TrueSeq stranded mRNA Library Prep Kit. Ribo-depletion was performed to remove the rRNA using Qiagen FastSelect Yeast rRNA Depletion Kit, followed by paired-end sequencing using the Novaseq-X platform.

value: Whole yeast cells

tag: background strain

value: Mot1 anchor away strain

tag: genotype

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4


title: H3K27me3 - CUT&RUN

city: Durham

first: Michael-Christopher

last: Keogh

state: NC

address: 6 Davis Dr

institute: EpiCypher, Inc

description: Library name: H3K27me3

data_processing:
Paired-end fastq files were aligned to the T2T reference genome using Bowtie2 (v2.2.5).
Duplicate reads were removed via SAMtools (v1.6).
Multi-aligned reads were removed via Picard (v2.26.2).
bigWig creation included RPKM normalization via bamCoverage in deeptools (v3.5.1).
Assembly: T2T
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

growth_protocol: K562 cells were grown in IMDM media + 10% FBS and cultured in T75 flasks. Handled according the ATCC guidelines.

extract_protocol:
Freshly cultured, native whole cells (500K) were utilized in each reaction.
5 ng of CUT&RUN DNA (for each antibody or GST-reader) was used to prepare sequencing libraries with the Ultra II DNA Library Prep Kit (NEB #E7645L). Libraries were sequenced on an Illumina NextSeq 2000 platform. See referenced text for further detail.

tag: cell line

tag: detection reagent

value: ThermoFisher #MA5-11198


title: Ovarian cancer, Patient7

description:
Library name: Patient_7
FFPE spatial transcriptome sequencing

value: Stage IIIC

value: Primary debulking surgery

value: TC ×8


title: 4C1272M

value: primary fibroblasts

tag: ephb4 ko status

value: bleomycin

tag: Sex


title: H3K9me3 - CUT&RUN

description: Library name: H3K9me3


title: MOT1AA SM_induced_with Rapamycin_Replicate 2

description: Library name: PM9460-8 (Rep. 8)

tag: cell type

tag: strain


title: 4C1271M


title: MOT1AA SM_induced_with Rapamycin_Replicate 1

description: Library name: PM9460-7 (Rep. 7)


title: H3K4me3 - CUT&RUN

description: Library name: H3K4me3


title: Ovarian cancer, Patient6

description:
Library name: Patient_6
FFPE spatial transcriptome sequencing

value: ovarian cancer

tag: age at_sample_colletion

value: TC ×6 → wPTX ×5 → PLD ×3 → PLD ×6 → CPT-11 ×2 → NGT ×2 → GEM ×3 → NDP ×10  wPTX ×10 → CBDCA ×3


title: ID42v0, SCI, Acute

description: Library name: ID42v0

value: Whole blood

tag: group

value: SCI

value: Acute

tag: age

value: Male

tag: ais

value: B

tag: nli


title: 4C1242F

value: Lung

value: Ephb4f/f; Col1a2-CreERT2 (corn oil)

value: female


title: WTAA SM_induced_with Rapamycin_Replicate 3

description: Library name: PM9460-6 (Rep. 6)

value: Whole yeast cells

value: WT anchor-away background strain

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: TAF3 Reader - CUT&RUN

description: Library name: GST-TAF3


title: 4C1233F


title: WTAA SM_induced_with Rapamycin_Replicate 2

description: Library name: PM9460-5 (Rep. 5)


title: Ovarian cancer, Patient3

description:
Library name: Patient_3
FFPE spatial transcriptome sequencing

tag: Stage

value: Stage IVA

tag: treatment before_sample_collection

value: TC ×5 +Bev ×3

tag: timing of_sample_collection

value: Interval debulking surgery

tag: sample

value: Ovary

tag: treatment before_olaparib_treatment

value: TC ×4 +Bev ×3 → Bev maintenance ×10 → TC + Bev ×9

value: CR


title: WTAA SM_induced_with Rapamycin_Replicate 1

description: Library name: PM9460-4 (Rep. 4)

tag: background strain

tag: genotype


title: Mutant A12_RNA-seq_3

data_processing:
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20), reads shorter than 40 bases were discarded for further analysis.
Reads mapping to rRNA were discarded (this mapping was performed using bowtie version 2.2.8).
Reads were mapped onto the hg38 assembly of human genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 98.
Assembly: hg38
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

extract_protocol:
Total RNA of CHD1L control NPC and CHD1L KO (Line 1 and Line 2) NPC was extracted using NucleoSpin RNA or RNA Plus Mini Kit (Macherey Nagel).
RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94°C for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: tissue

value: 2D culture

tag: cell line

value: hiPSC-derived mutant Line 2

value: Neural Progenitor Cells

value: Mutant CHD1L-/- Line 1

tag: treatment

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit


title: HP1beta Reader - CUT&RUN

description: Library name: GST-HP1beta

tag: detection reagent


title: WTAA uninduced_with Rapamycin_Replicate 3

description: Library name: PM9460-3 (Rep. 3)

tag: cell type

tag: strain


title: Ovarian cancer, Patient2

description:
Library name: Patient_2
FFPE spatial transcriptome sequencing

value: ovarian cancer

tag: age at_sample_colletion

value: Stage IVB

value: TC ×8 → TC ×10 → PLD ×10 → NGT + Bev ×5 → NGT ×3 → NDP ×3→ CPT-11 ×1

value: Surgery for recurrence

value: Fallopian tube

value: CPT-11 ×3 → TC ×6

tag: response to_prior_platinum_regimen


title: CBX7 Reader - CUT&RUN

description: Library name: GST-CBX7


title: Mutant A12_RNA-seq_1


title: WTAA uninduced_with Rapamycin_Replicate 2

description: Library name: PM9460-2 (Rep. 2)

value: Whole yeast cells

value: WT anchor-away background strain

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: Ovarian cancer, Patient1

description:
Library name: Patient_1
FFPE spatial transcriptome sequencing

value: Stage IIIC

value: TC ×6

value: Interval debulking surgery

value: Omentum

value: TC ×3

value: PR


title: Mutant A5_RNA-seq_3

value: 2D culture

value: hiPSC-derived mutant Line 1

value: Neural Progenitor Cells

value: Mutant CHD1L-/- Line 2


title: sample pool M for TCRseq

city: Palo Alto

first: Xiaorui

last: Han

state: CA

address: 240 Pasteur Dr. BMI

institute: Stanford University School of Medicine

description:
Library name: sample pool M for TCRseq
BD Rhapsody single-cell paired TCRseq

data_processing:
Raw Fastq files of targeted mRNA, TCRseq, and AbSeq processing, demultiplexing, barcoded processing, gene counting, normalizing, major cell type defination, multiplets identification were processed via the BD RhapsodyTM Sequence Analysis Pipeline (BD Biosciences) on the Seven Bridges platform (https://www.sevenbridges.com) per the manufacturers recommendations.
Assembly: For Targeted RNAseq reads were mapped to targeted-rnaseq-panel-index.fasta (supplementary file). For the targeted assay in combination with TCR, the pipeline automatically adds species appropriate TCR and BCR gene segments to the FASTA reference file. These gene segments are derived from the same Gencode transcriptome GTF as is used in the pre-built WTA assay reference archives.
Supplementary files format and content: matrix files with gene expression count, Abseq expression count, TCR contig annotations with cell barcode information, integrated data and RDS (R data) files for Seurat objects.
Library strategy: TCR-Seq

source_name: blood cells

extract_protocol:
PBMCs were thawed and each PBMC sample was rested for 6h at 37°C with 5% CO2 in 10% medium [RPMI (Gibico, cat. 11875085) + 10% FBS (Gibico, cat. A5670701), and 1% Pen-Strep (Gibico, cat. 15070063)]. Cells were counted and plated in 3 round-bottom wells of a 96-well plate at the density of 1.4 x106 cells in culture with 200 µL 5% medium [RPMI (Gibico, cat. 11875085) + 5% FBS (Gibico, cat. A5670701), and 1% Pen-Strep (Gibico, cat. 15070063)] per well and was stimulated with peanut protein solution (200ng/ul, peanut flour is from Stallergenes Greer cat. XPF171D3A25 and dissolved in PBS) for 18h. Then the cells were washed with Facs buffer (PBS with 0.25% BSA and 1mM EDTA) and stained with Fc block (Biolegend, cat. 422302) following with Single Cell Labeling with the human SMK SmapleTags (BD, cat. 633781) at room temperature for 20 minutes. Cells were surface stained with a panel of fluorochrome-conjugated antibodies including PE-CD154 and PE-CD137 (more details in Supplemental Table 18) in buffer (PBS with 0.25% BSA and 1mM EDTA) for 20 minutes on ice. Then we performed Anti-PE MicroBeads (Miltenyi, cat. 130-105-639) enrichment, following the product instruction to enrich the CD154 and/or CD137 positive cells. After enrichment, we pooled enriched cells from each of the 12 tagged samples to sort PE-positive CD4+ cells, including pr Teff CD4+ T cells (CD4+CD154+) and pr Treg CD4+ T cells (CD4+CD137+CD154-), using a BD FACS Aria at the Stanford FACS facility. We sorted as many pr CD4+ T cells as possible from the enriched cells, yielding between 33,000 and 85,000 cells per set of 12 pooled samples. At the same time, 1000 non-reactive (nr) CD4+ T cells (CD4+CD154-CD137-) were sorted into one single tube from the flowthrough cells from each individual sample. Then, all the pr Teff, Treg CD4+ T cells and nr CD4+ T cells were pooled together following with incubation with AbSeq oligo-linked mAbs pool(Supplemental Table 4, 2ul/mAb in 100ul 2%FBS PBS buffer, all AbSeq oligo-linked mAbs were validated titrated by BD company.).
Sorted cells were processed by using the BD RhapsodyTM platform. The libraries were prepared using the BD Immune Response Targeting Panel (BD RhapsodyTM Immune Response Panel HS, cat.633750) with addition of custom gene panel reagents, human TCR primers, BD RhapsodyTM Targeted mRNA and AbSeq Amplification Kit (cat. 633774) and sequenced on Illumina NovaSeq 6000 at Novogene USA (Davis, California).

value: blood cells

value: PBMC

value: T cells

tag: library type

value: TCRseq

tag: batch

value: M


title: GST Control - CUT&RUN

description: Library name: antiGSTcontrol

value: Bethyl A190-122A (Lot 11)


title: CUT&RUN HK4me2

extract_protocol:
Protocol was adapted from Hainer and Fazzio (2019) and Skene and Henikoff (2019).
P3010 : CUT&RUN samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). CUT&RUN libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (10 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: hiPSC-derived control

value: Control CHD1L+/+

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit

tag: antibody


title: WTAA uninduced_with Rapamycin_Replicate 1

description: Library name: PM9460-1 (Rep. 1)

value: Whole yeast cells

value: WT anchor-away background strain

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: Ovarian cancer, Patient5

description:
Library name: Patient_5
FFPE spatial transcriptome sequencing

value: ovarian cancer

tag: Stage

value: Stage IIIC

tag: treatment before_sample_collection

value: Primary debulking surgery

value: Peritoneum

value: TC ×8 → TC ×4 → TC ×8 → PLD ×5 → GEM ×3 → DTX ×4 → wPTX ×8 → CPT-11 ×3 → TC ×2 → GEM ×4  → NDP ×3

value: PR


title: Mutant A5_RNA-seq_2

value: 2D culture

value: hiPSC-derived mutant Line 1

value: Neural Progenitor Cells

value: Mutant CHD1L-/- Line 2


title: RAG2 Reader - CUT&RUN

description: Library name: GST-RAG2


title: MethylCseq_Anthers_rim-q

city: La Jolla

first: Julie

middle: A

last: Law

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

institute: Salk Institute for Biological Studies

description: Library name: sample208

data_processing:
Reads were mapped to the TAIR10 reference genome using the bs_seeker2-align.py function of BS-Seeker2 (v2.1.8) allowing 2 mismatches (-m 2). Redundant reads were removed using the remove_clonal.py function of picard tools (http://broadinstitute. github.io/picard/). The bs_seeker2-call_methylation.py function of BS-Seeker2 was used to call methylation at single cytosine resolution with read coverage greater than 4 (-r 4). To facilitate DNA methylation analyses and visualization, Tag Directory and BigWig data formats were generated as follows: (1) The CGmap output files from the BS-Seeker2 pipeline were converted to wig files using a previously published perl script (BSseeker2_2_wiggleV2_CG_CHG_CHH_allmC.pl), (2) the wig files were converted into BigWig files using wigToBigWig (v2.9) following default options, and (3) Tag Directories were made from the wig files using a previously published perl script (parseWig_noChr.v2.pl) and the makeTagDirectory function of HOMER (v4.10).
To identify differentially methylated regions (DMRs), the genome was split into 100 bp non-overlapping bins and the average levels of DNA methylation in the CG, CHG, and CHH contexts were compared between each mutant and three different wild-type controls. Thresholds used to declare significant DMRs are as follows: (1) The 100-bp bin should contain at least 4 cytosines in the specified context with read coverage greater than 4, (2) the methylation difference between mutant and wild-type control must be greater than 0.4, 0.2, or 0.1 for CG, CHG, and CHH contexts, respectively, and adjusted p-value must be less than 0.01, and (3) the DMR should pass the first two criteria when compared to three replicates of the wildtype control.
Assembly: TAIR10
Supplementary files format and content: wiggle (.wig) file, header with Chromosome, and two columns: position, % methylation

organism: Arabidopsis thaliana

source_name: Anthers (stage9)

growth_protocol: For transgenic lines that required drug selection, seeds were sterilized in sterilization buffer (70% ethanol, 0.05% SDS) for 10 minutes, followed by plating on half strength Linsmaier and Skoog medium (1/2 LS; Caisson Labs, Cat# LSP03) supplemented with 0.6% agar (Phyto Agar, Cat# P1003). The plates were placed in a 4˚C cold room for 4 days before growing in a growth chamber with 16h-light and 8h-dark cycles for 7 days. The seedlings were transplanted and grown under Salk greenhouse conditions. For the HEM EMS lines, the T-DNA insertion lines, and their corresponding control lines, seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. Approximately five weeks after planting, flower buds (stage 12 and younger), ovules (stage 12 unfertilized ovules), and anthers (stage 9) were collected and frozen in liquid nitrogen. Flower development stages were determined according to Smyth et al. Ovule collection was performed using a vacuum pump-based collection device that was engineered at the Salk Institute and was described previously.

extract_protocol:
Genomic DNA was extracted from anthers (stage 9) and ovules (stage 12) using the CTAB method followed by RNA digestion with RNase A (Thermo, #EN0531) according to the manufacturer’s instructions. 2 μg of genomic DNA was fragmented using a Covaris S2 sonicator. The sonicated DNA was size-selected using SpeedBeads (Thermo Scientific #65152105050250) to collect fragments 150-300 bp in length.
The DNA ends were repaired using the End-It DNA repair kit (epicenter # ER81050) and purified using SpeedBeads. The end-repaired fragments were adenylated using the polymerase activity of the Klenow Fragment (N-terminal truncation of DNA Polymerase I, NEB # M0212L), purified using SpeedBeads, and indexed using Trueseq Adapters (BIOO Scientific # 511911) and T4 DNA ligase (NEB # M0202). After purification using SpeedBeads, the fragments were subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, MECOV-50). Bisulfite-converted DNA was amplified by PCR using the KAPA HiFi HotStart DNA polymerase (KAPA BIOSYSTEMS # KK2801). The following program was used for the PCR amplification: 95˚C for 2 min; 98˚C for 30 s; 4 cycles of (98˚C for 15 s, 60˚C for 30 s, 72˚C for 4 min); and 72˚C for 10 minutes. The PCR product was purified using SpeedBeads and pooled for sequencing using the pair-end 50 bp kit (PE50) on the Illumina Nextseq 2000 or Novaseq X plus platform.

value: Anthers (stage9)

tag: ecotype

value: Columbia


title: A12_Mutant_multiome_RNA

description:
nuclear RNA 10x Genomics
NDLH4

data_processing:
BCLconvert 3.8.4, Cell Ranger arc 2.0.2 and the human reference cellranger-arc-GRCh38-2020-A-2.0.0 were used for demultiplexing, alignment, barcode and UMI filtering and counting.
Control CHD1L+/+ and CHD1L-/- samples were aggregated using cellranger-arc aggr function without performing the depth normalization.
Assembly: hg38
Supplementary files format and content: h5 file: contains both RNA-seq counts and ATAC-seq counts; tsv.gz: frangments file for ATAC-seq; tsv.gz.tbi: frangments file index for ATAC-seq

molecule: nuclear RNA

source_name: 3D cerebral organoid

extract_protocol:
Multiomes libraries were generated following the 10X Genomics Multiome Guidelines (protocol vA.01). Nuclei isolation were performed following the demonstrated protocol “Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing” available on 10XGenomics.com (cat #CG000375 Rev C). Briefly, 6 cerebral organoids per condition, control CHD1L+/+ and CHD1L-/-, were washed in PBS 1X. Lysis were performed using 1X NP40 Lysis Buffer with mechanical dissocation of tissues. Samples were filtered through 70µm strained and centrifugated for 5mn at 4°C 500rcf. Pellet were re-suspended in PBS + 1% BSA + 1U/µl RNAse Inhibitor and incubated for 5mn. After a second centrifugation, pellet was re-suspended in 0.1X Lysis Buffer and incubated 5mn on ice. Wash buffer was added and samples were centrifugated before a final resuspension in Diluted Nuclei Buffer. 10,000 nuclei were sent for analysis.
Multiomes libraries preparation were generated following the 10X Genomics Multiome Guidelines (protocol vA.01) and the protocol “Chromium Next Gem Single Cell Multiome ATAC + Gene expression User guide” (cat #CG000338 Rev E). Sequencing was performed by the GenomEast platform, a member of the ‘France Génomique’ consortium (ANR-10-INBS-0009)

treatment_protocol: Cerebral Organoids were generated from hiPSC lines  using the STEMCell Cerebral Organoid Kit (08570, STEMCELL) as precognized by the furnisher. Cerebral Organoids were maintained until day 60 in vitro.

value: 3D cerebral organoid

value: hiPSC-derived control

value: Complex

value: KO CHD1L-/-

value: hiPSC derived Cerebral Organoids using StemCell cerebral organoid differentiation kit


title: Mutant A5_RNA-seq_1

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit


title: Ovarian cancer, Patient4

description:
Library name: Patient_4
FFPE spatial transcriptome sequencing

value: ovarian cancer

value: Stage IIIB

value: TC ×6 → CPT-P ×3 → TC ×2 → PLD ×4 → TC ×3 → NDP ×5 → DTX ×3 → NGT ×7 → CPT-11 ×4

tag: timing of_sample_collection

value: Surgery for recurrence

tag: sample

value: Vaginal stump

tag: treatment before_olaparib_treatment

value: NED ×6


title: sample pool K for TCRseq

description:
Library name: sample pool K for TCRseq
BD Rhapsody single-cell paired TCRseq

tag: tissue

value: blood cells

value: PBMC

value: T cells

value: TCRseq

value: K


title: CUT&RUN CHD1L

value: 2D culture

tag: cell line

value: Neural Progenitor Cells

tag: genotype

value: Control CHD1L+/+


title: sample pool L for TCRseq

description:
Library name: sample pool L for TCRseq
BD Rhapsody single-cell paired TCRseq

value: L


title: Control 8 330_RNA-seq_3

value: hiPSC-derived control

tag: treatment


title: MethylCseq_Anthers_rim22-2

description: Library name: sample206

value: Anthers (stage9)

value: Columbia


title: Mutant A12_RNA-seq_2

value: hiPSC-derived mutant Line 2

tag: cell type

value: Mutant CHD1L-/- Line 1

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit


title: sample pool I for TCRseq

description:
Library name: sample pool I for TCRseq
BD Rhapsody single-cell paired TCRseq

value: I


title: Mouselungs_Bleo_Vehicle_1

description:
Library name: Mouselungs_Bleo_Vehicle_1
10X Genomics

extract_protocol:
Nuclei were isolated from frozen mouse lungs (n=12, weighing approximately 50 mg) by physical dissociation using a glass dounce homogenizer and were sorted using fluorescence-activated cell sorting (FACS) based on DAPI-positive fluorescence to obtain a single nuclei population. Nuclei concentration was manually determined using DAPI staining and hemocytometer and adjusted to 1000 nuclei/uL.
Single nuclei RNA sequencing libraries were generated using the 10X Genomics Chromium Instrument and Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1) from approximately 4000 nuclei. Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).

value: Lungs


title: A12_Mutant_multiome_ATAC

description:
chromatin accessibility 10x Genomics
NDLH2

library_source: genomic single cell

value: 3D cerebral organoid

value: Complex

value: KO CHD1L-/-

value: hiPSC derived Cerebral Organoids using StemCell cerebral organoid differentiation kit


title: Control 8 330_RNA-seq_2


title: 8330_Control_multiome_RNA

description:
nuclear RNA 10x Genomics
NDLH3


title: MethylCseq_Anthers_rim16

description: Library name: sample205


title: sample pool H for TCRseq

description:
Library name: sample pool H for TCRseq
BD Rhapsody single-cell paired TCRseq

value: blood cells

value: PBMC

value: T cells

value: TCRseq

value: H


title: Control 8 330_RNA-seq_1

value: 2D culture

value: hiPSC-derived control

value: Neural Progenitor Cells

value: Control CHD1L+/+


title: 8330_Control_multiome_ATAC

description:
chromatin accessibility 10x Genomics
NDLH1


title: MethylCseq_Anthers_clsy1,2

description: Library name: sample204

value: Anthers (stage9)

value: Columbia


title: sample pool G for TCRseq

description:
Library name: sample pool G for TCRseq
BD Rhapsody single-cell paired TCRseq

value: G


title: MethylCseq_Anthers_pol-iv

description: Library name: sample203


title: MethylCseq_Anthers_rim-cr

description: Library name: sample207


title: IgG Control - CUT&RUN

description: Library name: RbIgG

data_processing:
Paired-end fastq files were aligned to the T2T reference genome using Bowtie2 (v2.2.5).
Duplicate reads were removed via SAMtools (v1.6).
Multi-aligned reads were removed via Picard (v2.26.2).
bigWig creation included RPKM normalization via bamCoverage in deeptools (v3.5.1).
Assembly: T2T
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

tag: detection reagent


title: sample pool J for TCRseq

description:
Library name: sample pool J for TCRseq
BD Rhapsody single-cell paired TCRseq

value: J


title: A12_ATAC-seq_3

data_processing:
Data analysis was performed using the Encode ATAC-seq pipeline v1.9.3. Adapter sequences were removed and low quality ends were trimmed. Reads were mapped onto the hg38 assembly of Homo Sapiens genome using Bowtie2 (version 2.2.6) choosing the zero multi-mapping option. Mitocondrial reads were removed.
Assembly: hg38
Supplementary files format and content: Fold-enrichment bigwig files generated with the MACS2 bdgcmp command

extract_protocol:
Assay for transposase accessible chromatin was performed on hiPSC-derived hNPC using a derived protocol from Buenostro et al., 2013. Indeed, 50 000 cells from 8330 (control line CHD1L+/+), A12 and A5 (mutant for CHD1L) lines were resuspended in resuspension buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2) and then lysed in lysis buffer (Resuspension buffer + 0.1% NP40 + 0.1% tween-20+ 0.01% Digitonin) and incubated 3mn on ice. Then, 1mL of wash buffer was added (resuspension buffer + 0.1% Tween-20). Cells were centrifugated 10mn at 500G at 4°C and supernatant was trashed out. Transposition reaction mix (Kit Illumina Tagment DNA Enzyme and Buffer Small Kit #20034197) was added to pellet and incubated 30mn at 37°C in a thermomixer at 1000rpm. DNA fragment was isolated using Qiagen MinElut Reaction Cleanup kit.
DNA fragment were amplificated and library was generated by PCR using appropriate primers as described in Buenostro et al., 2013 and NEBNext High-Fidelity 2X PCR Master mix (NEB, #M0541S). Finally, library was purified using SRIselect beads (Beckman Coulter) by a one-sided purification to remove primers.

value: hiPSC-derived mutant Line 6

value: Mutant CHD1L-/- Line 1

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit


title: sample pool F for TCRseq

description:
Library name: sample pool F for TCRseq
BD Rhapsody single-cell paired TCRseq

value: F


title: MethylCseq_Anthers_clsy3,4

description: Library name: sample202


title: A12_ATAC-seq_2

value: hiPSC-derived mutant Line 5


title: sample pool E for TCRseq

description:
Library name: sample pool E for TCRseq
BD Rhapsody single-cell paired TCRseq

value: blood cells

value: PBMC

value: E


title: sample pool D for TCRseq

description:
Library name: sample pool D for TCRseq
BD Rhapsody single-cell paired TCRseq

value: T cells

value: TCRseq

value: D


title: A12_ATAC-seq_1

value: 2D culture

value: hiPSC-derived mutant Line 4

value: Neural Progenitor Cells


title: B cells, S728 GEX, Convalescent

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Pediatrics

institute: Weill Cornell Medicine

description: Library name: S728 GEX

data_processing:
Demultiplexing the Illumina sequencer's base call files (BCLs) for each flowcell directory into FASTQ files was performed by "cellranger mkfastq"  (cellranger version 3.02)
Gene counts were calculated using "cellranger count" (cellranger version 3.02) under default setting， BCR sequences were assembled using "cellranger vdj" (cellranger version 3.02) under default setting.
Assembly: GRCh38-1.2.0 for transccriptome, cellranger-vdj-GRCh38-alts-ensembl-5.0.0 for V(D)J
Supplementary files format and content: For each dataset, there are 5 files. Using dataset S68 as an example: S68_barcodes.tsv.gz, S68_features.tsv.gz, S68_matrix.mtx.gz are gene count files for scRNA-seq data, S68_barcodes.tsv.gz contains all cell barcodes information, S68_features.tsv.gz contains all features information (including genes and ADT features), and S68_matrix.mtx.gz contains expression matrix. S68_consensus.fasta, S68_filtered_contig_annotations.csv are sequence files for single cell BCR sequencing data. S68_consensus.fasta contains all assembled BCR sequences, S68_filtered_contig_annotations.csv contains all cell barcode information. For raw fastq data, we include a feature barcode file (feature_barcode_covid.csv/feature_barcode_covid1.csv) of ADT features for each dataset. Fastq files for 5'prime RNA-seq are named by ""RNA"", e.g. S68_RNA_..... Fastq files for surface protein and probe binding are named by ""ADT"", e.g. S68_ADT_.... For each sequence run, there are 12 fastq files: I1, R1, R2 for four lines (L001, L002, L003, L004). Users can run Cellranger on these fastq files by following offical documents: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

source_name: Peripheral Blood Mononuclear Cell

extract_protocol:
Cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum of 10,000 individual cells per sample.
Utilizing the Chromium Single Cell A Chip Kit(10x Genomics, PN-120236) and Chromium Single Cell 5' Library & Gel Bead Kit (10x Genomics, PN-1000006) , poly-adenylated mRNA from an individual cell was tagged with a unique 16 base pair 10x barcode and 10 base pair Unique Molecular Identifier.

treatment_protocol: PBMCs were isolated from whole blood (acute samples) or leukoreduction filters (convalescent samples) by use of a Lymphoprep Ficoll gradient and any contaminating red blood cells were lysed by ACK buffer. Cells were then frozen at -80 deg C in fetal bovine serum supplemented with 10% DMSO. On the day of sorting and sequencing cells were thawed and B cell were purified by human pan B cell EasySep enrichment kit from STEMCELL technologies.

value: Peripheral Blood Mononuclear Cell

value: B cells

tag: strain

tag: disease state

value: Convalescent


title: B cells, S728 VDJ, Convalescent

description: Library name: S728 VDJ


title: sample pool C for TCRseq

description:
Library name: sample pool C for TCRseq
BD Rhapsody single-cell paired TCRseq

tag: library type

value: C


title: MethylCseq_Anthers_WT_rep2

description: Library name: sample199

value: Anthers (stage9)

value: Columbia


title: B cells, S728 ADT, Convalescent

description: Library name: S728 ADT


title: A5_ATAC-seq_4

value: hiPSC-derived mutant Line 3

value: Mutant CHD1L-/- Line 2

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit


title: sample pool M for RNAseq Abseq

description:
Library name: sample pool M for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

data_processing:
Raw Fastq files of targeted mRNA, TCRseq, and AbSeq processing, demultiplexing, barcoded processing, gene counting, normalizing, major cell type defination, multiplets identification were processed via the BD RhapsodyTM Sequence Analysis Pipeline (BD Biosciences) on the Seven Bridges platform (https://www.sevenbridges.com) per the manufacturers recommendations.
Assembly: For Targeted RNAseq reads were mapped to targeted-rnaseq-panel-index.fasta (supplementary file). For the targeted assay in combination with TCR, the pipeline automatically adds species appropriate TCR and BCR gene segments to the FASTA reference file. These gene segments are derived from the same Gencode transcriptome GTF as is used in the pre-built WTA assay reference archives.
Supplementary files format and content: matrix files with gene expression count, Abseq expression count, TCR contig annotations with cell barcode information, integrated data and RDS (R data) files for Seurat objects.

value: blood cells

value: PBMC

value: targeted RNAseq and Abseq

tag: batch

value: M


title: B cells, S626 VDJ, Convalescent

description: Library name: S626 VDJ


title: MethylCseq_Anthers_WT_rep1

description: Library name: sample198


title: B cells, S626 GEX, Convalescent

description: Library name: S626 GEX


title: sample pool L for RNAseq Abseq

description:
Library name: sample pool L for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: T cells

value: L


title: A5_ATAC-seq_3

value: 2D culture

value: hiPSC-derived mutant Line 2


title: A5_ATAC-seq_2

value: hiPSC-derived mutant Line 1

value: Neural Progenitor Cells


title: MethylCseq_Ovules_rim-q

description: Library name: sample197

source_name: Ovules (stage12)

value: Ovules (stage12)


title: A12_ATAC-seq_4

value: hiPSC-derived mutant Line 7

value: Mutant CHD1L-/- Line 1


title: B cells, S451 VDJ, Convalescent

description: Library name: S451 VDJ

value: Peripheral Blood Mononuclear Cell

value: B cells

value: Convalescent


title: sample pool J for RNAseq Abseq

description:
Library name: sample pool J for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: J


title: A5_ATAC-seq_1

value: Mutant CHD1L-/- Line 2

value: hiPSC derived NPC using StemXVivo Neural Progenitor Differentiation kit


title: MethylCseq_Anthers_clsy3

description: Library name: sample201

value: Anthers (stage9)

value: Columbia


title: MethylCseq_Ovules_rim-cr

description: Library name: sample196


title: 8330_ATAC-seq_4

value: Control CHD1L+/+


title: MethylCseq_Ovules_rim22-2

description: Library name: sample195


title: B cells, S451 GEX, Convalescent

description: Library name: S451 GEX


title: 8330_ATAC-seq_3

value: hiPSC-derived control


title: B cells, S451 ADT, Convalescent

description: Library name: S451 ADT


title: MethylCseq_Ovules_rim16

description: Library name: sample194


title: MethylCseq_Anthers_WT_rep3

description: Library name: sample200


title: sample pool H for RNAseq Abseq

description:
Library name: sample pool H for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: blood cells

value: PBMC

value: T cells

value: targeted RNAseq and Abseq

value: H


title: 8330_ATAC-seq_2

value: 2D culture

value: Neural Progenitor Cells


title: MethylCseq_Ovules_clsy1,2

description: Library name: sample193

value: Ovules (stage12)


title: sample pool G for RNAseq Abseq

description:
Library name: sample pool G for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: G


title: 8330_ATAC-seq_1


title: B cells, S380 VDJ, Convalescent

description: Library name: S380 VDJ

value: Peripheral Blood Mononuclear Cell

value: B cells

value: Convalescent


title: B cells, S380 GEX, Convalescent

description: Library name: S380 GEX


title: sample pool F for RNAseq Abseq

description:
Library name: sample pool F for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: F


title: B cells, S626 ADT, Convalescent

description: Library name: S626 ADT


title: MethylCseq_Ovules_clsy3,4

description: Library name: sample191


title: MDA-MB-231dTOP CAR POS8

city: Leuven

first: Frederic

last: Lluis

state: Leuven

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description:
CARBP8
MDA-MB-231dTOP_CAR_POS8
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

data_processing:
Trimming of adapters, polyA/T tails, and low-quality reads was performed using the Trimgalore package with default parameters. Using the Salmon package with default parameters, the reads were aligned to the transcriptome and quantified using release 32 of the human reference transcriptome sequence and gene annotation. Counts were then imported into R using Tximport.
Assembly: Release 32 (GRCh38.p13)
Supplementary files format and content: raw counts per sample
Supplementary files format and content: normalized (VST) counts per sample

source_name: MDA-MB-231dTOP cell line treated with Carboplatin (35uM) for 72 hours - sorted for WNTHigh cells (GFP +)

extract_protocol:
Total RNA was extracte MDA-MB-231 cells using the GenElute™ Mammalian Total RNA Miniprep Kit according to the Manufacturer's instructions.
RNA sequencing (RNAseq) libraries were prepared from 4 µg of total RNA using the KAPA stranded mRNA-seq kit (Roche, KK8581) according to manufacturer’s specifications. 100 nM KAPA-single index adapters (Roche, KK8700) were added to A-tailed cDNA, and libraries were amplified for 10 cycles. Finally, 1x library cleanup was performed using Agencourt AMPure XP beads (Beckman Coulter, A63881). Library fragment size was assessed using Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). Each library was diluted to 4 nM and pooled for sequencing on an Illumina Hiseq4000, aiming at 15-20 million SE50 reads per sample (19 million reads on average).

value: Breast tumor-derived

value: Mesenchymal

value: Chemotherapy (Carboplatin - 35uM)

tag: timepoint

value: 72 hours


title: sample pool K for RNAseq Abseq

description:
Library name: sample pool K for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: blood cells

value: K


title: sample pool E for RNAseq Abseq

description:
Library name: sample pool E for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: PBMC

value: T cells

value: E


title: B cells, S380 ADT, Convalescent

description: Library name: S380 ADT


title: MDA-MB-231dTOP CAR POS7

description:
CARBP7
MDA-MB-231dTOP_CAR_POS7
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: MethylCseq_Ovules_clsy3

description: Library name: sample190

value: Columbia


title: MethylCseq_Ovules_WT_rep3

description: Library name: sample189


title: sample pool C for RNAseq Abseq

description:
Library name: sample pool C for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: targeted RNAseq and Abseq

value: C


title: MethylCseq_Ovules_WT_rep2

description: Library name: sample188

value: Ovules (stage12)


title: B cells, S270 ADT, Convalescent

description: Library name: S270 ADT

value: Peripheral Blood Mononuclear Cell


title: B cells, S270 GEX, Convalescent

description: Library name: S270 GEX

value: B cells


title: MDA-MB-231dTOP CAR POS4

description:
CARBP4
MDA-MB-231dTOP_CAR_POS4
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: sample pool D for RNAseq Abseq

description:
Library name: sample pool D for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: D


title: MethylCseq_Ovules_WT_rep1

description: Library name: sample187


title: Day 60, sublibrary 7

city: Singapore

first: John

middle: F

last: Ouyang

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Parse biosciences

data_processing:
Sequencing raw reads were demultiplexed and processed using the Parse Biosciences pipeline (v1.0.5), aligned to GrCH38 human genome.
Assembly: GrCH38
Supplementary files format and content: tab separated value files and matrix file

extract_protocol:
Midbrain organoids were dissociated into single cells using Papain-based dissociation. Samples were fixed and stored for scRNA sequencing according to Parse Biosciences Evercode Fixation kit (v2.0.2) and stored at -80°C until library preparation.
Library preparation was conducted using the Parse Biosciences Evercode Whole Transcriptome (WT) kit (v2.0.1). Sequencing sublibraries were quantified with the KAPA Library Quantification Kit (#KK4824). Sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Midbrain organoids


title: B cells, S195 VDJ, Convalescent

description: Library name: S195 VDJ

value: Convalescent


title: sample pool I for RNAseq Abseq

description:
Library name: sample pool I for RNAseq Abseq
BD Rhapsody single-cell targeted RNAseq and Abseq

value: I


title: MDA-MB-231dTOP CAR POS3

description:
CARBP3
MDA-MB-231dTOP_CAR_POS3
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

value: Breast tumor-derived

value: Mesenchymal

value: Chemotherapy (Carboplatin - 35uM)


title: MethylCseq_Ovules_pol-iv

description: Library name: sample192


title: B cells, S270 VDJ, Convalescent

description: Library name: S270 VDJ


title: smRNAseq_Anthers_b8_pUBQ10_3xFLAG-RIM12_col-0_line2_rep2

description: Library name: sample143

library_source: other

data_processing:
For each sample, fastq files were trimmed using cutadapt (v1.18) with the -a AGATCGGAAGAGC option to remove the adapter sequence and the -m 15 option to discard reads shorter than 15 nt. Clean reads were then mapped to the TAIR10 reference genome using ShortStack (v3.8.5) allowing one mismatch (--mismatches 1). The --mmap f option was also included to assign multiple-mapped reads to a specific locus using the fractional-seeded algorithm. The resulting bam files were then filtered to keep perfectly mapped reads or reads with a single mismatch at the 3’ end using bamtools (v2.5.1) together with an in-house script (JSON_findPerfectMatches_and_TerminalMisMatches_v3) to meet the characteristics of Pol-IV transcription. To facilitate downstream analyses, the filtered bam files were used to generate Tag Directories using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 1 -keepAll. To quantify the expression of smRNAs with specific sizes, the tag directories were split by size (20nt-25nt) using a custom perl script (splitTagDirectoryByLength.dev2.pl) and all subsequent analyses utilized the Tag Directories corresponding to 24nt siRNAs.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

molecule: other

source_name: anthers (stage9)

extract_protocol:
Total RNA extraction and smRNA enrichment was performed following a previously reported protocol. Briefly, 10 μg of total RNA extracted from flower buds (stage 12 and younger), ovules (stage 12 unfertilized ovules), and anthers (stage 9) were used for each smRNA library prep.
The smRNA-seq libraries were constructed using the NEBNext Small RNA Library Prep Kit (NEB, Cat# E7330L). The smRNA libraries were further purified using an 8% acrylamide gel and size selected (130-160 bp) relative to the O'RangeRuler 10 bp DNA Ladder (Thermo Scientific, Cat# SM1313). The size selected smRNA libraries were pooled for sequencing with single-end 50 bp kit (SE50) on Illumina Nextseq 2000 or Novaseq X plus platforms.

value: anthers (stage9)

value: experiment batch8


title: B cells, S195 GEX, Convalescent

description: Library name: S195 GEX


title: Day 60, sublibrary 6

description: Parse biosciences


title: MDA-MB-231dTOP CAR POS2

description:
CARBP2
MDA-MB-231dTOP_CAR_POS2
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

value: 72 hours


title: B cells, S195 ADT, Convalescent

description: Library name: S195 ADT


title: smRNAseq_Anthers_b8_clsy34,rim22_rep2

description: Library name: sample141


title: smRNAseq_Anthers_b8_pUBQ10_3xFLAG-RIM12_col-0_line2_rep1

description: Library name: sample142


title: B cells, S136 VDJ, Convalescent

description: Library name: S136 VDJ


title: MDA-MB-231dTOP CAR POS6

description:
CARBP6
MDA-MB-231dTOP_CAR_POS6
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: MDA-MB-231dTOP CAR NEG8

description:
CARBN8
MDA-MB-231dTOP_CAR_NEG8
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

source_name: MDA-MB-231dTOP cell line treated with Carboplatin (35uM) for 72 hours - sorted for WNTLow cells (GFP -)


title: Day 60, sublibrary 5

description: Parse biosciences


title: MDA-MB-231dTOP CAR POS1

description:
CARBP1
MDA-MB-231dTOP_CAR_POS1
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: smRNAseq_Anthers_b8_clsy34,rim22_rep1

description: Library name: sample140


title: MDA-MB-231dTOP CAR POS5

description:
CARBP5
MDA-MB-231dTOP_CAR_POS5
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: B cells, S136 GEX, Convalescent

description: Library name: S136 GEX


title: MDA-MB-231dTOP CAR NEG7

description:
CARBN7
MDA-MB-231dTOP_CAR_NEG7
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 60, sublibrary 8

description: Parse biosciences


title: Day 60, sublibrary 3

description: Parse biosciences


title: smRNAseq_Anthers_b8_clsy12,rim22_rep2

description: Library name: sample139


title: MDA-MB-231dTOP CAR NEG6

description:
CARBN6
MDA-MB-231dTOP_CAR_NEG6
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: B cells, S136 ADT, Convalescent

description: Library name: S136 ADT


title: Day 60, sublibrary 1

description: Parse biosciences


title: MDA-MB-231dTOP CAR NEG5

description:
CARBN5
MDA-MB-231dTOP_CAR_NEG5
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: smRNAseq_Anthers_b8_clsy12,rim22_rep1

description: Library name: sample138


title: smRNAseq_Anthers_b8_clsy4,rim22_rep2

description: Library name: sample137


title: B cells, S80 VDJ, Convalescent

description: Library name: S80 VDJ


title: B cells, S80 GEX, Convalescent

description: Library name: S80 GEX


title: Day 60, sublibrary 2

description: Parse biosciences


title: smRNAseq_Anthers_b8_clsy4,rim22_rep1

description: Library name: sample136


title: Day 50, sublibrary 7

description: Parse biosciences


title: Day 50, sublibrary 8

description: Parse biosciences


title: B cells, S80 ADT, Convalescent

description: Library name: S80 ADT


title: MDA-MB-231dTOP CAR NEG3

description:
CARBN3
MDA-MB-231dTOP_CAR_NEG3
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 60, sublibrary 4

description: Parse biosciences


title: Day 50, sublibrary 6

description: Parse biosciences


title: smRNAseq_Anthers_b8_clsy3,rim22_rep2

description: Library name: sample135


title: B cells, S68 VDJ, Convalescent

description: Library name: S68 VDJ


title: MDA-MB-231dTOP CAR NEG2

description:
CARBN2
MDA-MB-231dTOP_CAR_NEG2
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: smRNAseq_Anthers_b8_clsy3,rim22_rep1

description: Library name: sample134


title: B cells, S68 GEX, Convalescent

description: Library name: S68 GEX


title: Day 50, sublibrary 5

description: Parse biosciences


title: MDA-MB-231dTOP CAR NEG1

description:
CARBN1
MDA-MB-231dTOP_CAR_NEG1
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: smRNAseq_Anthers_b8_clsy2,rim22_rep2

description: Library name: sample133


title: Day 50, sublibrary 4

description: Parse biosciences


title: B cells, S68 ADT, Convalescent

description: Library name: S68 ADT


title: smRNAseq_Anthers_b8_clsy2,rim22_rep1

description: Library name: sample132


title: MDA-MB-231dTOP DOC POS6

description:
DOCP6
MDA-MB-231dTOP_DOC_POS6
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

source_name: MDA-MB-231dTOP cell line treated with Docetaxel (4.5nM) for 72 hours - sorted for WNTHigh cells (GFP +)

value: Chemotherapy (Docetaxel - 4.5nM)


title: HLF5_NVP-BHG712

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample.
Cutadapt (v1.18) is used to maintain minimum read length of 25 bp post trimming of adapters as well as trimming of N’s.
Splice-aware alignment of reads using a Hierarchical Graph FM index (HGFM) method is performed using HISAT2 software (v2.1.0) with parameters (--rna-strandness RF –dta) against human reference genome (vGRCh38).
To obtain the abundance of each of these transcripts based only on the known reference genome and transcriptome, StringTie was run again using different parameters (-e -B -G referencetranscripts.gtf) to generate output of Ballgown software as compatible table files.
A script named ‘prepDE.py’ by StringTie software was used to extract the read count information.
Assembly: GRCh38
Supplementary files format and content: 1 tab-delimited text file includes raw gene expression values for each sample.

growth_protocol: Primary human IPF lung fibroblasts and human lung fibroblasts (HLF; from control donors) were seeded in 6-well culture dishes at 2 x 10^6 cells in 10% FBS/DMEM for 24 h (5% CO2).

extract_protocol:
Total RNA is extracted from treated IPF and HLF cells using standard TRIzol method and quantified using the Qubit RNA BR assay (Denovix). Quality of RNA is assessed using the Agilent RNA Nano chips on a Bioanalyzer instrument. For all the samples, RNA integrity number (RIN) was 10.
Total RNA libraries are prepared from 200 ηg total RNA using the TruSeq Stranded total RNA library preparation kit (Illumina Cat# 20020596) as per manufacturer’s recommendations.  Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries prepared for sequencing (volumetrically pooled, diluted and denatured): 75 paired end read-cycles on an Illumina NextSeq 550 sequencer.

treatment_protocol: One day after seeding, cells were treated for 24 h with either 250 nM of the EphB4 inhibitor NVP-BHG712 or an equivalent volume of DMSO (as control)

value: Lung

value: 250 nM NVP-BHG712


title: MDA-MB-231dTOP CAR NEG4

description:
CARBN4
MDA-MB-231dTOP_CAR_NEG4
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 50, sublibrary 3

description: Parse biosciences


title: MDA-MB-231dTOP DOC POS5

description:
DOCP5
MDA-MB-231dTOP_DOC_POS5
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: HLF3_NVP-BHG712


title: smRNAseq_Anthers_b8_clsy1,rim22_rep2

description: Library name: sample131

value: Columbia


title: Day 50, sublibrary 2

description: Parse biosciences


title: smRNAseq_Anthers_b8_clsy1,rim22_rep1

description: Library name: sample130


title: HLF2_NVP-BHG712


title: Day 50, sublibrary 1

description: Parse biosciences


title: smRNAseq_Anthers_b8_rim-q_rep2

description: Library name: sample129


title: MDA-MB-231dTOP DOC POS3

description:
DOCP3
MDA-MB-231dTOP_DOC_POS3
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 40, sublibrary 8

description: Parse biosciences


title: MDA-MB-231dTOP DOC POS2

description:
DOCP2
MDA-MB-231dTOP_DOC_POS2
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: smRNAseq_Anthers_b8_rim-q_rep1

description: Library name: sample128


title: Day 40, sublibrary 7

description: Parse biosciences


title: HLF5_Vehicle

value: 0.1% DMSO


title: MDA-MB-231dTOP DOC POS1

description:
DOCP1
MDA-MB-231dTOP_DOC_POS1
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: HLF3_Vehicle


title: smRNAseq_Anthers_b8_rim-cr_rep2

description: Library name: sample127


title: MDA-MB-231dTOP DOC NEG6

description:
DOCN6
MDA-MB-231dTOP_DOC_NEG6
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

source_name: MDA-MB-231dTOP cell line treated with Docetaxel (4.5nM) for 72 hours - sorted for WNTLow cells (GFP -)


title: Day 40, sublibrary 6

description: Parse biosciences


title: smRNAseq_Anthers_b8_rim-cr_rep1

description: Library name: sample126


title: MDA-MB-231dTOP DOC NEG5

description:
DOCN5
MDA-MB-231dTOP_DOC_NEG5
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: smRNAseq_Anthers_b8_rim22-2_rep2

description: Library name: sample125


title: HLF1_Vehicle


title: Day 40, sublibrary 4

description: Parse biosciences


title: HLF2_Vehicle


title: MDA-MB-231dTOP DOC POS4

description:
DOCP4
MDA-MB-231dTOP_DOC_POS4
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: HPB-ALL, ATAC-seq

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

institute: University of Michigan

data_processing:
Data processing was performing using Chipseq ATACseq Pipelines 1.0.1 (https://github.com/russell-ryan-lab/ChIPseq_ATACseq_pipelines).
Paired-end reads were aligned to hg19 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to retain only paired reads in a proper pair (flags: 0x1, 0x2), and to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800).
Reads were filtered to retain only read-pairs mapping to <=2 sites genome-wide (X0 tag <=2 for both reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg19 fragment coverage, normalized to fragments per million post-filtering)

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Nuclei were isolated from 50,000 cells for each sample using Nuclei EZ prep-Nuclei Isolation Kit (Sigma-Aldrich, USA).
The transposition reaction mix (25μl of 2X TD buffer, 2.5μl of Tn5 transposase (Illumina, San Diego, CA, USA), 15ul of PBS and 7.5μl of nuclease free water) was added to nuclei and incubated at 37°C for 1hour in an orbital shaker at 300RPM. 50uL Qiagen buffer PB was added to each sample to stop the reaction and DNA was isolated with AMPure XP beads (Beckman Coulter). 15 cycles of PCR were performed with transposed DNA using the dual index primers and NEBNext PCR Master Mix, followed by AMPure XP purification.

value: T-cell acute lymphoblastic leukemia

value: HPB-ALL


title: MDA-MB-231dTOP DOC NEG4

description:
DOCN4
MDA-MB-231dTOP_DOC_NEG4
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: MDA-MB-231dTOP DOC NEG3

description:
DOCN3
MDA-MB-231dTOP_DOC_NEG3
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: smRNAseq_Anthers_b8_rim16_rep2

description: Library name: sample123


title: Day 40, sublibrary 3

description: Parse biosciences


title: DU.528, ATAC-seq


title: HLF1_NVP-BHG712


title: smRNAseq_Anthers_b8_rim22-2_rep1

description: Library name: sample124


title: MDA-MB-231dTOP DOC NEG2

description:
DOCN2
MDA-MB-231dTOP_DOC_NEG2
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 40, sublibrary 2

description: Parse biosciences


title: Day 40, sublibrary 1

description: Parse biosciences


title: smRNAseq_Anthers_b8_clsy1,2_rep2

description: Library name: sample121


title: CUTLL1, ATAC-seq