title: Bulk RNAseq of HBECs (U19_KD_C2)

description: Library name: U19_KD_C2


title: Bulk RNAseq of HBECs (U19_WT_C2)

status: Public on Nov 24 2025

type: SRA

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

country: USA

institute: Harvard T. H. Chan School of Public Health

description: Library name: U19_WT_C2

library_source: transcriptomic

data_processing:
Bulk RNA Sequencing
Alignment to GRCh38 using Salmon 1.5.2
Differential expression analysis using DESeq2
Assembly: GRCh38 release 101
Supplementary files format and content: Digital gene expression count matrix generated by Salmon.

molecule: total RNA

organism: Homo sapiens

source_name: Bronchus

growth_protocol: As previously described (11, 12, 49, 53), primary HBE cells were seeded on transwells and maintained in ALI culture until the cells were well-differentiated. We used primary HBE cells from thirteen distinct donors with no history of smoking or lung disease (Supplementary Table).

extract_protocol:
As we previously described (12), we isolated total RNA from HBE cells (n = 3 donors without a history of lung disease) using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Bulk RNA sequencing was performed on a NovaSeq instrument (Illumina, San Diego, CA, USA) by the Bauer Core Facility at Harvard University.
Bulk RNA Seq

treatment_protocol: To mimic bronchoconstriction, well-differentiated HBE cells were exposed to apical-to-basal pressure with a magnitude of 30cm H2O for 3 hrs, as previously described (11, 12, 49, 53). Time-matched control cells received 0cm H2O pressure. Cells and conditioned media were collected between 3 and 72 hrs. In experiments using recombinant human (rh) TGF-β1 (Cell Signaling Technologies, Danvers, MA), we spiked 10 ng/ml into the basolateral media of HBE cells in ALI cultures. Cells were collected between 24 and 72 hrs for further analysis. To determine the signaling pathways that regulate mechanical compression-induced Hic-5 protein expression, we used pharmacological inhibitors of the TGF-β receptor (SB431542; 10 µM, Tocris, Bristol, UK), MEK (U0126; 10 µM, Tocris), and EGFR (AG1478; 10 µM, Tocris). Each inhibitor was added to the basolateral media of HBE cells 1 hr prior to exposure to mechanical compression or TGF- β. As a control, 0.1% DMSO was used.To knock down Hic-5 expression in HBE cells, we used antisense oligonucleotides designed and provided by Ionis Pharmaceuticals. We initially tested five ASOs targeting TGFB1I1(denoted as Hic-5 ASO). Then, we  selected the most effective ASO and used for subsequent experiments. HBE cells maintained in ALI culture were treated with 10µM of either a non-targeting control (scrambled) ASO or Hic-5 ASO between ALI days 9 and 20 prior to the application of mechanical compression. We confirmed the knockdown efficiency of the Hic-5 ASO in well-differentiated HBE cells by RT-qPCR and western blot analysis.

tag: tissue

value: Bronchus

value: WT

tag: cell type

value: Airway epithelial cells

tag: genotype

value: Wild type

tag: treatment

value: Control


title: Bulk RNAseq of HBECs (U19_WT_C1)

description: Library name: U19_WT_C1


title: Combination_Anlotinib3

city: luzhou

first: Tao

last: Ma

state: si chuan

address: taiping jie

department: Department of Hematology

country: China

institute: Affiliated Hospital of Southwest Medical University

description: Library name: 3_3

data_processing:
1.mRNA data quality control: FastQC software and R were used to evaluate the quality of raw sequencing data；2. mRNA reference genome alignment, using STAR software to align the filtered reads with the reference database；3.mRNA analysis, using Stringtie's analysis workflow to quantify the expression of known genes and transcripts, using Deseq2 software to analyze differential genes, and significantly differentially differentiated gene GO and KEGG enrichment analysis
Assembly: hg38
Supplementary files format and content: gene expression matrix(FPKM)

molecule: polyA RNA

source_name: T-ALL Jurkat

extract_protocol:
The concentration of RNA samples was ≥ 100 ng/μL, the total amount was > 2 μg, the OD value was between 1.8~2.2, the OD was ≥ 2.0, and Agilent 2100 was required The Bioanalyzer assays RIN ≥ 6.5 to ensure the construction of downstream high-quality mRNA-seq libraries
Library concentration and fragment length distributions were measured using Qubit and Agilent 2100 Bioanalyzers, respectively. The concentration is required to be >5ng/μl and the fragment length is concentrated Between 300-400 bp

tag: cell line

value: T-ALL Jurkat

value: T-ALL cell

value: Combination of Chidamide (5 μM) and Anlotinib (1 μM) treated


title: Anlotinib3

description: Library name: 3_2

value: Anlotinib (1 μM) treated


title: Chidamide3

description: Library name: 3_1

value: Chidamide (5 μM)  treated


title: Bulk RNAseq of HBECs (U19_KD_P2)

description: Library name: U19_KD_P2

value: KD

value: Pressure


title: Bulk RNAseq of HBECs (U16_KD_C1)

description: Library name: U16_KD_C1


title: Combination_Anlotinib2

description: Library name: 2_3


title: Anlotinib2

description: Library name: 2_2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, SON (Input)_rep2

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

country: South Korea

institute: KAIST

description: Library name: IAA_12hr, SON_INPUT_rep2

library_source: genomic

data_processing:
Raw sequencing reads were first mapped to the human genome (UCSC hg38) using Bowtie 2 version 2.5.4 with default parameters. PCR duplicates reads were removed using samtools version 1.3.1 with default parameters. The normalized SON-TSA score was calculated as the log 2 ratio of (TSA-Seq pulldown reads in a 20 kb window divided by total mapped reads for this pulldown sample) / (input reads in the same 20 kb window divided by total mapped reads for this input). The window slides on the genome with a step size of 100 bp.
Assembly: GRCh38
Supplementary files format and content: BigWig (.bw) files

molecule: genomic DNA

extract_protocol:
Cell were fixed with 1.6% paraformaldehyde for 20 minutes. After quenching, TSA-reaction (proximity-labelling) and cell lysis, genomic DNA was sonicated using Covaris S220 sonicator.
TSA-Seq libraries were constructed using TruSeq Nano DNA High Throughput Library Prep Kit. 0.1 ug of genomic DNA was sheared using adaptive focused acoustic technology (Covaris) and the fragmented DNA is end-repaired to create 5’-phosphorylated, blunt-ended dsDNA molecules. Following end-repair, DNA was size selected with bead-based method. These DNA fragments go through the addition of a single ‘A’ base, and ligation of the TruSeq DNA UD Indexing adapters. The products are then purified and enriched with PCR to create the final DNA library.


title: Anlotinib1

description: Library name: 1_2


title: Combination_Anlotinib1

description: Library name: 1_3


title: Chidamide1

description: Library name: 1_1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, SON (Input)_rep1

description: Library name: IAA_12hr, SON_INPUT_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, SON (TSA)_rep1

description: Library name: IAA_12hr, SON_TSA_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, SON (TSA)_rep2

description: Library name: IAA_12hr, SON_TSA_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, SON (Input)_rep2

description: Library name: IAA_3hr, SON_INPUT_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, SON (Input)_rep1

description: Library name: IAA_3hr, SON_INPUT_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, SON (TSA)_rep2

description: Library name: IAA_3hr, SON_TSA_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, SON (TSA)_rep2

description: Library name: DMSO, SON_TSA_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, SON (TSA)_rep1

description: Library name: IAA_3hr, SON_TSA_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, SON (Input)_rep1

description: Library name: DMSO, SON_INPUT_rep1


title: HCT116, THZ1, 3hr, SAF-A CUT&Tag_rep2

description: Library name: SAF-A_CnT_THZ1_rep2

data_processing:
Raw sequencing reads were trimmed with the use of Trim Galore (v0.6.7: Cutadapt v3.5 and FastQC v0.11.9) with the default setting (-q 20 –length 20) and were then aligned to mm10 with Bowtie2 (v2.4.4)69. After removal of low-quality reads, duplicate reads, and reads in blacklisted regions using samtools (v1.14)72 and Picard MarkDuplicates (v2.26.3). Peak calling was performed with MACS3 (v3.0.0b1)74, and narrowPeak files were used for downstream analysis. For signal visualization, the local bias signal was subtracted from the normalized read pileup (generated by the -B -SPMR option of MACS3) with the use of the bdgcmp command of MACS3, and the results in bedGraph files were converted to bigwig files with bedGraphToBigwig (v4). For differential signal enrichment analysis, overlapping regions between biological replicates for each experimental condition were generated with bedtools intersect70. All peaks detected in conditions to be compared were merged into one peak set file with bedtools merge and reads overlapping peaks were quantified with featurecount, with the result count table being used as input to DESeq2. Motif enrichment analysis was performed with findMotifsGenome.pl (-d 200) from HOMER (v4.11).
Assembly: GRCh38
Supplementary files format and content: BigWig (.bw) files
Library strategy: CUT&Tag

extract_protocol:
The library for CUT&Tag was prepared with the use of a CUT&Tag-IT Assay Kit (AT53165, Active Motif) according to the manufacturer’s protocol. Nuclei were bound to concanavalin A beads, incubated overnight at 4°C with antibodies to SAF-A, and then incubated with secondary antibodies and subjected to tagmentation for 60 min at 37°C. DNA was purified with the use of DNA purification column before library preparation.
Library preparation for ATAC-seq was performed with the use of an ATAC-seq kit (AT53150, Active Motif) and the Omni-ATAC protocol (Corces et al. 2017).


title: HCT116, DRB, 3hr, SAF-A CUT&Tag_rep2

description: Library name: SAF-A_CnT_DRB_rep2


title: HCT116, DRB, 3hr, SAF-A CUT&Tag_rep1

description: Library name: SAF-A_CnT_DRB_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, ATAC-seq_rep2

description: Library name: ATAC-seq_IAA_12hr_rep2

data_processing:
Raw sequencing reads were trimmed with the use of Trim Galore (v0.6.7: Cutadapt v3.5 and FastQC v0.11.9) with the default setting (-q 20 –length 20) and were then aligned to mm10 with Bowtie2 (v2.4.4)69. After removal of low-quality reads, duplicate reads, and reads in blacklisted regions using samtools (v1.14)72 and Picard MarkDuplicates (v2.26.3). Peak calling was performed with MACS3 (v3.0.0b1)74, and narrowPeak files were used for downstream analysis. For signal visualization, the local bias signal was subtracted from the normalized read pileup (generated by the -B -SPMR option of MACS3) with the use of the bdgcmp command of MACS3, and the results in bedGraph files were converted to bigwig files with bedGraphToBigwig (v4). For differential signal enrichment analysis, overlapping regions between biological replicates for each experimental condition were generated with bedtools intersect70. All peaks detected in conditions to be compared were merged into one peak set file with bedtools merge and reads overlapping peaks were quantified with featurecount, with the result count table being used as input to DESeq2. Motif enrichment analysis was performed with findMotifsGenome.pl (-d 200) from HOMER (v4.11).
Assembly: GRCh38
Supplementary files format and content: BigWig (.bw) files

extract_protocol:
Library preparation for ATAC-seq was performed with the use of an ATAC-seq kit (AT53150, Active Motif) and the Omni-ATAC protocol(Corces et al. 2017). In brief, nuclear suspensions obtained from 100,000 cells were treated with assembled Tn5 transposase for 30 min at 37°C. Tagmented DNA was cleaned up with a MinElute PCR Purification Kit (28006, Qiagen) before library preparation.
ATAC-seq sequencing libraries were constructed with the use of Nextera PCR primers.


title: HCT116, DMSO, 3hr, SAF-A CUT&Tag_rep1

description: Library name: SAF-A_CnT_DMSO_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, SON (Input)_rep2

description: Library name: DMSO, SON_INPUT_rep2


title: HCT116, DMSO, 3hr, SAF-A CUT&Tag_rep2

description: Library name: SAF-A_CnT_DMSO_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 12hr, ATAC-seq_rep1

description: Library name: ATAC-seq_IAA_12hr_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, SON (TSA)_rep1

description: Library name: DMSO, SON_TSA_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, ATAC-seq_rep2

description: Library name: ATAC-seq_DMSO_rep2


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, DMSO, ATAC-seq_rep1

description: Library name: ATAC-seq_DMSO_rep1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, ATAC-seq_rep1

description: Library name: ATAC-seq_IAA_3hr_rep1


title: Chidamide2

description: Library name: 2_1


title: HCT116 osTIR1(F74G) SAF-A-mAID-Halo, 5-Ph-IAA, 3hr, ATAC-seq_rep2

description: Library name: ATAC-seq_IAA_3hr_rep2


title: GFP-exon 6 XISTrep3

city: Bronx

first: Kevin

middle: Sean

last: O'Leary

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: Library name: XIST-3

data_processing:
Reads were mapped to the GRCh38 human genome, together with GENCODE v46 annotation, by the STAR aligner (v2.7.9a), and gene counts were determined using RSEM (v1.2.28).
Assembly: GRCh38
Supplementary files format and content: raw read counts in csv format

growth_protocol: HEK293T cells were cultured in DMEM with 10% FBS and 1% pen/strep solution (Corning) in 5% CO2 at 37°C.

extract_protocol:
For ectopic GFP and GFP-short hXIST expression, HEK293T cells were transfected with 10mg of pLV-eGFP and pLV-eGFP-short hXIST lentiviral construct, 10mg packing plasmids (psPAX2, pMD2.G, from Addgene plasmids #12259 and #12260), and 40ml jetPEI transfection regent (Polyplus) according to the manufacturer’s instructions. Cells were replaced with fresh DMEM medium after 24 hours post-transfection. Lentivirus-containing DMEM was collected 48 hours post-transfection and filtered through a 0.45mm filter. HEK293T was cultured with lentivirus-containing media and supplemented with 4mg/ml polybrene (Millipore Sigma). Virus-containing media were replaced 24 hours post-infection with fresh DMEM, and cells were cultured for an additional 24 hours. Virus-transfected cells were selected with 5μg/mL puromycin (Millipore Sigma) for 3 days.
GFP and GFP-short hXIST-expressed cells were collected directly into RLT Plus buffer (QIAGEN), and total RNA was isolated with the RNeasy Plus Mini Kit (QIAGEN) and RNase-free DNaseI treatment (QIAGEN) according to the manufacturer’s instructions. For bulk mRNA-seq library preparation, the total RNA quality was measured using a Bioanalyzer (Agilent), and samples with RNA integrity numbers (RIN) > 8 were used. Libraries were constructed from 100ng of total RNA using the Universal Plus mRNA-Seq with NuQuant® (Tecan). Following the manufacturer’s instructions of mRNA elution, mRNA was subjected to fragmentation at 94°C for 8 minutes. First strand, second-strand cDNA synthesis, end repair, adapter ligation, and amplification were carried out by following the manufacturer’s instructions. The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed mRNA-seq libraries were sequenced at GENEWIZ (Azenta) on the Illumina Nova-seq platform, obtaining 150-nucleotide paired-end reads.

value: immortalised cells


title: GFP-exon 6 XISTrep2

description: Library name: XIST-2


title: GFP-exon 6 XISTrep1

description: Library name: XIST-1


title: GFP rep3

description: Library name: GFP-3


title: GFP rep2

description: Library name: GFP-2


title: HCT116, THZ1, 3hr, SAF-A CUT&Tag_rep1

description: Library name: SAF-A_CnT_THZ1_rep1


title: BT549-NOVA1-knockdown2

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

description: Library name: Sample10

data_processing:
FASTQ files were merged by sample and aligned to human genome reference (GRCh38) using STAR (v2.5);
Gene read number was estimated using HTSeq-count based on Ensembl v93.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values (tsv) files include gene count values for each sample

growth_protocol: MCF-7 and BT-549 human breast cancer cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained at 37°C in a humidified atmosphere containing 5% CO₂. Cells were passaged every 2–3 days

extract_protocol:
Total RNA was extracted from MCF-7 and BT-549 cells using the QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions. Briefly, cells were lysed in RLT buffer containing β-mercaptoethanol and homogenized by pipetting. The lysate was then applied to RNeasy spin columns, followed by on-column DNase I treatment (QIAGEN RNase-Free DNase Set) to remove genomic DNA. After a series of wash steps with RW1 and RPE buffers, total RNA was eluted in RNase-free water. RNA quantity and purity were assessed using a NanoDrop spectrophotometer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: MCF-7 and BT-549 breast cancer cell lines were transduced with lentiviral particles carrying either an ESRP1 overexpression construct, ESRP1-targeting shRNA, or NOVA1-targeting shRNA. Lentiviruses were generated in HEK293T cells using GeneJuice Transfection Reagent (Novagen) and collected 48 hours post-transfection. For transduction, target cells were incubated with viral supernatant for 24 hours, after which the medium was replaced with fresh DMEM. Stable cell lines were selected using 1 μg/mL puromycin for 3 days. Cells transduced with lentivirus carrying an empty vector served as controls. After selection, cells were harvested for total RNA extraction and bulk RNA sequencing.

value: human breast cancer cell line

value: NOVA1 knockdown


title: BT549-NOVA1-knockdown1

description: Library name: Sample9


title: GFP rep1

description: Library name: GFP-1


title: BT549-control1

description: Library name: Sample7

value: negative control


title: MCF7-ESRP1-overexpression1

description: Library name: Sample5

value: ESRP1 overexpression


title: MCF7-ESRP1-knockdown1

description: Library name: Sample3

value: ESRP1 knockdown


title: Bulk RNAseq of HBECs (U30_WT_C1)

description: Library name: U30_WT_C1

value: Bronchus

value: WT


title: MCF7-control1

description: Library name: Sample1


title: d15_vCM_ZNF436kd_r3

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

description: Library name: d15_vCM_ZNF436kd_r3

data_processing:
Libraries were sequenced in 100 bp paired-end format on the NovaSeq 6000 sequencer. RNA-seq reads were mapped to the hg19 human genome assembly using hisat2 v2.2.1 with parameters hisat2 -k 5 --seed 42. Only uniquely mapped reads were used for creating gene read counts with a mapping quality over 10 (MAPQ > 10) using featureCounts v2.0.1. Only uniquely mapped reads were used for counting. Finally, the features for which the sum of reads across all samples was lower than the number of samples were discarded from the analysis. Counts on genes were used as the library size to correct gene expression.
Assembly: hg19
Supplementary files format and content: gene and TE count tables

source_name: H9 ESC

growth_protocol: Human embryonic stem cell (hESC) line H9 was grown at 37ºC in 95% air, 5% CO2 in mTeSR plus media (STEMCELL Technologies, 100-0276) on plates previously coated with Matrigel (Corning, 354277). Cells were differentiated into cardiomyocytes using a ventricular cardiomyocyte differentiation kit (STEMCELL Technologies, 05010) following the manufacturer’s protocol. At day 15 of differentiation, ventricular-like cardiomyocytes (vCMs) were dissociated using 0.25% trypsin (Thermo Fisher Scientific, 25300054) for 5 min at 37ºC, which was quenched using cardiomyocyte support media (STEMCELL Technologies, 05027).

extract_protocol:
Total RNA-extraction was done using NucleoSpin RNA XS, Micro kit for RNA purification (Machery-Nagel) by the protocol.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA kit.

value: H9 ESC

value: cardiomyocyte differentiation


title: MCF7-ESRP1-overexpression2

description: Library name: Sample6


title: d15_vCM_ZNF436kd_r2

description: Library name: d15_vCM_ZNF436kd_r2


title: d15_vCM_ZNF436kd_r1

description: Library name: d15_vCM_ZNF436kd_r1


title: MCF7-ESRP1-knockdown2

description: Library name: Sample4


title: d15_vCM_ctrl_r1

description: Library name: d15_vCM_ctrl_r1


title: d15_vCM_ctrl_r3

description: Library name: d15_vCM_ctrl_r3


title: PTBP1ko_UT_rep3

city: Nanjing

first: Erguang

last: Li

address: Hankou Road 22, Nanjing, Jiangsu Province, China

department: Medical School

institute: Nanjing University

description: Library name: Sample 12

data_processing:
RNA-seq raw files (fastq, PE150) were aligned to the GRCh38/hg38 version of the human reference genome, using TopHat2 with default parameters. Read counts were imported by FeatureCounts.  Differential gene expression was performed with DESeq2 packages from R. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
TopHat2
DESeq2
R
Adjusted p-value < 0.05
Assembly: GRCh38/hg38
Supplementary files format and content: gene_sample_count_with_symbol

source_name: cervical tissue

growth_protocol: HeLa cells (human cervical carcinoma cells, ATCC, CCL-2) were cultured in DMEM (Life Technologies) plus 10% fetal bovine serum (FBS) and penicillin/streptomycin (Life Technologies) at 37 °C in an incubator with 95% humidified air and 5% CO2. The cells were tested routinely for Mycoplasma contamination with a PCR detection kit (Beyotime, Shanghai).

extract_protocol:
three 10 cm plates of PTBP1-ko HeLa cells were collected and total RNA was extracted using TRIzol reagent for generating mRNA-seq library using KAPA stranded mRNA library preparation kit (KK8421, KAPA Biosystems)
The RNA-seq library preparation was followed by the instructions of Genergy bio-technology CO., Ltd.

treatment_protocol: PTBP1  ko cells were generated in the lab using the CRISPR/Cas9 system. A CRISPR design tool (available at crispr.mit.edu) was used to select a single-guide RNA (sgRNA) targeting PTBP1 (accession NM_002819.5, 5’-CTTCATCGAGATGAACACGG) and was synthesized by Genscript (Nanjing, China). To generate PTBP1  knockout cells, HeLa cells were transfected with the sgRNA and GenCrispr Cas9-C-NLS Nuclease (Z03385, Genscript) using Lipofectamine 2000 (Life Technologies). Individual clones were selected and validated by DNA sequencing and correctly edited cell clones were confirmed by immunoblotting analysis for the absence of gene expression. HSV-1 strain F was used throughout this study. The viruses were cultured and titrated according to ATCC instructions.

value: cervical tissue

value: HeLa

value: cervical cancer cell

value: PTBP1 knockout

value: Mock


title: PTBP1ko_HSV_rep2

description: Library name: Sample 8

value: HSV-1 infection


title: PTBP1ko_HSV_rep3

description: Library name: Sample 9


title: HeLa_UT_rep2

description: Library name: Sample 5


title: PTBP1ko_UT_rep1

description: Library name: Sample 10


title: PTBP1ko_HSV_rep1

description: Library name: Sample 7


title: HeLa_HSV_rep3

description: Library name: Sample 3


title: HeLa_UT_rep3

description: Library name: Sample 6


title: BT549-control2

description: Library name: Sample8


title: PTBP1ko_UT_rep2

description: Library name: Sample 11


title: HeLa_HSV_rep2

description: Library name: Sample 2


title: HeLa_HSV_rep1

description: Library name: Sample 1


title: HeLa_UT_rep1

description: Library name: Sample 4


title: EXP2_CONTROL_ASO_sample19

city: Carlsbad

first: Sagar

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: Library name: 259591

data_processing:
Reads were aligned to the human genome (GRCh38) using STAR  and gene assignments were performed with FeatureCounts.
Unique molecular identifiers (UMIs) were used to remove PCR duplicates via umi_tools (version 1.1), discarding reads mapping to the same gene with identical 12 nt UMIs.
Post-deduplication, unique reads were quantified using Salmon (version 0.7.2) in pseudoalignment mode with default parameters, leveraging gene models from Ensembl Human Transcriptome Build 96.
Assembly: GRCh38
Supplementary files format and content: quant.sf files contain per-transcript counts for each sample

growth_protocol: A431 cells were cultured in DMEM high-glucose medium (Thermo Fisher Scientific, Cat: 11965092) supplemented with 10% fetal bovine serum at 37°C in a 10% CO₂ atmosphere.

extract_protocol:
Total RNA was purified using a 384-well glass fiber filter plate with chaotropic salts and on-column DNase I digestion.
Libraries were constructed using the 3’QuantSeq FWD kit (Lexogen, Cat: #015.2x96) with custom first-strand synthesis primers

treatment_protocol: ASOs were incubation for  48-72 hours at 37°C in 10% CO₂ and cells were lysed for total RNA isolation

value: cell line

value: Control ASO

tag: treatment concentration


title: MCF7-control2

description: Library name: Sample2

value: human breast cancer cell line


title: EXP2_CONTROL_ASO_sample20

description: Library name: 259350


title: EXP2_CONTROL_ASO_sample14

description: Library name: 259420


title: d15_vCM_ctrl_r2

description: Library name: d15_vCM_ctrl_r2


title: EXP2_CONTROL_ASO_sample17

description: Library name: 259589


title: EXP2_CONTROL_ASO_sample16

description: Library name: 259545


title: EXP2_CONTROL_ASO_sample18

description: Library name: 259429


title: EXP2_CONTROL_ASO_sample15

description: Library name: 259457


title: EXP2_CONTROL_ASO_sample12

description: Library name: 259362


title: EXP2_CONTROL_ASO_sample7

description: Library name: 259333


title: EXP2_CONTROL_ASO_sample13

description: Library name: 259464


title: EXP2_CONTROL_ASO_sample9

description: Library name: 259616


title: EXP2_CONTROL_ASO_sample10

description: Library name: 259515


title: EXP2_CONTROL_ASO_sample8

description: Library name: 259390


title: EXP2_CONTROL_ASO_sample11

description: Library name: 259629


title: EXP2_CONTROL_ASO_sample3

description: Library name: 259611


title: EXP2_CONTROL_ASO_sample2

description: Library name: 259473


title: EXP2_CONTROL_ASO_sample4

description: Library name: 259540


title: EXP2_CONTROL_ASO_sample6

description: Library name: 259644


title: EXP2_CONTROL_ASO_sample5

description: Library name: 259383


title: EXP2_UTC8

description: Library name: 259367

value: UTC


title: EXP2_CONTROL_ASO_sample1

description: Library name: 259341


title: EXP2_UTC5

description: Library name: 259535


title: EXP2_UTC4

description: Library name: 259587


title: EXP2_UTC6

description: Library name: 259456


title: EXP2_UTC3

description: Library name: 259366


title: EXP2_UTC2

description: Library name: 259656


title: EXP1_ACTN_ASO_sample17

description: Library name: 168768


title: EXP1_ACTN_ASO_sample14

description: Library name: 168420


title: EXP1_ACTN_ASO_sample15

description: Library name: 168694


title: EXP2_UTC7

description: Library name: 259397


title: EXP2_UTC1

description: Library name: 259382


title: EXP1_ACTN_ASO_sample12

description: Library name: 168350


title: EXP1_ACTN_ASO_sample16

description: Library name: 168746


title: EXP1_ACTN_ASO_sample13

description: Library name: 168520


title: EXP1_ACTN_ASO_sample10

description: Library name: 168570


title: EXP1_ACTN_ASO_sample6

description: Library name: 168604


title: EXP1_ACTN_ASO_sample7

description: Library name: 168309


title: EXP1_ACTN_ASO_sample5

description: Library name: 168721


title: EXP1_ACTN_ASO_sample8

description: Library name: 168727


title: EXP1_ACTN_ASO_sample4

description: Library name: 168263


title: EXP1_ACTN_ASO_sample3

description: Library name: 168325


title: EXP1_ACTN_ASO_sample2

description: Library name: 168262


title: EXP1_UTC7

description: Library name: 168637


title: EXP1_ACTN_ASO_sample1

description: Library name: 168514


title: EXP1_UTC4

description: Library name: 168492


title: EXP1_UTC5

description: Library name: 168565


title: EXP1_UTC6

description: Library name: 168675


title: EXP1_UTC8

description: Library name: 168374


title: EXP1_UTC1

description: Library name: 168342


title: EXP1_UTC2

description: Library name: 168745


title: sq, control, mb16

city: St. Louis

first: Gretchen

last: Meyer

state: MO

address: 507 S Euclid Ave

department: Department of Physical Therapy

institute: Washington University School of Medicine in Saint Louis

description:
Library name: Sample 16
mb16sq

data_processing:
RNA-seq reads were then aligned and quantitated to the Human Ensembl GRCh38.76 assembly on the HTCF Coffee version 1.0 pipeline.
Assembly: hg38
Supplementary files format and content: tab-seperated text files(tsv) include raw counts for each sample

source_name: adipose, sq

extract_protocol:
RNA was extracted via a combination Trizol/chloroform extraction and RNEasy mini kit (Qiagen, Hilden, Germany) with DNAse treatment.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems).

value: adipose, sq

tag: subject status

value: control

tag: subject id


title: sq, diabetes, mb15

description:
Library name: Sample 14
mb15sq

value: diabetes


title: EXP1_ACTN_ASO_sample11

description: Library name: 168543


title: sq, diabetes, mb12

description:
Library name: Sample 12
mb12sq


title: sq, control, mb22

description:
Library name: Sample 18
mb22sq


title: imat, diabetes, mb15

description:
Library name: Sample 13
mb15edb

source_name: adipose, imat

value: adipose, imat


title: EXP1_ACTN_ASO_sample9

description: Library name: 168298


title: sq, diabetes, mb11

description:
Library name: Sample 10
mb11sq


title: imat, diabetes, mb12

description:
Library name: Sample 11
mb12ah


title: imat, control, mb16

description:
Library name: Sample 15
mb16ah


title: sq, diabetes, mb08

description:
Library name: Sample 8
mb08lsq_2


title: imat, diabetes, mb11

description:
Library name: Sample 9
mb11ah


title: imat, diabetes, mb08

description:
Library name: Sample 7
mb08lah


title: sq, control, mb06

description:
Library name: Sample 4
mb06sq


title: imat, control, mb06

description:
Library name: Sample 3
mb06ah


title: imat, diabetes, mb07

description:
Library name: Sample 5
mb07ah


title: imat, diabetes, mb01

description:
Library name: Sample 1
mb01ah


title: leptomeninges, patient 29, TCR

city: New York

first: Ryan

last: Hobson

state: New York

institute: Columbia University

description: Library name: 29M_TCR

data_processing:
RNA and TCR reads were aligned to the Hg38 genome and clonotype/contig matrices were generated using Cell Ranger (v6.1.2).
Assembly: Hg38
Supplementary files format and content: comma separated value files containing barcoded matrices
Library strategy: TCR-Seq

source_name: leptomeninges

extract_protocol:
Leptomeninges were placed in 1mg/mL of Collagenase D (Roche cat. #51657128) dissolved in PBS and incubated at 37C for 10 minutes. Tissue was then mashed through a 70um strainer using the plunger of a 3mL syringe to achieve a single cell suspension. Cells were subsequently spun at 300g for 10 minutes and subjected to debris removal using a commercially available density gradient-based Debris Removal Solution (Miltenyi cat. #130-109-398). Postmortem brain was mechanically dissociated using a combination of mincing with a razor blade and dounce homogenization in a 15mL glass tissue homogenizer. Dissociated tissues were passed through a 70um filter and cleared of myelin using Myelin Removal Beads (Miltenyi cat. #130-096-433) and the MultiMacs Cell24 Separator. After debris removal, leptomeninges and brain cells were pelleted at 300xg for 10 minutes and incubated with anti-CD11b APC/Cy7 (BioLegend cat. #101226) and anti-CD45 BV510 (BD Biosciences cat. #563204) antibodies at 1:100 dilution in staining buffer (2% FBS in PBS) for 20 minutes. Cells were pelleted and resuspended in staining buffer containing propidium iodide (PI) at a 1:1000 dilution (Sigma Aldrich Cat. #P4864). CD45+/PI- cells were sorted on the Sony MA900 (Sony Biotechnology, USA) into the A1 well of a 96 well plate (Eppendorff cat. #951020401) pre-coated with 2% FBS. All sorting was performed using a 100um nozzle.
Cell capture, amplification, and library construction was performed on the 10x Chromium platform using the manufacturer’s publicly available protocol. Briefly, after sorting a fraction of cell suspension was used to estimate total cell count and viability. All remaining sorted cells were loaded in the Chromium platform using the 10x Genomics Next GEM Single Cell 5’ v2 for scRNA and TCR-seq. Libraries were prepared using 10x library reagents in accordance with their 5’ RNA and TCR sequencing library protocol and sequenced on the NovaSeq 6000.

value: leptomeninges

value: immune cells


title: leptomeninges, patient 20, RNA

description: Library name: 20M_RNA

library_source: transcriptomic single cell

data_processing:
RNA and TCR reads were aligned to the Hg38 genome and clonotype/contig matrices were generated using Cell Ranger (v6.1.2).
Assembly: Hg38
Supplementary files format and content: comma separated value files containing barcoded matrices


title: parietal, patient 35, TCR

description: Library name: 35P_TCR

source_name: brain

value: brain


title: leptomeninges, patient 28, TCR

description: Library name: 28M_TCR


title: imat, control, mb22

description:
Library name: Sample 17
mb22ah


title: hippocampus, patient 29, TCR

description: Library name: 29H_TCR

source_name: hippocampus

value: hippocampus


title: hippocampus, patient 29, RNA

description: Library name: 29H_RNA


title: hippocampus, patient 35, TCR

description: Library name: 35H_TCR


title: motor cortex, patient 33, TCR

description: Library name: 33B_TCR


title: hippocampus, patient 34, TCR

description: Library name: 34H_TCR


title: parietal, patient 30, TCR

description: Library name: 30P_TCR


title: hippocampus, patient 26, TCR

description: Library name: 26H_TCR


title: motor cortex, patient 19, TCR

description: Library name: 19B_TCR


title: hippocampus, patient 27, TCR

description: Library name: 27H_TCR


title: sq, diabetes, mb07

description:
Library name: Sample 6
mb07sq


title: motor cortex, patient 17, TCR

description: Library name: 17B_TCR


title: motor cortex, patient 32, TCR

description: Library name: 32B_TCR


title: hippocampus, patient 16, TCR

description: Library name: 16H_TCR


title: hippocampus, patient 13, TCR

description: Library name: 13H_TCR


title: sq, diabetes, mb01

description:
Library name: Sample 2
mb01sq


title: motor cortex, patient 15, TCR

description: Library name: 15B_TCR


title: motor cortex, patient 10, TCR

description: Library name: 10B_TCR


title: motor cortex, patient 18, TCR

description: Library name: 18B_TCR


title: parietal, patient 8, TCR

description: Library name: 8P_TCR


title: hippocampus, patient 7, TCR

description: Library name: 7H_TCR


title: hippocampus, patient 6, TCR

description: Library name: 6H_TCR


title: hippocampus, patient 3, TCR

description: Library name: 3H_TCR


title: parietal, patient 3, TCR

description: Library name: 3P_TCR


title: hippocampus, patient 4, TCR

description: Library name: 4H_TCR


title: motor cortex, patient 2, TCR

description: Library name: 2B_TCR


title: leptomeninges, patient 27, TCR

description: Library name: 27M_TCR


title: hippocampus, patient 30, TCR

description: Library name: 30H_TCR


title: EXP1_UTC3

description: Library name: 168282


title: leptomeninges, patient 26, TCR

description: Library name: 26M_TCR


title: leptomeninges, patient 24, TCR

description: Library name: 24M_TCR


title: leptomeninges, patient 25, TCR

description: Library name: 25M_TCR


title: leptomeninges, patient 23, TCR

description: Library name: 23M_TCR


title: leptomeninges, patient 21, TCR

description: Library name: 21M_TCR


title: substantia nigra, patient 17, TCR

description: Library name: 17SN_TCR


title: leptomeninges, patient 19, TCR

description: Library name: 19M_TCR


title: leptomeninges, patient 18, TCR

description: Library name: 18M_TCR


title: leptomeninges, patient 22, TCR

description: Library name: 22M_TCR


title: leptomeninges, patient 15, TCR

description: Library name: 15M_TCR


title: Parental

city: Darlinghurst

first: Leila

last: Eshraghi

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Library name: MCF7-P

data_processing:
Cultured cells were captured with DropSeq microfluidic devices and sequenced in one batch to reduce batch effects. Data were analysed with the McCarroll lab cookbook, custom genome (hg38 plus Trinity assemblies), and gen-code vM14. Seurat (v Seurat_5.1.0) was the main platform for visualisation and expression analysis, with DGE matrices filtered in R (>200 genes, <15% mitochondrial reads, >1200 UMI and genes expressed in at least 3 cells).
Assembly: hg38 plus Trinity assemblies
Supplementary files format and content: Seurat Object with MetaData "scRNA_seuratObj_GEO.RDS"

source_name: Parental MCF-7 cells grown without fulvestrant

growth_protocol: MCF-7 cells were obtained from the Michigan Cancer Foundation. Normally cycling MCF-7 cells were cultured in phenol red free RPMI1640 supplemented with 5% charcoal stripped FBS, 1% penicillin/streptomycin (P/S), and 10 pM 17-β estradiol.

extract_protocol:
Trypsinised cells were prepared as a single cell suspension. Dissociated cells were mixed with DropSeq barcoded beads and droplet generation oil to generate droplets containing single cells and beads. This was performed using syringes with set flow rates on a PDMS co-flow microfluidic droplet generation chip (FlowJem). Droplet captures were performed for 7 mins to obtain 0.5 mL of beads, with ~2.5% of beads associated with a cell. Cells were captured using the microfluidic devices described for Dropseq following the Online Drop-seq Laboratory Protocol version 3.1 (www.mccarrolllab.com/dropseq).
Following droplet lysis, beads with barcoded RNAs were retrotranscribed, treated with exonuclease I, and amplified by PCR. Pooled cDNAs were then tagmented with the Nextera XT DNA Library kit (Illumina Cat# FC-131-1024) and custom primers. The tagmented and multiplexed cDNA libraries were sequenced in Nextseq 500 using Nextseq500 High Output v.2 kit (75 cycles, Illumina Cat# FC-404-2005) following Macosko et al. recommendations and additional modifications described in PMID 33852842.

treatment_protocol: To analyse changes in cells following fulvestrant-mediated cell cycle arrest and release, cells were treated with fulvestrant and subsequently stimulated to re-enter the cell cycle by addition of 17-β estradiol. Samples were derived as follows (1) 48h of 10nM fulvestrant arrest; (2) 6h of 100nM 17-β estradiol treatment following 48h of fulvestrant arrest, and (3) 24h of 100nM 17-β estradiol treatment following 48h of fulvestrant arrest.  Two fulvestrant resistant cell lines (a slow growing and a fast growing derivative) derived by long term exposure to 100nM fulvestrant were also analysed.

value: breast cancer epithelial cell line

value: WT

value: no fulvestrant exposure

tag: group

value: long-term exposure

tag: technology

value: DropSeq


title: leptomeninges, patient 16, TCR

description: Library name: 16M_TCR


title: leptomeninges, patient 13, TCR

description: Library name: 13M_TCR


title: Fast Growing

description: Library name: MCF7-L

source_name: Fast growing fulvestrant resistant MCF-7 cells

value: >12 months fulvestrant exposure


title: hippocampus, patient 8, TCR

description: Library name: 8H_TCR


title: parietal, patient 16, TCR

description: Library name: 16P_TCR


title: Endocrine Tolerant

description: Library name: MCF7-EH

source_name: Slow growing fulvestrant resistant MCF-7 cells


title: leptomeninges, patient 14, TCR

description: Library name: 14M_TCR


title: 6h estrogen

description: Library name: e2_6hr

source_name: MCF-7 cells that were fulvestrant arrested, then stimulated with 17-β estradiol for 6h

value: 48h fulvestrant, 6h 17-β estradiol

value: short-term treatment


title: 24h estrogen

description: Library name: e1_24hr

source_name: MCF-7 cells that were fulvestrant arrested, then stimulated with 17-β estradiol for 24h

value: 48h fulvestrant, 24h 17-β estradiol


title: leptomeninges, patient 11, TCR

description: Library name: 11M_TCR


title: asynchronous

description: Library name: async_2109

source_name: Untreated MCF-7 cells


title: leptomeninges, patient 10, TCR

description: Library name: 10M_TCR


title: Resistant Clone 7 Biological Replicate 3

city: Philadelphia

first: Gianna

middle: T

last: Busch

state: Pennsylvania

address: 415 Curie Blvd, 415 CRB

department: Bioengineering

institute: University of Pennsylvania

description:
Library name: Sample 22
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V22

data_processing:
We pseudoaligned RNA-seq reads to the human genome (hg19) with Kallisto to obtain the counts matrix and transcripts per million.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: WM989 A6-G3 melanoma cell line, first described in Shaffer et al, 2017, and kindly provided by the lab of Dr. Meenhard Herlyn, were derived by twice single-cell bottlenecking the WM989 melanoma cell line. The identities of WM989 A6-G3 was verified by DNA STR microsatellite fingerprinting at the Wistar Institute. Resistant clones were generated by expanding isolated colonies of the WM989 A6-G3 cell line, which grew out following treatment with either 1 μM vemurafenib or 250nM dabrafenib/2.5 nM trametinib. Cells were grown in Tu2% (80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4mM CaCl2, 50 U ml−1 penicillin and 50 μg ml−1 streptomycin) in humdified atmosphere with 5% CO2 at 37C. Cells listed as vemurafenib-resistant had 1 μM vemurafenib added to the media. Cells listed as dabrafenib/trametinib-resistant had 250 nM dabrafenib and 2.5 nM trametinib added to the media.

extract_protocol:
We conducted standard bulk paired-end (37:8:8:38) RNA sequencing using RNeasy Micro (Qiagen 74004) for RNA extraction, NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S), and an Illumina NextSeq 1000/2000 P4 XLEAP-SBS 100 cycles kit.
Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases.

value: vemurafenib-resistant melanoma cells


title: leptomeninges, patient 6, TCR

description: Library name: 6M_TCR


title: Untreated Biological Replicate 1

description:
Library name: Sample 21
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V21

value: untreated melanoma cells


title: leptomeninges, patient 7, TCR

description: Library name: 7M_TCR


title: leptomeninges, patient 5, TCR

description: Library name: 5M_TCR


title: Resistant Clone 13 Biological Replicate 3

description:
Library name: Sample 23
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V23


title: leptomeninges, patient 17, TCR

description: Library name: 17M_TCR


title: leptomeninges, patient 20, TCR

description: Library name: 20M_TCR


title: Resistant Clone 9 Biological Replicate 2

description:
Library name: Sample 19
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V19


title: leptomeninges, patient 8, TCR

description: Library name: 8M_TCR


title: Resistant Clone 10 Biological Replicate 2

description:
Library name: Sample 20
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V20


title: leptomeninges, patient 4, TCR

description: Library name: 4M_TCR


title: Resistant Clone 10 Biological Replicate 1

description:
Library name: Sample 18
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V18


title: leptomeninges, patient 2, TCR

description: Library name: 2M_TCR


title: leptomeninges, patient 1, TCR

description: Library name: 1M_TCR


title: leptomeninges, patient 3, TCR

description: Library name: 3M_TCR


title: Resistant Clone 12 Biological Replicate 2

description:
Library name: Sample 16
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V16


title: leptomeninges, patient 12, TCR

description: Library name: 12M_TCR


title: 48h fulvestrant

description: Library name: fas_2109

source_name: Fulvestrant arrested MCF-7 cells

value: 48h fulvestrant


title: Resistant Clone 8 Biological Replicate 1

description:
Library name: Sample 15
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V15


title: parietal, patient 35, RNA

description: Library name: 35P_RNA


title: leptomeninges, patient 9, TCR

description: Library name: 9M_TCR


title: Untreated Biological Replicate 3

description:
Library name: Sample 14
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V14


title: hippocampus, patient 34, RNA

description: Library name: 34H_RNA


title: Untreated Biological Replicate 2

description:
Library name: Sample 13
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V13


title: Resistant Clone 9 Biological Replicate 1

description:
Library name: Sample 12
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V12


title: motor cortex, patient 33, RNA

description: Library name: 33B_RNA


title: Resistant Clone 11 Biological Replicate 3

description:
Library name: Sample 11
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V11


title: motor cortex, patient 32, RNA

description: Library name: 32B_RNA


title: Resistant Clone 10 Biological Replicate 3

description:
Library name: Sample 9
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V9


title: hippocampus, patient 31, RNA

description: Library name: 31H_RNA


title: Resistant Clone 7 Biological Replicate 2

description:
Library name: Sample 8
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V8


title: Resistant Clone 12 Biological Replicate 3

description:
Library name: Sample 17
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V17


title: Resistant Clone 13 Biological Replicate 2

description:
Library name: Sample 10
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V10


title: hippocampus, patient 30, RNA

description: Library name: 30H_RNA


title: Resistant Clone 13 Biological Replicate 1

description:
Library name: Sample 7
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V7


title: hippocampus, patient 26, RNA

description: Library name: 26H_RNA


title: parietal, patient 30, RNA

description: Library name: 30P_RNA


title: Resistant Clone 9 Biological Replicate 3

description:
Library name: Sample 5
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V5


title: motor cortex, patient 19, RNA

description: Library name: 19B_RNA


title: Resistant Clone 8 Biological Replicate 3

description:
Library name: Sample 6
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V6


title: Resistant Clone 7 Biological Replicate 1

description:
Library name: Sample 4
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V4


title: substantia nigra, patient 17, RNA

description: Library name: 17SN_RNA


title: hippocampus, patient 35, RNA

description: Library name: 35H_RNA


title: Resistant Clone 8 Biological Replicate 2

description:
Library name: Sample 3
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V3


title: motor cortex, patient 17, RNA

description: Library name: 17B_RNA


title: Resistant Clone 11 Biological Replicate 2

description:
Library name: Sample 2
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V2


title: Resistant Clone 12 Biological Replicate 1

description:
Library name: Sample 1
Column name in GTB_07102024_Step1_TxImport_myCounts.tsv: V1


title: parietal, patient 16, RNA

description: Library name: 16P_RNA


title: motor cortex, patient 15, RNA

description: Library name: 15B_RNA


title: TIE2-TGF-192

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

country: Netherlands

institute: Utrecht University

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.9).
TrimGalore (v0.6.7) as used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA (v4.3.6) after which the resulting reads were aligned to the reference genome fasta (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna) using the STAR (v2.7.10b) aligner.
Followup QC on the mapped (bam) files was done using Sambamba (v0.8.2), RSeQC (v5.0.1) and PreSeq (v3.2.0).
Readcounts were then generated using the Subread FeatureCounts module (v2.0.3) with the Homo_sapiens.GRCh38.106.ncbi.gtf gtf file as annotation.
Assembly: GRCh38
Supplementary files format and content: tab delimited counts
Supplementary files format and content: tab delimited meta data

source_name: Nucleus pulposus-derived

growth_protocol: The iPSC line were expanded in mTESR1 medium until the start of the experiment.

extract_protocol:
Cell pellets were crushed with a pestle after snap freezing in liquid nitrogen. RNA was extracted using the RNeasy® Micro kit (74004, Qiagen) according to the manufacturer’s instructions.
Trueseq RNA stranded polyA

treatment_protocol: The iPSC lines were differentiated into mesendoderm progenitor cells (MEPCs) according to the publish protocol by Warin et al. (2024) (https://doi.org/10.1016/j.isci.2024.109018).  At this timepoint the cells were transfected with NOTO mRNA and simulteneously plated into low-adherent culture plates to obtain 3D cell pellets of 35,000 cells in NP-genic medium (hgDMEM  (11965, Thermo Fisher) supplemented with 1% ITS+, 40 µg/ml L-proline (P5607, Sigma-Aldrich), 1% NEAA, 50 µg/mL Ascorbic acid-2-Phosphate (ASAP; A8960, Sigma-Aldrich), and 10 ng/mL TGF-β1 (240-B-010, R&D Systems, Minneapolis, USA)). On day 7, half of the samples were switched to NP-genic medium in which the TGF-β1 was replaced by decellularized notochordal cell-derived matrix, the other half was continued in TGF-β1.

value: Nucleus pulposus-derived

value: iPSCs

value: TGF-β1 10ng/mL


title: hippocampus, patient 13, RNA

description: Library name: 13H_RNA

value: brain

value: immune cells


title: hippocampus, patient 27, RNA

description: Library name: 27H_RNA


title: TIE2-TGF-190


title: TIE2-NCM-191

value: dNCM 3 mg/mL


title: TIE2-NCM-190


title: parietal, patient 8, RNA

description: Library name: 8P_RNA


title: TIE2-NCM-192


title: hippocampus, patient 8, RNA

description: Library name: 8H_RNA


title: motor cortex, patient 10, RNA

description: Library name: 10B_RNA


title: motor cortex, patient 18, RNA

description: Library name: 18B_RNA


title: hippocampus, patient 7, RNA

description: Library name: 7H_RNA


title: hippocampus, patient 4, RNA

description: Library name: 4H_RNA


title: PBMC-TGF-190

source_name: Blood-derived

value: Blood-derived


title: parietal, patient 3, RNA

description: Library name: 3P_RNA


title: PBMC-TGF-191


title: PBMC-NCM-191


title: hippocampus, patient 3, RNA

description: Library name: 3H_RNA


title: PBMC-NCM-190


title: hippocampus, patient 16, RNA

description: Library name: 16H_RNA


title: leptomeninges, patient 28, RNA

description: Library name: 28M_RNA

value: leptomeninges


title: motor cortex, patient 2, RNA

description: Library name: 2B_RNA


title: hippocampus, patient 6, RNA

description: Library name: 6H_RNA


title: leptomeninges, patient 27, RNA

description: Library name: 27M_RNA


title: KO_24hr_2

city: Frederick

first: Ian

last: Bettencourt

state: MD

address: 1050 Boyles Street Rm 31-16A

department: CIL

institute: NCI

description: Library name: K

data_processing:
Basecalling with RTA 3.9.25
Demulitplexing with Bcl2fastq v2.20
Filtering (Adaptor and quality) with Cutadapt 1.18
Alignment with STAR 2.7.0f to reference genome mm10
Gene expression quantification with RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: raw count output from RSEM

organism: Mus musculus

source_name: isolated splenocyte

growth_protocol: 1-2x10^5 isolated T cells were plated in complete RPMI media cotaning 10% FBS, glutamine (2mM), fresh 2-Mercaptoethanol (55uM), Pen/Strep and 25ng/mL human IL7

extract_protocol:
RNA was extracted from positively selected CD4 T cells using PureLink RNA Mini Kit and DNase treated with PureLink DNase.
RNA libraries were constructed using the llumina Stranded mRNA ligation kit

treatment_protocol: for stimulation, 96-well non-tissue cutlure treated flat bottom plate was treated overnight with 100uL PBS containg 1ug/mL anti-CD3 and 2ug/mL anti-CD28.  The next day, plates we washed 3x with PBS and T cells were plated.

value: isolated splenocyte

value: CD4 T cell

value: Pkm2 knockout

value: isolated splenocytes cultured overnight with platebound aCD3 and aCD28, and supplementary IL7


title: KO_24hr_3

description: Library name: L


title: KO_24hr_1

description: Library name: J


title: WT_24hr_3

description: Library name: I

value: Wild type


title: PBMC-TGF-192


title: leptomeninges, patient 26, RNA

description: Library name: 26M_RNA


title: leptomeninges, patient 25, RNA

description: Library name: 25M_RNA


title: leptomeninges, patient 24, RNA

description: Library name: 24M_RNA


title: WT_24hr_2

description: Library name: H


title: leptomeninges, patient 23, RNA

description: Library name: 23M_RNA


title: KO_resting_2

description: Library name: E

value: isolated splenocytes cultured overnight with supplementary IL7


title: PBMC-NCM-192


title: WT_24hr_1

description: Library name: G


title: leptomeninges, patient 22, RNA

description: Library name: 22M_RNA


title: KO_resting_3

description: Library name: F


title: KO_resting_1

description: Library name: D


title: leptomeninges, patient 29, RNA

description: Library name: 29M_RNA


title: leptomeninges, patient 19, RNA

description: Library name: 19M_RNA


title: WT_resting_2

description: Library name: B


title: WT_resting_3

description: Library name: C


title: WT_resting_1

description: Library name: A


title: leptomeninges, patient 18, RNA

description: Library name: 18M_RNA


title: leptomeninges, patient 17, RNA

description: Library name: 17M_RNA


title: leptomeninges, patient 15, RNA

description: Library name: 15M_RNA


title: leptomeninges, patient 16, RNA

description: Library name: 16M_RNA


title: leptomeninges, patient 14, RNA

description: Library name: 14M_RNA


title: leptomeninges, patient 13, RNA

description: Library name: 13M_RNA


title: leptomeninges, patient 12, RNA

description: Library name: 12M_RNA


title: leptomeninges, patient 10, RNA

description: Library name: 10M_RNA


title: leptomeninges, patient 21, RNA

description: Library name: 21M_RNA


title: leptomeninges, patient 9, RNA

description: Library name: 9M_RNA


title: leptomeninges, patient 11, RNA

description: Library name: 11M_RNA


title: leptomeninges, patient 8, RNA

description: Library name: 8M_RNA


title: leptomeninges, patient 6, RNA

description: Library name: 6M_RNA


title: leptomeninges, patient 7, RNA

description: Library name: 7M_RNA


title: WT_Female_Vehicle_inVitro_3

city: Chicago

first: Rogan

middle: A

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

description: Library name: WTF3_veh

data_processing:
FASTQ files were generated using bcl-convert 4.0.3 using default parameters. To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.16.1 implemented in Nextflow 22.10.1 using Singularity 3.8.1 with the minimal command nextflow run nf-core/rnaseq \ -r ‘3.16.1’ \ -profile nu_genomics \--additional_fasta ‘transgenes.fa’ \ --star_index false \ --genome ‘GRCm38’. Briefly, lane-level reads were trimmed using trimGalore! 0.6.7 and aligned to the hybrid genome described above using STAR 2.7.10a. Gene-level assignment was then performed using salmon 1.10.1.
Assembly: GRCm38
Supplementary files format and content: Raw gene counts and associated metadata

source_name: Hippocampus

growth_protocol: Primary neonate microglia cultures Neonatal primary microglia were isolated from mixed glial cultures made from hippocampal tissue from P2-P5 mice. Hippocampal tissue was dissected from the neonate brain using a dissection scope and ice-cold Hank’s balanced salt solution (HBSS; 14175-095, Gibco). Tissues were enzymatically digested with 0.25% trypsin (15090046, Invitrogen) and DNaseI (1mg/ml, 1014159001, Roche) for 18 mins in 37°C water bath with inverting the tube every 5 mins. Tissue was washed twice with HBSS followed by mechanical titration in culture media containing 10% fetal bovine serum (FBS; 26140-079, Gibco) and 1% penicillin-streptomycin (pen-strep; 15140122, Gibco) in Dulbecco’s modified Eagle’s medium (DMEM; 10-013-CM, Corning). Cells were strained through a 70μm cell strainer and collected and cultured on poly-L-lysine (P4707, Sigma-Aldrich, USA) coated 25mm2 tissue culture flasks with 10ml of culture medium. On the second day of culture, media was completely exchanged and OH-tamoxifen (1μM) was added to the culture media. Half of the culture medium was exchanged every 3 to 4 days for about 12 to 14 days. Subsequently, microglia were forcibly removed from the astrocyte layer by shaking cells in an incubator for 1 hour at 200 rpm and 37°C. Cells and media were collected and centrifuged at 300xg for 5 mins at 4°C. The supernatant was aspirated, and the cells plated on poly-L-lysine dishes in a serum free media for two days prior to conducting functional assays. The serum free media contained N-acetyl cysteine (5µg/ml, Sigma), apo-transferrin (100µg/ml, Sigma), sodium selenite (100ng/ml, Sigma), oleic acid (0.1µg/ml, Caymen Chemical), gondoic acid (0.001µg/ml, Caymen Chemical), 1x glutamax (Gibco), 1x penicillin-streptomycin (Gibco), TGF-β2(2ng/ml, Preprotech), CSF1 (10ng/ml, BioLegend), hepran sulfate (1µg/ml, Galen Laboratory Supplies), and ovine wool cholesterol (1.5µg/ml, Avanti Polar Lipids)(83). Microglia were plated at 40,000 cells per well in a 24 well plate for RNA-seq experiments and 60,000 cells per well for metabolomics experiments.  Isolation of microglia from adult mice Orai1fl/fl and Orai1fl/fl Cx3CR1-cre/ERT2 were taken at week 10-14 weeks of age after waiting 30 to 35 days after the last injection of tamoxifen and perfused with 20ml of ice cold HBSS to remove blood from the brain. The brain was dissected out and the cerebellum was chopped off. The brain was minced up in cold HBSS and transferred to a 15ml conical. HBSS was aspirated off and 500ul of HBSS was added along with 500ul of enzymatic digestion buffer. The digestion buffer contained papain (NC9199962, Worthington Biochemical Corporation) in 4.5ml of HBSS (14025092, Gibco) and 500ul of 10mg/ml of DNaseI (1014159001, Roche) added to the papain vial. Brains were incubated in the digestion buffer at 37°C for 20mins with tubes being tapped on the lab bench every 5mins to agitate the solution. Brain tissue was then titrated with P1000 and P200 pipettes before adding 1% Bovine Serum Albumin (BSA; A3294, Sigma-Aldrich) to neutralize. Cells were centrifuged at 400xg for 10 mins at 4°C followed by reconstitution in 40% percoll (17-0891-09, GE Healthcare). Cells were centrifuged at 500xg for 30 mins. Myelin layer was carefully aspirated off and cells were washed with PBS twice. Cells were then taken for downstream for isolation of microglia via FACS or MACS for downstream applications.

extract_protocol:
RNA isolation with QIAGEN RNeasy Plus Mini kit (74134, QIAGEN) was performed according to the manufacturer’s protocol. For adult microglia isolated via FACS,  RNA was isolated following manufacturer’s instructions using QIAGEN RNeasy Micro kit (74004, QIAGEN).
RNA quality and quantity were assessed using TapeStation 4200 RNA tapes (Agilent), and RNA-seq libraries were prepared from 100ng(microglia from in vitro assays) and 0.97ng (adult microglia isolated vis FACS)  of total RNA using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB E7370L) and the SMARTer Stranded Total RNA-seq kit v2 (Takara Bio), respectively. Library QC was then performed using TapeStation 4200 DNA tapes (Agilent).

treatment_protocol: For culture experiments, microglia were cultured as described above and treated with Tg (0.2µM)+PDBu(50nM), LPS (10ng/ml, Escherichia coli O111:B4), or equivalent volume of DMSO for 6h. For in vivo experiments, Orai1fl/fl and Orai1fl/fl Cx3CR1-cre/ERT2 were injected with tamoxifen for five consecutive days (see Transgenic mouse for more information). Following the 30 to 35-day waiting period after the final injection, mice (10-12 weeks old) received an intrapreneurial injection with sterile PBS or Lipopolysaccharide (LPS) from Escherichia coli O111:B4 (1mg/kg; L4391, Sigma-Aldrich) dissolved in sterile PBS.

value: Hippocampus

value: Cultured Primary Microglia

value: Orai1 WT

value: Vehicle

tag: Sex

value: Female

tag: timepoint


title: WT_Male_Vehicle_inVitro_2

description: Library name: WTM4_veh

value: Male


title: WT_Male_LPS_inVitro_1

description: Library name: WTM10_LPS

value: LPS


title: WT_Male_LPS_inVitro_2

description: Library name: WTM4_LPS


title: WT_Female_Tg+PDBu_inVitro_3

description: Library name: WTF3_Tgplus_PDBu

value: Tg+PDBu


title: WT_Male_LPS_inVitro_3

description: Library name: WTM9_LPS


title: WT_Male_Tg+PDBu_inVitro_1

description: Library name: WTM10_Tgplus_PDBu


title: WT_Male_Vehicle_inVitro_3

description: Library name: WTM9_veh


title: leptomeninges, patient 5, RNA

description: Library name: 5M_RNA

value: immune cells


title: leptomeninges, patient 4, RNA

description: Library name: 4M_RNA


title: WT_Female_Vehicle_inVitro_2

description: Library name: WTF14_veh


title: WT_Male_Tg+PDBu_inVitro_2

description: Library name: WTM4_Tgplus_PDBu


title: WT_Male_Vehicle_inVitro_1

description: Library name: WTM10_veh


title: WT_Female_LPS_inVitro_3

description: Library name: WTF3_LPS


title: leptomeninges, patient 3, RNA

description: Library name: 3M_RNA


title: leptomeninges, patient 2, RNA

description: Library name: 2M_RNA


title: WT_Male_Tg+PDBu_inVitro_3

description: Library name: WTM9_Tgplus_PDBu


title: WT_Female_Tg+PDBu_inVitro_2

description: Library name: WTF14_Tgplus_PDBu


title: WT_Female_LPS_inVitro_2

description: Library name: WTF14_LPS


title: leptomeninges, patient 1, RNA

description: Library name: 1M_RNA


title: WT_Female_Vehicle_inVitro_1

description: Library name: WTF12_veh


title: WT_Female_Tg+PDBu_inVitro_1

description: Library name: WTF12_Tgplus_PDBu


title: ND20 CR5 iPSC WGS

city: Piscataway

first: Ziyuan

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

description: KAPA HYper Prep Library Preparation

data_processing:
Reads were aligned to the human genome using the GATK DRAGMAP tool, followed by variant calling with GATK HaplotypeCaller. Variants were then filtered using a quality threshold of “QUAL < 10.4139.”
Assembly: Human GRCh38
Supplementary files format and content: Single nucleotide polymorphisms (SNPs) in filtered variant call format (VCF) files.
Library strategy: WGS

source_name: Cultured iPSCs

extract_protocol:
Genomic DNA was extracted from human pluripotent stem cells using the Qiagen DNA Mini Kit
Libraries were contructed for whole genome sequencing.
Libraries were prepared by KAPA HYper Prep kit.

value: Cultured iPSCs

value: Human iPSC

value: CSF2RB A455D mutation


title: WT_Female_LPS_inVitro_1

description: Library name: WTF12_LPS


title: DS A455D PMPs transplanted, DSAD-tau treated, 10 mo, rep 2

description: 10x Genomics 3' Gex v3.1

data_processing:
The demuiltiplexing, barcoded processing, gene counting were made using the Cell Ranger (version v7.1.0) using the Human (GRCh38) and mouse (mm10) reference - 2020-A (10x Genomics).
Assembly: Human (GRCh38) and mouse (mm10) reference - 2020-A
Supplementary files format and content: Filtered cell-associated barcodes in MEX format (feature-barcode matrices).

source_name: Brain

growth_protocol: PMPs were generated from the three pairs of Cont and DS hiPSC cell lines using a previously established protocol. The yolk sac embryoid bodies (YS-EBs) were generated by treating the YS-EBs with mTeSR 1 media (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To stimulate myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). At 4-6 weeks after plating, human PMPs emerged into the supernatant and were continuously produced for more than 3 months. PMPs were collected from the supernatant and suspended at a concentration of 100,000 cells/µl in PBS. Cells were then injected into the brains of P0 Rag2−/−hCSF1 immunodeficient mice (C;129S4-Rag2tm1.1FlvCsf1tm1(CSF1)FlvIl2rgtm1.1Flv/J, The Jackson Laboratory) as previously described. The transplantation sites were bilateral from the midline = ±1.0 mm, posterior from bregma = −2.0 mm, and dorsoventral depths = −1.5 and −1.2 mm 43. All pups were placed in ice for 4-5 mins to anesthetize. The pups were then injected with 0.5 μl of cells into each site (four sites total), using a digital stereotaxic device (David KOPF Instruments) that was equipped with a neonatal mouse adapter (Stoelting). The pups were weaned at three weeks and kept for further experimentation at different time points.

extract_protocol:
Chimeric mice were anesthetized and perfused with cold DPBS (1x). Brains were dissected and dissociated using Adult Brain Dissociation Kit (Miltenyi) according to the manufacturer’s instructions. Human cells were isolated by mouse cell depletion kit (Miltenyi) following the manufacturer’s protocols. Isolated cell suspension then loaded to the Chromium controller for mRNA barcoding and reverse transcription using Chromium Next GEM Single Cell 3' Kit v3.1.
scRNA-seq libraries were constructed using Chromium Next GEM Single Cell 3' Kit v3.1 and Dual Index Kit TT Set A, following the manufacturer’s protocols. Quality control of the scRNA-seq libraries were performed by Agilent 2100 Bioanalyzer, and libraries were sequenced in Novaseq 6000 S4 flow cells.

treatment_protocol: Soluble S1 fractions from human samples (provided by the University of California Alzheimer's Disease Research Center (UCI-ADRC) and the Institute for Memory Impairments and Neurological Disorders) were prepared as described before. The human tissues were homogenized in TBS (20 mM Tris-HCl, 140 mM NaCl, pH 7.5) containing protease and phosphatase inhibitors (Roche). Homogenates were ultracentrifuged (4 °C for 60 min) at 100,000×g (Optima MAX Preparative Ultracentrifuge, Beckman Coulter). Supernatants, S1 fractions, were aliquoted and stored at −80 °C. The total amount of soluble tau in S1 fractions was determined by using an ELISA kit (human Tau, Invitrogen), according to the manufacturer’s protocol. The ELISA experiments were repeated in three independent experiments using triplicate replicas. All adult brain injections were performed using a Kopf stereotaxic apparatus (David Kopf, Tujunga, CA). Stereotaxic surgery was performed on two months old transplanted Rag2−/−hCSF1 immunodeficient mice. The mice were aseptically injected with human brain extracts (Cont tau or DSAD tau) in the dorsal hippocampus and the overlying cortex (bregma: −2.5 mm; lateral: +2 mm; depth: −2.4 mm and −1.8 mm from the skull). A dose of tau at 3.2 µg, which was previously shown to be able to induce tau pathology in tau transgenic mice, was injected into each human microglial chimeric mouse. Concentrations of tau per injection site were 0.8 μg/µl each site for both DSAD- Tau and Cont-Tau. The mice were injected with 1 μl of Cont or DSAD tau into each site (four sites total). After the injection, the mice were kept for further experiments.

value: Brain

value: DS A455D iPSC-differentiated PMP

value: Human microglia

value: DSAD tau


title: KO_Male_Tg+PDBu_inVitro_3

description: Library name: KOM8_Tgplus_PDBu

value: Orai1 KO


title: KO_Male_Tg+PDBu_inVitro_2

description: Library name: KOM6_Tgplus_PDBu

value: Hippocampus


title: KO_Male_LPS_inVitro_3

description: Library name: KOM8_LPS

value: Cultured Primary Microglia


title: KO_Male_Vehicle_inVitro_3

description: Library name: KOM6_veh


title: G53_CM_mRNA

city: BETHESDA

first: Cihan

last: Oguz

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

data_processing:
The fastq and count files generated by CellRanger (v3.1.1) mkfastq and count (utilizing the 10X hg38/GRCh38-3.0.0 reference transcriptome) pipelines, respectively.
Assembly: hg38
Supplementary files format and content: Cell Ranger scRNA-seq count matrices are in h5 data format (one h5 file per sample).

source_name: ileal mucosa

extract_protocol:
Tissue samples were collected into ice-cold MACS tissue storage solution (Miltenyi Biotech). After washing with DPBS (Thermo Fisher Scientific), mucosal tissues were minced into small pieces by dissecting scissors.  The minced tissues were digested in 5 ml TrypLE Express (Thermo Fisher Scientific) in gentleMACS C tubes (Miltenyi Biotech) using GentleMACS Octo Dissociator (Miltenyi Biotech) at 37oC for 30 min.  The digested cells were passed through a 40 micromete strainer (Greiner Bio-One), collected into 1% BSA DPBS-treated 50 ml conical tube.  After washing twice with ice-cold DPBS, the cells were incubated with anti-FcR antibody (Miltenyi Biotech) and then stained with PE-conjugated anti-EpCAM antibody (Novus Biological), Alexa Fluor 647-conjugated anti- CD45 antibody (BioLegend) and DAPI (Kirkegaard & Perry Laboratories) in 400 microliter DPBS.  After washing with DPBS twice, cells were resuspended in phenol-free DMEM (Thermo Fisher Scientific).  Live DAPI-negative EpCAM+ cells were sorted by FACS using a BD FACSAriaTM Fusion (Becton Dickinson) and collected into 1% BSA DPBS-treated microfuge tube containing 800 microliter phenol-free DMEM.
Single cell RNA-seq libraries were produced using Chromium 3’ v3 kit (10X Genomics) according to the standard manufacturer’s protocol and sequenced on Illumina NovaSeq6000.

value: ileal mucosa

value: epithelial


title: KO_Male_LPS_inVitro_2

description: Library name: KOM6_LPS


title: G51_CM_mRNA


title: G48_CM_mRNA


title: KO_Male_Vehicle_inVitro_2

description: Library name: KOM18_veh

value: Vehicle


title: G50_CM_mRNA


title: DS A455D PMPs transplanted, DSAD-tau treated, 10 mo, rep 1

description: 10x Genomics 3' Gex v3.1


title: G47_CM_mRNA


title: KO_Male_Tg+PDBu_inVitro_1

description: Library name: KOM18_Tgplus_PDBu

value: Male


title: KO_Male_LPS_inVitro_1

description: Library name: KOM18_LPS

value: LPS


title: KO_Male_Vehicle_inVitro_1

description: Library name: KOM17_veh


title: KO_Female_Vehicle_inVitro_3

description: Library name: KOF7_veh

value: Female


title: KO_Female_Tg+PDBu_inVitro_2

description: Library name: KOF7_Tgplus_PDBu

value: Tg+PDBu


title: hicut, CEBPA_4d_rep3

city: Beijing

first: Cheng

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

description: Library name: CEBPA_4d_rep3

data_processing:
distiller is used to process data and produce .cool file which was then transform to .hic files
Assembly: hg19
Supplementary files format and content: hic
Supplementary files format and content: bw

growth_protocol: HL-60 cell was cultured in a 5% CO2 incubator at 37 °C . The complete medium consist of ATCCformulated Iscove's Modified Dulbecco's Medium with 20% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde in RTfor 10min and then suspended with Hi-C lysis buffer on ice for 30min. DNA was then digested with DdeI and DpnII enzyme,. End-filling master mix was used to fill in restriction fragment overhangss and ligation master mix was used to ligate the DNA fragments.   Add the proximity ligated nuclei in Wash Buffer to activated beads abd then treated with primary CEBPA Rabbit mAb and Secondary Anti-Rabbit.  Chromatin was incubated pA/G-Tn5 transposase then DNA for tagmentation and extracted using DNA Extract Beads Pro.
After PCR amplification(14 cycles), size selection was performed using Ampure XP beads.

treatment_protocol: 1 μM all-trans-Retinoic acid (ATRA ) was applied to induce neutrophil differentiation

value: promyelocytic

value: RA 4d


title: G44_PTM_mRNA


title: hicut, CEBPA_4d_rep4

description: Library name: CEBPA_4d_rep4


title: hicut, CEBPA_4h_rep4

description: Library name: CEBPA_4h_rep4

value: RA 4h


title: KO_Female_Vehicle_inVitro_2

description: Library name: KOF16_veh


title: hicut, CEBPA_4d_rep2

description: Library name: CEBPA_4d_rep2


title: CAGG WT ESC WGS

description: KAPA HYper Prep Library Preparation

source_name: Cultured ESCs

value: Cultured ESCs

value: CAGG  WT

value: Human ESC

value: Wild type


title: KO_Female_Tg+PDBu_inVitro_1

description: Library name: KOF16_Tgplus_PDBu

value: Orai1 KO


title: hicut, CEBPA_4h_rep3

description: Library name: CEBPA_4h_rep3


title: G43_PTM_mRNA


title: G42_PM_mRNA


title: hicut, CEBPA_4h_rep2

description: Library name: CEBPA_4h_rep2


title: G35_PTM_mRNA


title: KO_Female_LPS_inVitro_1

description: Library name: KOF15_LPS

value: Hippocampus


title: KO_Male_LPS_6hrs_inVivo_2

description: Library name: 72_KO_LPS

source_name: Whole Brain

value: Whole Brain

value: FACS-Purified Microglia

value: Ora1 KO


title: KO_Male_LPS_6hrs_inVivo_3

description: Library name: 73_KO_LPS


title: KO_Male_LPS_6hrs_inVivo_1

description: Library name: 71_KO_LPS


title: hicut, CEBPA_0h_rep4

description: Library name: CEBPA_0h_rep4

value: RA 0h


title: hicut, CEBPA_0h_rep2

description: Library name: CEBPA_0h_rep2


title: WT_Male_LPS_6hrs_inVivo_2

description: Library name: 69_WT_LPS

value: Ora1 WT

value: Male


title: G34_PTM_mRNA

value: ileal mucosa

value: epithelial


title: G33_PM_mRNA


title: WT_Male_LPS_6hrs_inVivo_3

description: Library name: 70_WT_LPS

value: LPS


title: WT_Male_LPS_24hrs_inVivo_4

description: Library name: 3402_WTM_LPS


title: G32_PM_mRNA


title: DE, PDHB+/-_2, rep2

city: WuHan

first: liming

last: meng

address: No. 115, Donghu Road

institute: WuHan university

description: Library name: Sample 6

data_processing:
The sequencing data was assessed using FastQC 0.12.1 for quality control.
The clean data were then aligned to the human GRCh38 genome using Bowtie2 2.3.5.1.
The aligned reads were subsequently counted for different gene regions using featureCounts, and the TPM values were calculated.
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values of all samples

growth_protocol: Undifferentiated human embryonic stem cells (HUES8) were cultured on Matrigel-coated plates (Corning, Cat#354277). And the cells cultured at 37 °C with 5% CO2, maintaining in mTesR1 medium (STEMCELL Technologies, Cat#85850). Subculturing was performed every 4 days using Accutase (STEMCELL Technologies, Cat#07922), and the culture medium was changed daily.

extract_protocol:
RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For the induction of definitive endoderm (DE) differentiation, experiments were conducted using 24-well cell culture plates coated with growth factor-reduced Matrigel (Corning, Cat# 354230). The initial cell seeding density was 100,000 cells per well. After culturing the cells in mTeSR1 for one day, when the cells began to reach confluence, the DE differentiation medium was switched. The DE differentiation medium was based on DMEM (Gibco, Cat# C11995500BT) and supplemented with 100 ng/mL Activin A (PeproTech, Cat# 120-14P), 1x penicillin/streptomycin (Gibco, Cat# 10378016), and 0.2% bovine serum albumin (Yeasen Biotechnology, Cat# 36104ES25).

value: embryonic stem cells

value: PDHB heterozygous cell line

value: DE differentiation


title: WT_Male_LPS_6hrs_inVivo_1

description: Library name: 68_WT_LPS


title: G30_PTM_mRNA


title: KO_Male_LPS_24hrs_inVivo_4

description: Library name: 3399_KOM_LPS


title: WT_Male_Vehicle_inVivo_3

description: Library name: 3401_WTM_sal

value: Vehicle


title: KO_Male_Vehicle_inVivo_3

description: Library name: 3398_KOM_sal


title: DE, PDHB+/-_2, rep1

description: Library name: Sample 5


title: KO_Female_LPS_inVitro_2

description: Library name: KOF16_LPS

value: Cultured Primary Microglia

value: Female


title: G25_PTM_mRNA


title: DE, PDHB+/-_1, rep2

description: Library name: Sample 4


title: KO_Female_Vehicle_inVivo_3

description: Library name: 3397_KOF_sal


title: KO_Female_Vehicle_inVitro_1

description: Library name: KOF15_veh

value: Orai1 KO


title: KO_Female_LPS_24hrs_inVivo_3

description: Library name: 3396_KOF_LPS


title: hicut, CEBPA_0h_rep3

description: Library name: CEBPA_0h_rep3

value: promyelocytic


title: G24_PTM_mRNA


title: DE, PDHB+/-_1, rep1

description: Library name: Sample 3


title: KO_Female_Vehicle_inVivo_2

description: Library name: 3395_KOF_sal

value: Whole Brain


title: G23_PTM_mRNA


title: KO_Female_LPS_24hrs_inVivo_2

description: Library name: 3394_KOF_LPS

value: FACS-Purified Microglia


title: WT_Female_Vehicle_inVivo_3

description: Library name: 3393_WTF_sal


title: DE, WT, rep2

description: Library name: Sample 2

value: WT


title: WT_Female_LPS_24hrs_inVivo_4

description: Library name: 3392_WTF_LPS


title: DE, WT, rep1

description: Library name: Sample 1


title: WT_Female_LPS_24hrs_inVivo_3

description: Library name: 3377_WTF_LPS


title: G22_PTM_mRNA


title: WT_Female_Vehicle_inVivo_2

description: Library name: 3376_WTF_sal


title: G21_PTM_mRNA


title: WT_Female_LPS_24hrs_inVivo_2

description: Library name: 3315_WTF_LPS


title: WT_Female_LPS_24hrs_inVivo_1

description: Library name: 3312_WTF_LPS


title: G19_PTM_mRNA


title: hESCs, SMAD2/3, ChIP

description: Library name: ChIP-seq, hESCs, SMAD2/3, ChIP

data_processing:
The sequencing data was assessed and processed by FastQC 0.12.1 for quality control.
The clean data were then aligned to the human GRCh38 genome using Bowtie2 2.3.5.1.
Subsequent data visualization finished by deeptools 2.5.7 and IGV.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
The cells were initially crosslinked with 1% formaldehyde for 10 minutes at room temperature while gently rotating. Then the cross-linking reaction was finished by 0.125 M glycine, followed by a 5 minutes incubation. Next, cells were harvested and resuspended in cell lysis buffer (10 mM Tris-HCl, pH 8.0; 140 mM NaCl; 0.2% NP-40), supplemented with 1x cOmplete Protease Inhibitor (Roche), and incubated on ice for 10 minutes to isolate nuclei. After washing with cold DBPS, the nuclei were broken in nuclear lysis buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA, pH 8.0; 1% SDS). And sonication was carried out, aiming to generate chromatin fragments ranging from 200 to 500 bp. Following sonication, the lysates were centrifuged, and the soluble chromatin fragments were incubated with SMAD2/3 antibody and Protein A/G Dynabeads to enrich for the fragmented chromatin. The DNA was eluted by elution buffer (100 mM NaHCO₃, 1% SDS) and reverse-crosslinked at 67°C overnight.
The libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody


title: WT_Male_Vehicle_inVivo_2

description: Library name: 3311_WTM_sal


title: hESCs, SMAD2/3, Input

description: Library name: ChIP-seq, hESCs, SMAD2/3, Input


title: WT_Female_Vehicle_inVivo_1

description: Library name: 3314_WTF_sal


title: ATAC-seq, DE, PDHB+/-, rep2

description: Library name: ATAC-seq, PDHB+/-, rep2

data_processing:
The sequencing data was assessed and processed by FastQC 0.12.1 and fastp 0.23.4 for quality control.
The clean data were then aligned to the human GRCh38 genome using Bowtie2 2.3.5.1.
The duplicates were removed with sambamba 1.0.
Subsequent data visualization finished by deeptools 2.5.7 and IGV.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
Cells were prepared for ATAC-seq library construction using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711-01).
The library was constructed by the TruePrep Index Kit V2 for Illumina (Vazyme, TD202).


title: WT_Male_LPS_24hrs_inVivo_3

description: Library name: 3310_WTM_LPS


title: G17_PTM_mRNA


title: WT_Male_Vehicle_inVivo_1

description: Library name: 3308_WTM_sal


title: WT_Male_LPS_24hrs_inVivo_2

description: Library name: 3309_WTM_LPS


title: G18_PTM_mRNA


title: KO_Male_LPS_24hrs_inVivo_3

description: Library name: 3306_KOM_LPS

value: Ora1 KO


title: G16_PM_mRNA


title: KO_Male_Vehicle_inVivo_2

description: Library name: 3304_KOM_sal


title: G15_PM_mRNA


title: KO_Male_LPS_24hrs_inVivo_2

description: Library name: 3305_KOM_LPS


title: KO_Male_LPS_24hrs_inVivo_1

description: Library name: 3303_KOM_LPS


title: KO_Female_LPS_24hrs_inVivo_1

description: Library name: 3300_KOF_LPS


title: G14_CM_mRNA


title: G11_CM_mRNA


title: Ripk1KO NIT-1 beta-cells TNF_IFN replicate 6

city: Indianapolis

first: Madeline

last: Peyton

state: IN

address: 410 W 10th St

institute: Indiana University

description:
Library name: Ripk1KO_TNF_IFN_rep6
Ripk1KO NIT-1 beta-cells treated with TNF_IFN, biological replicate 6

data_processing:
Raw paired-end reads (2×100 bp) were quality-checked and aligned to the Mus musculus reference genome GRCm39 using STAR (v2.7.11a). Gene-level counts were obtained using featureCounts (Subread v2.0.6) with Ensembl GRCm39 GTF annotation, counting reads overlapping exons summarized at the gene_id level (paired-end, reverse-stranded, exon-based counting).
Differential expression analysis was performed in R (v4.3.1) using DESeq2 (v1.42.1). Genes with fewer than 10 reads in at least 3 samples were excluded prior to modeling. DESeq2's median-of-ratios method was used for library size normalization and dispersion parameters were estimated with empirical Bayes shrinkage.
A design formula including genotype (CTL vs Ripk1Δ), treatment (vehicle vs TNFα+IFNγ), and their interaction was used (~ genotype + treatment + genotype:treatment). Wald tests computed statistics, and p-values were adjusted using the Benjamini-Hochberg method; genes with FDR < 0.05 were considered significantly differentially expressed.
Assembly: Mus musculus GRCm39 (Ensembl)
Supplementary files format and content: normalized_counts_NIT1.csv: comma-separated file with DESeq2-normalized counts; rows = genes (Ensembl gene IDs); columns = normalized counts for each sample plus group means and gene category annotations.
Supplementary files format and content: sample_metadata.csv: comma-separated file with sample-level metadata including genotype, treatment, replicate, and FASTQ/BAM prefix for each sample.

source_name: pancreatic beta-cells

growth_protocol: NIT-1 beta-cells derived from NOD/ShiLtJ mice were cultured in DMEM with 25 mM glucose supplemented with 10% FBS, 1% sodium pyruvate, and 1% penicillin-streptomycin at 37°C in 5% CO2. Ripk1 gene-edited (Ripk1Δ) and control (CTL) NIT-1 cell lines were generated using CRISPR/Cas9 with gRNAs targeting exons 2-3 of mouse Ripk1 and a non-targeting control gRNA delivered via lentiCRISPR v2 followed by puromycin selection.

extract_protocol:
Total RNA was extracted from NIT-1 CTL and Ripk1Δ beta-cells treated with vehicle or TNFα+IFNγ. RNA integrity was assessed prior to library preparation according to sequencing core facility guidelines.
RNA-seq libraries were prepared from total RNA by the institutional sequencing core using a stranded mRNA-seq workflow with poly(A) selection following standard protocols. Libraries were barcoded, quantified, pooled, and sequenced on an Illumina NovaSeq 6000 as paired-end 2×100 bp reads.

treatment_protocol: For RNA-seq experiments, CTL and Ripk1Δ NIT-1 cells were treated with either vehicle or TNFα (40 ng/mL) plus IFNγ (100 ng/mL) for the indicated times before RNA isolation.

value: pancreatic beta-cells

value: beta-cell

value: TNFα (40 ng/mL) + IFNγ (100 ng/mL)


title: Ripk1KO NIT-1 beta-cells TNF_IFN replicate 5

description:
Library name: Ripk1KO_TNF_IFN_rep5
Ripk1KO NIT-1 beta-cells treated with TNF_IFN, biological replicate 5


title: Ripk1KO NIT-1 beta-cells TNF_IFN replicate 4

description:
Library name: Ripk1KO_TNF_IFN_rep4
Ripk1KO NIT-1 beta-cells treated with TNF_IFN, biological replicate 4


title: Mutant+RAdiet 4

city: Aurora

first: Christina

last: Como

state: CO

institute: University of Colorado

data_processing:
Library sequencing was performed by the Genomics and Microarray core at the University of Colorado, Anschutz Medical Campus. ATAC-seq data was analyzed using the nf-core ataceq analysis pipeline with the following parameters: aligned with bwa and macs2 narrow peak calling. ATAC-seq peak data was visualized using IGV and Signac, and DiffBind was used to determine statistical differences in peak size.
Assembly: mm10/GRCm38
Supplementary files format and content: narrow peak bed files

source_name: forebrain

extract_protocol:
Zymo ATACseq kit
Zymo ATAClibrary kit

value: forebrain

value: Foxc1 hith/LacZ

value: RA diet


title: Mutant+RAdiet 5


title: Mutant+RAdiet 6


title: Ripk1KO NIT-1 beta-cells TNF_IFN replicate 3

description:
Library name: Ripk1KO_TNF_IFN_rep3
Ripk1KO NIT-1 beta-cells treated with TNF_IFN, biological replicate 3


title: Mutant+RAdiet 3


title: Mutant+RAdiet 2


title: G8_PTM_mRNA

value: ileal mucosa

value: epithelial


title: WT_Male_LPS_24hrs_inVivo_1

description: Library name: 3307_WTM_LPS

value: Ora1 WT

value: LPS

value: Male


title: ATAC-seq, DE, PDHB+/-, rep1

description: Library name: ATAC-seq, PDHB+/-, rep1

value: embryonic stem cells

value: PDHB heterozygous cell line

value: DE differentiation


title: Ripk1KO NIT-1 beta-cells TNF_IFN replicate 1

description:
Library name: Ripk1KO_TNF_IFN_rep1
Ripk1KO NIT-1 beta-cells treated with TNF_IFN, biological replicate 1


title: G7_PTM_mRNA


title: Ripk1KO NIT-1 beta-cells TNF_IFN replicate 2

description:
Library name: Ripk1KO_TNF_IFN_rep2
Ripk1KO NIT-1 beta-cells treated with TNF_IFN, biological replicate 2


title: Control+RAdiet 4

value: Foxc1 WT


title: G9_PM_mRNA


title: Mutant+RAdiet 1


title: G10_PM_mRNA


title: KO_Male_Vehicle_inVivo_1

description: Library name: 3302_KOM_sal

value: Whole Brain

value: FACS-Purified Microglia

value: Vehicle


title: KO_Female_Vehicle_inVivo_1

description: Library name: 3299_KOF_sal

value: Ora1 KO

value: Female


title: Control+RAdiet 3

value: forebrain


title: ATAC-seq, DE, WT, rep1

description: Library name: ATAC-seq, WT, rep1

value: WT


title: ATAC-seq, DE, WT, rep2

description: Library name: ATAC-seq, WT, rep2


title: Ripk1KO NIT-1 beta-cells Vehicle replicate 6

description:
Library name: Ripk1KO_Vehicle_rep6
Ripk1KO NIT-1 beta-cells treated with Vehicle, biological replicate 6

value: pancreatic beta-cells

value: beta-cell


title: Control+RAdiet 2

value: RA diet


title: G5_PTM_mRNA

value: ileal mucosa

value: epithelial


title: G4_PM_mRNA


title: Foxc1Mutant 3

value: Foxc1 hith/LacZ

value: no diet


title: Control+RAdiet 1


title: Ripk1KO NIT-1 beta-cells Vehicle replicate 5

description:
Library name: Ripk1KO_Vehicle_rep5
Ripk1KO NIT-1 beta-cells treated with Vehicle, biological replicate 5


title: Foxc1Mutant 2


title: Control+RAdiet 5


title: Ripk1KO NIT-1 beta-cells Vehicle replicate 4

description:
Library name: Ripk1KO_Vehicle_rep4
Ripk1KO NIT-1 beta-cells treated with Vehicle, biological replicate 4


title: Foxc1Mutant 1


title: G2_CM_mRNA


title: Ripk1KO NIT-1 beta-cells Vehicle replicate 3

description:
Library name: Ripk1KO_Vehicle_rep3
Ripk1KO NIT-1 beta-cells treated with Vehicle, biological replicate 3


title: Control 3


title: G1_CM_mRNA


title: Control 4


title: Ripk1KO NIT-1 beta-cells Vehicle replicate 2

description:
Library name: Ripk1KO_Vehicle_rep2
Ripk1KO NIT-1 beta-cells treated with Vehicle, biological replicate 2


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day44, Lot.3-2

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

data_processing:
The raw sequences were initially trimmed using Trim Galore (v0.6.5). Subsequently, the trimmed sequences were aligned to the reference genome with bowtie2 (v2.3.5.1). Mitochondrial genome-derived reads and PCR duplicates were removed using samtools (v1.14) and Picard (v2.21.4), respectively. Finally, bigWig files were generated by calculating coverage with deepTools (v3.5.1).
Assembly: GRCh38
Supplementary files format and content: bigwig

source_name: Umbilical Vein

growth_protocol: hiHepPCs were cultured in DMEM/F12 and Fibrolife mixture medium with 4% FBS, 1 µg/ml insulin, 10^-7 M dexamethasone, 10 mM nicotinamide, 2 mM L-glutamine, 50 µM 2-mercaptoethanol, and penicillin/streptomycin, containing 20 ng/ml HGF, 1 µM A83-01, 2 µM SB431542, and 5 µM Y27632.

extract_protocol:
The cultured cells were collected at specified time points by trypsinization. Using 50,000 cells per reaction, the experiment was conducted following the publicly available standard Omni ATAC-seq protocol (PMID: 28846090).
The collected genomic DNA fragments were purified using a PCR purification kit (QIAGEN), and indexing and amplification were performed with the NEBNext High-Fidelity 2X PCR Master Mix (NEB). The amplified library was then purified and size-selected using AMPure XP (BECKMAN COULTER).

treatment_protocol: Induction of hiHepPCs was carried out with or without 3 µM CHIR99021.

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Forced expression of FOXA3, HNF1A and HNF6

tag: time

value: Day 44


title: Control 2

value: Foxc1 WT


title: Control 1


title: Ripk1KO NIT-1 beta-cells Vehicle replicate 1

description:
Library name: Ripk1KO_Vehicle_rep1
Ripk1KO NIT-1 beta-cells treated with Vehicle, biological replicate 1

value: Vehicle


title: Foxc1Mutant 4


title: Control NIT-1 beta-cells TNF_IFN replicate 6

description:
Library name: Control_TNF_IFN_rep6
Control NIT-1 beta-cells treated with TNF_IFN, biological replicate 6

value: Control

value: TNFα (40 ng/mL) + IFNγ (100 ng/mL)


title: Apex1 KO 6 days post fracture rep 2

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

data_processing:
bcl2fastq v2.20 was used to demultiplex and FASTQ files were aligned to the mouse genome (mm39) using STAR (v2.7.0d). Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.4.3) counting uniquely mapped paired-end reads with reverse strandness. The Ensembl v104 gene annotation was considered as the reference.
Normalization, processing and differential expression analyses were performed using DEseq2 (v1.32.0)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Fracture callus

extract_protocol:
RNA was extracted using Trizol reagent after homogenizing the fracture callus with liquid nitrogen and a mortar
RNA-seq libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus according to the manufacturer’s instructions

value: Fracture callus

value: Male

value: Apex1 KO

value: 6 days post fracture


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.3-2

value: Day 9


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day44, Lot.3-1


title: WT 6 days post fracture rep 5

value: Female

value: WT


title: Apex1 KO 6 days post fracture rep 3


title: Apex1 KO 6 days post fracture rep 1


title: Control NIT-1 beta-cells TNF_IFN replicate 5

description:
Library name: Control_TNF_IFN_rep5
Control NIT-1 beta-cells treated with TNF_IFN, biological replicate 5

value: pancreatic beta-cells

value: beta-cell


title: G3_PM_mRNA

value: ileal mucosa

value: epithelial


title: WT 6 days post fracture rep 3


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.3-1

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells

value: Forced expression of FOXA3, HNF1A and HNF6


title: WT 6 days post fracture rep 1


title: WT 6 days post fracture rep 2


title: Apex1 KO 3 days post fracture rep 4

value: 3 days post fracture


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.3-2

value: Day 44


title: WT 6 days post fracture rep 4

value: Fracture callus


title: Control NIT-1 beta-cells TNF_IFN replicate 3

description:
Library name: Control_TNF_IFN_rep3
Control NIT-1 beta-cells treated with TNF_IFN, biological replicate 3

value: Control

value: TNFα (40 ng/mL) + IFNγ (100 ng/mL)


title: Apex1 KO 3 days post fracture rep 3

value: Apex1 KO


title: Apex1 KO 3 days post fracture rep 2

value: Male


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.3-1


title: Control NIT-1 beta-cells TNF_IFN replicate 2

description:
Library name: Control_TNF_IFN_rep2
Control NIT-1 beta-cells treated with TNF_IFN, biological replicate 2


title: Apex1 KO 3 days post fracture rep 1


title: Control NIT-1 beta-cells TNF_IFN replicate 4

description:
Library name: Control_TNF_IFN_rep4
Control NIT-1 beta-cells treated with TNF_IFN, biological replicate 4


title: Control NIT-1 beta-cells Vehicle replicate 6

description:
Library name: Control_Vehicle_rep6
Control NIT-1 beta-cells treated with Vehicle, biological replicate 6

value: Vehicle


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day44, Lot.2-2


title: WT 10 days post fracture rep 4

value: WT

value: 10 days post fracture


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day16, Lot.3-1

value: Day 16


title: Apex1 KO 10 days post fracture rep 3


title: WT 14 days post fracture rep 4

value: 14 days post fracture


title: WT 3 days post fracture rep 4


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.2-2

value: Day 9


title: Control NIT-1 beta-cells Vehicle replicate 4

description:
Library name: Control_Vehicle_rep4
Control NIT-1 beta-cells treated with Vehicle, biological replicate 4

value: pancreatic beta-cells

value: beta-cell


title: Control NIT-1 beta-cells Vehicle replicate 5

description:
Library name: Control_Vehicle_rep5
Control NIT-1 beta-cells treated with Vehicle, biological replicate 5


title: Apex1 KO 10 days post fracture rep 2


title: WT 14 days post fracture rep 3


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day16, Lot.2-2

value: Umbilical Vein

value: Primay Cells

value: Endothelial Cells


title: Control NIT-1 beta-cells Vehicle replicate 3

description:
Library name: Control_Vehicle_rep3
Control NIT-1 beta-cells treated with Vehicle, biological replicate 3


title: WT 10 days post fracture rep 3


title: WT 3 days post fracture rep 2

value: Female

value: 3 days post fracture


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day44, Lot.2-1

value: Forced expression of FOXA3, HNF1A and HNF6

value: Day 44


title: Control NIT-1 beta-cells TNF_IFN replicate 1

description:
Library name: Control_TNF_IFN_rep1
Control NIT-1 beta-cells treated with TNF_IFN, biological replicate 1

value: Control

value: TNFα (40 ng/mL) + IFNγ (100 ng/mL)


title: Control NIT-1 beta-cells Vehicle replicate 2

description:
Library name: Control_Vehicle_rep2
Control NIT-1 beta-cells treated with Vehicle, biological replicate 2

value: Vehicle


title: WT 14 days post fracture rep 2

value: Fracture callus

value: Male

value: WT


title: WT 3 days post fracture rep 3


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day9, Lot.2-1


title: WT 3 days post fracture rep 1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.3-1


title: Apex1 KO 14 days post fracture rep 2

value: Apex1 KO

value: 14 days post fracture


title: WT 10 days post fracture rep 2

value: 10 days post fracture


title: Control NIT-1 beta-cells Vehicle replicate 1

description:
Library name: Control_Vehicle_rep1
Control NIT-1 beta-cells treated with Vehicle, biological replicate 1

value: pancreatic beta-cells

value: beta-cell


title: WT 14 days post fracture rep 1


title: HUVECs transduced with FOXA3, HNF1A and HNF6, with CHIR99021, Day16, Lot.2-1

value: Umbilical Vein

value: Primay Cells

value: Day 16


title: Cyp2c29 KO mouse liver 7

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Library name: Sample 14

data_processing:
Counts generated with Salmon and GENCODE vM36
Assembly: mm39
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: Liver

extract_protocol:
Qiagen Midiprep
Total RNA-seq libraries were generated in the NIEHS Epigenomics Core using Ribo-Zero Gold and sequenced on the Illumina NovaSeq 6000 to over 140 million reads per biological replicate.

value: Liver

value: Cyp2c29 KO

value: CDAA diet


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day44, Lot.2-2

value: Endothelial Cells

value: Forced expression of FOXA3, HNF1A and HNF6

value: Day 44


title: Apex1 KO 10 days post fracture rep 1

value: Fracture callus

value: Female


title: Cyp2c29 KO mouse liver 6

description: Library name: Sample 13


title: HUVECs transduced with FOXA3, HNF1A and HNF6, Day9, Lot.2-2

value: Day 9


title: WT 10 days post fracture rep 1

value: WT