title: HumanBrain-Tumor-WU1221-Core2

type: RNA

first: Allegra

middle: A

last: Petti

state: Massachusetts

address: 185 Cambridge St.

department: Department of Neurosurgery

institute: Massachusetts General Hospital

description: Samples were processed similarly as previously published20. In brief, formalin-fixed, paraffin-embedded (FFPE) tumor samples were sectioned into 5-um sections using a microtome onto Xenium slides according to Protocol CG000578 published by 10X Genomics. The Xenium slides were then deparaffinized and decrosslinked according to the Protocol CG000580. Both a pre-designed gene expression panel (Human Brain Probe set) and a custom probe set were used during probe hybridization, ligation, and amplification according to Protocol CG000582. The Xenium slide was then loaded into the Xenium Analyzer using Protocol CG000584 and regions of interest (ROIs) were initially selected using the on-instrument software.

data_processing: Raw FASTQ files were analyzed in Xenium Ranger (version 2.0.0.10) using the Xenium Multi-Tissue Stain cell segmentation method. Data were then processed using the Seurat R package (5.0.1). Initial filtering, and subsequent analysis, was performed on a per-sample basis. Counts were then log-normalized and PCA was performed with the optimal number of PCs determined based upon elbow plots, jackstraw resampling, and PC expression heatmaps. Dimensionality reduction and visualization were performed with the UMAP algorithm (Seurat implementation) followed by unsupervised graph-based clustering. Clusters with overall low nCount and nFeature were removed, and PCA and UMAP visualization was performed again on the filtered object. Cell types in each sample were individually characterized using marker genes and differentially expressed genes (Table S6-S7). Samples were then merged using SCTransform (Seurat implementation) and PCA and UMAP visualization was performed again on the merged object. Cell types were then standardized by performing hierarchical clustering on different groups of cell types, such as immune cells, tumor cells, etc. Cell types with consistent gene expression profiles were labeled similarly and differentially expressed genes of each cell type were analyzed to confirm correct identification.

label: 10X Xenium Probe Panel

source_name: Brain tumor section (IDH wildtype Glioblastoma)

label_protocol: We designed a panel of oligonucleotides targeting transcripts from 362 genes, comprising 266 genes from the predesigned 10X Genomics human brain-and-glioblastoma panel and 96 custom genes indicated by our scRNA-seq analyses (Table S4). Together, this customized panel captures diverse neurons, glia, endothelial cells, microglia, immune cells, GBM cells (including both spatial GBM cell states derived from our Visium data and published scRNA-seq-derived GBM cell states), and ligand-receptor pairs that putatively mediate tumor/neuron, tumor/T cell, and tumor/macrophage interactions.

tag: gender

value: female

tag: age

tag: tumor location

value: Left frontal-temporal

tag: tumor size

tag: mgmt methylation

value: Methylated

tag: egfr methylation

tag: patient id


title: Rex1-EmGFPd2 Ddb1 gRNA#1 mESCs, BrdU-IP Late

status: Public on Jun 12 2026

type: SRA

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
DEP_01_066_25_Ddb1_25_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
03_Ddb1_mean_w200ks40k.bedGraph

library_source: genomic

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 genome.
Duplicated reads were filtered out.
Reads per million (rpm) normalization were calculated for early- and late-S-phase BrdU-IP samples in sliding windows of 200-kb at 40-kb intervals and a nonoverlapping 200-kb bins for Robust scaling analysis, respectively.
The ratio of early-S-phase to total read counts [(early-S reads)/(early-S reads + late-S reads)] was calculated for each bin, and their distribution was converted to fit within a ±1 scale. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Assembly: mm9
Supplementary files format and content: bedGraph
Library strategy: BrdU-IP Repli-seq

molecule: genomic DNA

organism: Mus musculus

growth_protocol: C57BL/6N mESCs were grown in serum free medium NDiff 227 (Cellartis, Y40002), 1 μM PD0325901 (Wako, 162-25291) and 3 μM CHIR99021 (Wako, 034-23103), 0.1 mM 2-mercaptoethanol and 1000 U/ml mLIF on iMatrix-511 (Matrixome, 892012) coated dishes.

extract_protocol:
We followed the BrdU-IP-based protocol as described (Ryba et al., 2011). 75% ethanol fixed cells were stained with Propidium iodide (Nacalai tesque, 29037), then early-S phase and late-S phase cell population (at least 10,000 cells/fraction) were sorted by a Sony SH800 cell sorter (ultra-purity mode). For nocodazole/5-Ph-IAA removal experiments, only early-S phase cells were collected. Extracted DNA was sonicated by a Bioruptor BR2012A (Sonic Bio). BrdU-incorporated DNA was immunoprecipitated using anti-BrdU antibody (BD Biosciences Pharmingen, #555627).
BrdU-immunoprecipitated DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed from early- and late-replicating DNA after WGA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

treatment_protocol: (1) Transfection of gRNA-carrying vector was performed with Lipofectamine LTX&PLUS (ThermoFisher, 15338100) according to the manufacturer’s instructions. Cells were collected 4 days after transfection. (2) 5-Ph-IAA treatment: 5-Ph-IAA solution was added at a final concentration of 1 µM to the medium. (3) Nocodazole removal: after 15 hours of 50 ng/ml nocodazole treatment, the medium containintg nocodazole was replaced with normal culture medium. (4) 5-Ph-IAA removal: after 15 hours of 1 µM 5-Ph-IAA treatment, the medium containing 5-Ph-IAA was replaced with normal culture medium.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: strain

tag: genetic modification

value: EmGFPd2 knockin at Rex1 locus, Cas9 knockin at Rosa26 locus

tag: treatment

value: pU6-Ddb1-gRNA#1-CBA-PuroR transfection


title: Rex1-EmGFPd2 Control mESCs Replicate 2, BrdU-IP Early

description:
DEP_01_066_19_vector_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
01_vec_mean_w200ks40k.bedGraph

value: pU6-sgRNAscaff-CBA-PuroR transfection


title: TTchemSeq 15min recovery after h2o2 with OGG1i replicate 2 exp5

city: København

first: Lea

middle: Haarup

last: Gregersen

address: Blegdamsvej 3B,

department: ICMM

country: Denmark

institute: University of Copenhagen

description: Library name: TT5_15_ogg1i_r2

library_source: transcriptomic

data_processing:
Raw fastq files for Read 1 were labelled with appropriate UMI reads using UMItools
adapter trimming with cutadapt (v4.5) within trim_galore (v0.6.10) and read length filtering > 19nt
samples were mapped with STAR75 (v2.7.11b) against a merged human-yeast genome assemblies (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Genome alignments BAM files were filtered for multimapped reads with samtools (v1.21) view function (-q 10)
UMI duplicates were then removed with UMItools dedup function. A yeast gene-level count matrix was generated with Subread (v2.0.6) featureCounts76 and used to calculate yeast size-factors with DEseq277 (v1.42.0) “estimateSizeFactors” function. Strand specific and spike-in normalised BigWig files were generated from strand-specific bam files using Deeptools78 (v3.5.5) bamCoverage function (--scaleFactor = 1/ yeast size-factor) with bin size of 25 nt (-bs 25)
Assembly: (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Supplementary files format and content: bigwig forward and reverse strands

molecule: nuclear RNA

organism: Homo sapiens

source_name: HEK293 Flp-in T-Rex

growth_protocol: Flp-InTM T-REx HEK293 cells (HEK293, R78007, ThermoFisher Scientific, human embryonic kidney epithelial, female origin) were cultured at 37C with 5% CO2 in high glucose DMEM (Biowest, Cat#L0104) supplemented with 10% v/v FBS (Gibco, Cat#10270106), 100 U/mL penicillin, 100 μg/mL streptomycin (Gibco, 10378016) 2 mM L-glutamine.

extract_protocol:
80% confluent cells RNA were labelled in vivo for 15 min with 4sU by adding it directly to the tissue culture media to a final concentration of 1 mM. Per samples 80-100 μg of total RNA resuspended in 100 μL RNAse-free H2O was complemented with 1 % (relative to total RNA concentration) of S. cerevisiae 4tU-labelled RNA spike-in. Total RNA was fragmented by adding 20 μL of freshly prepared 1 M NaOH per sample, thoroughly mixed and incubated for 40 min on ice to < 400 nt fragments. Resuspended and purified 4sU labelled RNA in RNAse-free water was biotinylated in 10 mM Tris-HCl pH = 7.4; 1 mM EDTA complemented with 0.5 mg/ μL MTSEA biotin-XX linker (Biotum, Cat# BT90066) for 30 min in the dark at room temperature. Biotinylated RNA was immediately purified by ROTI®Aqua-P/C/I extraction and isopropanol precipitation and resuspended in 50 μL RNAse-free water. and isolated with μMACS Streptavidin Kit (Miltenyi, Cat#130-074-101). A total of 100uL μMACS Streptavidin MicroBeads were added to denatured 4sU total RNA and incubated for 15 min at room temperature with agitation. Beads bound to 4sU biotinylated RNA were applied to magnetic μColumns and transferred to the magnetic field of the μMACS magnetic separator (Miltenyi).
Approx. 30 ng of purified 4sU biotinylated RNA was used to prepare libraries with NEBNext® Ultra™ II RNA library prep kit (NEB, Cat#E7760) according to manufacturer’s protocol (protocol 5 for fragmented RNA) with ligation of two barcodes of 8 nt and 11 nt UMIs (NEB, Cat#E7416).

treatment_protocol: Inhibitors treatments were carried out by direct addition to the cell culture media with the following concentration 100 μM DRB (Sigma, D1916) or/and 10 μM Olaparib (PARPi, MedchemExpress, Cat#HY-10162) or/and 10 μM TH5487 (OGG1i, MedchemExpress, Cat#HY-125276). Oxidative stress induction treatments were carried out for 15 min (or 30 min for EU-labelling) with direct addition of freshly prepare 1000x concentrate to cell culture media, fresh H2O2 (maximum 3 month old kept at 4CC) to final concentration of 1 mM H2O2 (Sigma, H1009) or freshly resuspended Menadione sodium bisulfite (MND, Sigma, M5750) in water to final concentration of 0.25 mM.

value: HEK293 Flp-in T-Rex


title: L-fHP_40

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

country: USA

institute: University of Viginia

description: Library name: 79053351

data_processing:
Clusters were generated using ExAmp chemistry on patterned flow cells and sequenced with the NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles) on the NovaSeq 6000 system (Illumina, San Diego, CA), following the manufacturer's instructions. Approximately 60 million reads by were generated for each cDNA library by 150bp paired end (PE) sequencing cycle.
Assembly: hg38
Supplementary files format and content: .csv file includes raw counts for each Sample

molecule: total RNA

source_name: venous blood

extract_protocol:
RNA was extracted using PAXgene Blood RNA kit (Qiagen, cat#762164) following manufacturer’s protocol. RNA quality and integrity were confirmed by Quant-iT RiboGreen RNA Assay Kit (ThermoFisher, cat#R11490) and TapeStation RNA ScreenTape (Agilent, Santa Clara, CA)
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, cat# 470-2020-003-A).

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: L-fHP

tag: Sex

value: Female

tag: age blood_draw

tag: smoking history

value: No

tag: cigyears

tag: race

value: White

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival

value: alive

tag: surv months

tag: tissue

value: venous blood


title: HumanBrain-Tumor-WU1221-Edge1

city: Boston

tag: gender

tag: age

tag: tumor location

tag: tumor size

tag: mgmt methylation

tag: egfr methylation

tag: patient id


title: Rex1-EmGFPd2 Control mESCs Replicate 1, BrdU-IP Late

description:
DEP_01_066_01_vector_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
01_vec_mean_w200ks40k.bedGraph

tag: cell line

tag: cell type

tag: strain

tag: genetic modification

tag: treatment


title: TTchemSeq 15min recovery after h2o2 with OGG1i replicate 1 exp5

description: Library name: TT5_15_ogg1i_r1


title: L-fHP_39

description: Library name: 79050450

tag: diagnosis

tag: endotype

tag: Sex

tag: age blood_draw

tag: smoking history

value: Yes

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: HumanBrain-Tumor-WU1220-3

description: Formalin-fixed, paraffin-embedded (FFPE) tumor samples were sectioned into 5-um sections using a microtome onto Xenium slides according to Protocol CG000578 published by 10X Genomics. The Xenium slides were then deparaffinized and decrosslinked according to the Protocol CG000580. Both a pre-designed gene expression panel (Human Brain Probe set) and a custom probe set were used during probe hybridization, ligation, and amplification according to Protocol CG000749, which also contained cell segmentation staining. The Xenium slide was then loaded into the Xenium Analyzer using Protocol CG000584 and regions of interest (ROIs) were initially selected using the on-instrument software.

tag: gender

value: Male

tag: age

tag: tumor location

value: Left parietal-occipital

tag: tumor size

tag: mgmt methylation

value: Unmethylated

tag: egfr methylation

tag: patient id


title: L-fHP_64

description: Library name: 79091450

tag: cell type

tag: diagnosis

tag: endotype

tag: Sex

tag: medical center

tag: tissue


title: TTchemSeq 15min recovery after h2o2 with olaparib replicate 2 exp5

description: Library name: TT5_15_olaparib_r2

tag: cell line


title: Rex1-EmGFPd2 Control mESCs Replicate 1, BrdU-IP Early

value: embryonic stem cells

tag: strain

tag: genetic modification

tag: treatment


title: L-fHP_38

description: Library name: 79048950

tag: age blood_draw

tag: smoking history

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: transplant free_survival

tag: surv months


title: HumanBrain-Tumor-WU1220-01

tag: gender

tag: age

tag: tumor location

tag: tumor size

tag: mgmt methylation

tag: egfr methylation

tag: patient id


title: L-fHP_37

description: Library name: 79048850

tag: cell type

tag: diagnosis

tag: endotype

tag: Sex

tag: age blood_draw

tag: smoking history

tag: medical center

value: deadtx

tag: tissue


title: TTchemSeq 15min recovery after h2o2 with olaparib replicate 1 exp5

description: Library name: TT5_15_olaprib_r1

tag: cell line


title: Dppa2-EmGFPd2 ERCE del mESCs Replicate 2, BrdU-IP Late

description: DEP_01_037_3_del95_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph

tag: strain

tag: genetic modification

value: EmGFPd2 knockin at Dppa2 locus, ERCEs deletion

tag: treatment


title: HumanBrain-Tumor-ST073021-04

tag: gender

value: female

tag: age

tag: tumor location

value: Right frontal


title: Dppa2-EmGFPd2 ERCE del mESCs Replicate 2, BrdU-IP Early


title: L-fHP_36

description: Library name: 79048550

value: whole blood cells

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: transplant free_survival

tag: surv months


title: TTchemSeq 15min recovery after h2o2 replicate 2 exp5

description: Library name: TT5_15_dmso_r2

value: HEK293 Flp-in T-Rex


title: HumanBrain-Tumor-ST073021-02

tag: tumor size

tag: mgmt methylation

tag: egfr methylation

tag: patient id


title: Dppa2-EmGFPd2 ERCE del mESCs Replicate 1, BrdU-IP Late

tag: cell line

tag: cell type

tag: strain

tag: genetic modification

tag: treatment


title: TTchemSeq 15min recovery after h2o2 replicate 1 exp5

description: Library name: TT5_15_dmso_r1


title: L-fHP_35

description: Library name: 79045050

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: L-fHP

tag: Sex

tag: age blood_draw

tag: smoking history

tag: cigyears

tag: race

tag: medical center

tag: tissue


title: HumanBrain-Tumor-GBM025A

hyb_protocol: The Xenium slides were then deparaffinized and decrosslinked according to the Protocol CG000580. Both a pre-designed gene expression panel (Human Brain Probe set) and a custom probe set were used during probe hybridization, ligation, and amplification according to Protocol CG000749, which also contained cell segmentation staining. The Xenium slide was then loaded into the Xenium Analyzer using Protocol CG000584 and regions of interest (ROIs) were initially selected using the on-instrument software.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor samples were sectioned into 5-um sections using a microtome onto Xenium slides according to Protocol CG000578 published by 10X Genomics.

tag: gender

tag: age

tag: tumor location

value: Right temporal-parietal

tag: tumor size

tag: mgmt methylation


title: Dppa2-EmGFPd2 ERCE del mESCs Replicate 1, BrdU-IP Early

tag: cell line

tag: cell type

tag: strain


title: L-fHP_34

description: Library name: 79044950

tag: diagnosis

value: No

value: White

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: TTchemSeq treated (h2o2) with 1hour OGG1i and 1hour Olaparib replicate 2 exp5

description: Library name: TT5_no_double_r2


title: HumanBrain-Tumor-GBM026I

value: Left frontal

value: Methylated

tag: egfr methylation

tag: patient id


title: Dppa2-EmGFPd2 mESCs Replicate 2, BrdU-IP Late

description: DEP_01_037_1_con_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph

tag: genetic modification

value: EmGFPd2 knockin at Dppa2 locus

tag: treatment


title: L-fHP_33

description: Library name: 79043650

tag: endotype

tag: Sex

value: Female

tag: age blood_draw

tag: smoking history

tag: cigyears

tag: race

tag: medical center

tag: transplant free_survival

value: alive

tag: surv months

tag: tissue

value: venous blood


title: HumanBrain-Tumor-GBM034

tag: gender

value: Male

tag: age

tag: tumor location

value: Right occipital

tag: tumor size

tag: mgmt methylation

value: Unmethylated

value: Yes


title: L-fHP_32

description: Library name: 79040350

tag: cell type

value: whole blood cells

tag: diagnosis

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: deadtx


title: Dppa2-EmGFPd2 mESCs Replicate 2, BrdU-IP Early

tag: cell line

value: embryonic stem cells

tag: strain

tag: genetic modification

tag: treatment


title: TTchemSeq treated (h2o2) with 1hour OGG1i replicate 2 exp5

description: Library name: TT5_no_ogg1i_r2

value: HEK293 Flp-in T-Rex


title: TTchemSeq treated (h2o2) with 1hour OGG1i and 1hour Olaparib replicate 1 exp5

description: Library name: TT5_no_double_r1


title: HumanBrain-Tumor-GBM026M

tag: egfr methylation

tag: patient id


title: Dppa2-EmGFPd2 mESCs Replicate 1, BrdU-IP Late


title: HumanBrain-Tumor-GBM030

tag: gender

tag: age

value: Right temporal


title: L-fHP_31

description: Library name: 79040150

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: L-fHP

tag: Sex

tag: age blood_draw

tag: smoking history

value: No

tag: cigyears

tag: race

tag: medical center

tag: transplant free_survival

tag: surv months

tag: tissue


title: TTchemSeq treated (h2o2) with 1hour OGG1i replicate 1 exp5

description: Library name: TT5_no_ogg1i_r1

tag: cell line


title: Dppa2-EmGFPd2 mESCs Replicate 1, BrdU-IP Early

tag: cell type

tag: strain

tag: genetic modification


title: TTchemSeq treated (h2o2) with 1hour olaparib replicate 2 exp5

description: Library name: TT5_no_olaparib_r2


title: L-fHP_30

description: Library name: 79039750

tag: diagnosis

value: White

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: L-fHP_29

description: Library name: 79039150

tag: endotype

tag: Sex

tag: age blood_draw

tag: smoking history


title: HumanBrain-Tumor-GBM024I

tag: gender

tag: age

tag: tumor location

value: Right frontal

tag: tumor size

tag: mgmt methylation

tag: egfr methylation

tag: patient id


title: HumanBrain-Tumor-GBM024H


title: MOC2 cells, EphA4 knockout, Sample 3

city: Aurora

first: Sophia

last: Corbo

state: CO

address: 12801 E 17th ave, L18-4402E RC1 South/4th Floor

institute: University of Colorado-Denver (UCDenver) (Anschutz Medical Campus)

description:
Library name: MOC2_EphA4_S3
bulk RNA-Seq

data_processing:
Samples were sequenced on a Illumina NovaSeq 6000 sequencer as paired end 150bp reads and aligned with STAR aligner in gene counts mode.
Assembly: GRCm39
Supplementary files format and content: .tsv file containing bulk RNA-Seq raw counts

molecule: polyA RNA

growth_protocol: All cells were cultured at 37°C at 5% CO2. MOC2 cells were cultured in DMEM-F12:IMDM (1:2) (Gibco, Cat # 21-041-025) supplemented with 10% FBS (Fisherbrand, Cat # FB12999102) and 1% primocin/fungin (InvivoGen, Cat # ANTPM2), 1.75 µg EGF (Sigma Millipore, Cat # GF144), 20 µg hydrocortisone (Sigma, Cat # H0135-1MG), and 0.1% insulin (Suply Solutions, Cat # I9278-5ML). MOC2 control knockout and MOC2 EphA4 knockout H3 clone cell lines were harvested from T-75 (Fisherbrand Cat#: FB012939). Cells were thawed and passaged 2 times before being harvested for analysis.

extract_protocol:
RNA was extracted as follows. Cells were grown in a monolayer and 1 mL of TRI Reagent was added directed to flask and homogenized. Homogenate was supplemented with 0.1 ml BCP or 0.2 ml chloroform per 1 ml of TRI Reagent. The sample was then incubated at room temperature for 2-15 minutes and then centrifuged at 12,000 g for 14 minutes at 4C. Following centrifugation the aqueous phase was transferred to a fresh tube. The RNA was then precipitated from the aqueous phase with 0.5 mL of isopropanol per 1 mL of TRI Reagent used for the initial homogenization.
Libraries were constructed with a polyA-selection kit according to manufacturer's instructions

treatment_protocol: No treatments were applied.

tag: cell line

tag: cell type

value: HPV negative HNSCC

tag: genotype

value: EphA4 Knockout

tag: treatment

value: untreated

tag: batch


title: TTchemSeq treated (h2o2) with 1hour olaparib replicate 1 exp5

description: Library name: TT5_no_olaparib_r1


title: Mouse thoracic spine IVD spatial transcriptomics

city: Austin

first: Ryan

last: Gray

state: TX

address: 1400 Barbara Jordan Ave

department: Nutritional Sciences

institute: University of Texas at Austin

description:
Library name: IVD2
10x Genomics Visium Spatial Gene Expression (FFPE, probe-based) library IVD2 from mouse thoracic spine intervertebral disc. Slide V11A19-364 capture area D1. Both mutant and control tissue regions are present within this single capture area. Raw FASTQs: 8 files across two lanes (IVD2_S2_L001_* and IVD2_S2_L002_*) from run 220311_A00842_0226_BH5FJYDRX2. Space Ranger v1.3.1 count used both lanes (162,323,544 reads). Manual Loupe ROI outputs: https://github.com/xuziyi0909/Mouse_Spine_Intervertebral_Disc_SpatialTranscriptomics/tree/main/raw_data

data_processing:
All 8 IVD2 raw FASTQs (lanes L001 and L002) submitted with this GEO submission for SRA deposition by GEO staff. FASTQs processed with Space Ranger v1.3.1 (martian v4.0.5) using mm10-2020-A reference and Visium Mouse Transcriptome Probe Set v1.0.
Default Space Ranger auto-alignment used for the original IVD2 library with both lanes (162,323,544 reads). Manual Loupe ROI reruns on lane-2-only FASTQs are on GitHub.
Probe filtering and count matrices were generated with Space Ranger count. Filtered and raw feature-barcode matrices, spatial spot coordinates, and tissue images were exported from Space Ranger outs.
H&E image for capture area D1 provided as IVD2_D1.tif (V11A19-364-D1.tif).
Assembly: mm10-2020-A
Supplementary files format and content: IVD2_filtered_feature_bc_matrix.h5 IVD2_raw_feature_bc_matrix.h5 IVD2_tissue_positions_list.csv IVD2_tissue_hires_image.png IVD2_metrics_summary.csv IVD2_D1.tif IVD2_filtered_barcodes.tsv.gz IVD2_filtered_features.tsv.gz IVD2_filtered_matrix.mtx.gz
Supplementary files format and content: Manual ROI Space Ranger outputs for IVD2 Adgrg6-cKO vs wildtype control: https://github.com/xuziyi0909/Mouse_Spine_Intervertebral_Disc_SpatialTranscriptomics/tree/main/raw_data

source_name: Thoracic Spine

growth_protocol: Mouse thoracic spine tissues from Adgrg6-cKO mouse and wildtype control mouse was prepared for 10x Genomics Visium Spatial Gene Expression (FFPE) according to the manufacturer's protocol.

extract_protocol:
Total RNA was extracted from FFPE tissue sections on Visium slide V11A19-364 area D1 using the 10x Genomics Visium Spatial Gene Expression workflow with the Visium Mouse Transcriptome Probe Set v1.0 (mm10-2020-A).
Visium Spatial Gene Expression library IVD2 was prepared using the 10x Genomics Visium FFPE probe-based workflow and sequenced on an Illumina NovaSeq 6000 across two lanes (run 220311_A00842_0226_BH5FJYDRX2).

treatment_protocol: No drug treatment.

tag: tissue

value: Thoracic Spine

value: mixed

value: Adgrg6-cKO and Wildtype


title: TTchemSeq treated replicate 2 exp5

description: Library name: TT5_no_dmso_r2


title: MOC2 cells, EphA4 knockout, Sample 2

description:
Library name: MOC2_EphA4_S2
bulk RNA-Seq


title: HumanBrain-Tumor-GBM024E

value: Male

value: Unmethylated

value: Yes


title: L-fHP_28

description: Library name: 79038650

value: whole blood cells

tag: diagnosis

tag: endotype

value: Female

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival

value: alive

tag: surv months

value: venous blood


title: TTchemSeq treated replicate 1 exp5

description: Library name: TT5_no_dmso_r1

tag: cell line

value: HEK293 Flp-in T-Rex


title: L-fHP_27

description: Library name: 79037650

tag: cell type

value: Fibrotic hypersensitivity pneumonitis

value: L-fHP

tag: Sex

tag: age blood_draw

tag: smoking history

value: No


title: Rex1-EmGFPd2 Tbcc gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_45_Tbcc_7_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
16_Tbcc_mean_w200ks40k.bedGraph

value: embryonic stem cells

tag: strain

tag: genetic modification

value: EmGFPd2 knockin at Rex1 locus, Cas9 knockin at Rosa26 locus

tag: treatment

value: pU6-Tbcc-gRNA#2-CBA-PuroR transfection


title: HumanBrain-Tumor-GBM024D

tag: gender

tag: age

tag: tumor location

value: Right frontal

tag: tumor size

tag: mgmt methylation

tag: egfr methylation

tag: patient id


title: TTchemSeq Untreated (h2o2) with 1hour OGG1i and 1hour Olaparib replicate 2 exp5

description: Library name: TT5_unt_double_r2


title: MOC2 cells, Control CRISPR, Sample 3

description:
Library name: MOC2_Ctrl_KO_S3
bulk RNA-Seq

value: HPV negative HNSCC

tag: genotype

value: CRISPR Control

value: untreated

tag: batch


title: Cdc45-mAID G1-KD 5-Ph-IAA 15h ESCs Replicate 2, Hi-C

description: Library name: Sample257

data_processing:
Read pairs were individually mapped to the mouse genome (mm9) using the 4dn-hic pipeline (https://github.com/4dn-dcic/docker-4dn-hic). After mapping, the aligned reads were further processed to remove duplicates (https://github.com/mirnylab/pairtools) and obtain a set of filtered reads defined as valid pairs.
Valid pairs were binned into contact matrices at resolutions of 200 kb and then normalized using the cooler (Abdennur and Mirny, 2020). The bias-corrected contact heatmaps were used to generate the A/B compartment profiles (200-kb bins) in each chromosome and saddle plots using cooltools (https://github.com/open2c/cooltools).
Assembly: mm9
Supplementary files format and content: .cool
Supplementary files format and content: bigWig

extract_protocol:
Hi-C experiments were performed as previously reported with some modifications (Kadota et al., 2020). Cells were fixed with 1% formaldehyde for 10 min at room temperature. Glycine was added to 0.125 M final concentration and incubated for 5 min at room temperature. Tubes were placed on ice for 15 min. Cells were washed in ice-cold PBS by centrifuging at 400 g at 4°C. Then, 1–2 x 10^6 fixed cell pellets were used for the following steps. Cell pellets were resuspended in 400 µl of lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40) with 1x protease inhibitor cocktail (Roche, 11873580001), transferred to 1.5 ml Protein LoBind Tubes (Eppendorf) and incubated on ice for 20 min. The samples were spun down for 5 min at 1000 g at 4℃. After removing the supernatants carefully, pellets were resuspended in 250 µl of 1x NEBuffer 2 with 0.3% SDS and incubated for 1 h at 37°C in the Thermomixer C3 at 1100 rpm (Eppendorf). Then, 28 µl of 20% Triton X-100 were added to 2% final concentration and the samples were incubated for 1 h at 37°C. Next, 100 U of DpnIII (NEB, R0543S) was added and the samples were incubated overnight at 37°C in the Thermomixer C3 at 1100 rpm. The next day, after the inactivation of enzyme activity with 65˚C for 20 min, the samples were spun down for 5 min at 4°C. After removing the supernatants carefully, pellets were resuspended in 100 µl of “Biotin fill-in mix” (1 x NEBuffer 2, 15 µM each of dCTP, dGTP, dTTP and 15 µM of Biotin-14-dATP (Invitrogen, 19524-016), 15 U of Klenow (NEB, M0210S), 1% Triton X-100) and incubated for 45 min at 25°C. After spinning down for 5 min at 4°C and removing the supernatants carefully, the pellets were resuspended in 100 µl of “Ligation Mix” (1x T4 DNA ligase buffer (NEB), 6 µl of T4 DNA ligase (1 U/µl, Invitrogen, 15224-025), 1% Triton X-100) and incubated 6 hours at 16°C. The sample volumes were brought up to ~100 µl by adding 10 mM Tris-HCl (pH 8.0) / 5 mM EDTA and RNaseA-treated for 30 min at 37°C by adding 5 µl of 10 mg/ml RNaseA. Reverse-crosslinking and proteinase K treatment were performed overnight at 65°C by adding ""Reverse-crosslink Mix"" (1.5% SDS, 375 mM NaCl, 1 mg/ml Proteinase K). The next day, 5 µl of 20 mg/ml Proteinase K was added and incubated for 2 h at 55°C. Samples were then extracted twice with phenol/chloroform and once with chloroform. After this, 500 µl of 2-propanol was added. The samples were incubated for 10 min and spun down for 30 min at 20,000 g at 4°C for DNA precipitation. After 70% EtOH washes (add 1 ml, cfg for 5 min at 20,000 g at 4°C), the DNA pellets were resuspended in 30 µl of EB (QIAGEN, 19086).
For generating next-generation sequencing libraries, 1-2 µg of Hi-C DNA was used per library. To remove biotin from unligated ends, Hi-C DNA was mixed with 50 µl of “T4 DNA pol mix” (1x NEBuffer 2.1, 100 µM dATP, 100 µM dGTP, 2.5 U of T4 DNA polymerase (NEB, M0203S)) and incubated for 30 min at 37°C. The sample volumes were brought up to ~130 µl by adding TE buffer. DNA samples were sheared (300–500 bp) using the following settings in Covaris S220 (Duty Factor: 5.0, Peak incident power: 175 W, Cycles per burst: 200, Treatment time: 120 sec) using microTUBE with snap cap (Covaris, 520045). After DNA shearing, DNA size selection was performed using AMPure XP beads (Beckman Coulter). Using the size-selected DNA samples, biotin pull-down and sequencing library preparations were performed using 30 µl of Dynabeads M-280 Streptavidin (Invitrogen, 11206D) and a part of KAPA LTP kit (KAPA BIOSYSTEMS, KK8232) following the kit’s protocol. For library amplification, KAPA Real-Time Amplification Kits (KAPA BIOSYSTEMS, KK2701) were used to determine the optimal PCR cycles (5–8 cycles) and the final PCR products were purified by AMPure XP beads.

treatment_protocol: (1) Nocodazole treatment: nocodazole was added to the culture medium at a final concentration of 50 ng/ml for 7-10 hours, then G2/M cell population was sorted by cell sorter based on the relative levels of Propidium iodide. (2) Thymidine treatment: after nocodazole treatment, cells were released to G1 phase with thymidine at a final concentration of 2.5 mM for certain time, then G1 population was sorted. (3) 5-Ph-IAA treatment: after nocodazole treatment, cells were released to G1 phase with 5-Ph-IAA at a final concentration of 1 µM for certain time, then G1 population was sorted.

tag: cell line

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Cdc45

value: 5-Ph-IAA treatment 15h, G1 sort


title: L-fHP_26

description: Library name: 79037550

tag: cell type

value: whole blood cells

tag: diagnosis

tag: endotype

tag: cigyears

tag: race

value: White

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival

tag: surv months

tag: tissue


title: TTchemSeq Untreated (h2o2) with 1hour OGG1i and 1hour Olaparib replicate 1 exp5

description: Library name: TT5_unt_double_r1


title: L-fHP_25

description: Library name: 79037250

tag: Sex

value: Male

tag: age blood_draw

tag: smoking history

value: deadtx


title: MOC2 cells, EphA4 knockout, Sample 1

description:
Library name: MOC2_EphA4_S1
bulk RNA-Seq

tag: cell line

tag: cell type

tag: genotype

value: EphA4 Knockout

tag: treatment

tag: batch


title: MOC2 cells, Control CRISPR, Sample 2

description:
Library name: MOC2_Ctrl_KO_S2
bulk RNA-Seq


title: Cdc45-mAID G1-KD 5-Ph-IAA 15h ESCs Replicate 1, Hi-C

description: Library name: Sample256


title: TTchemSeq Untreated (h2o2) with 1hour OGG1i replicate 2 exp5

description: Library name: TT5_unt_ogg1i_r2

value: HEK293 Flp-in T-Rex


title: L-fHP_24

description: Library name: 79036350

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: L-fHP

value: Yes

tag: cigyears

tag: race

tag: fvc pred

value: venous blood


title: Cdc45-mAID G1-Control Thymidine 15h ESCs Replicate 2, Hi-C

description: Library name: Sample255

value: embryonic stem cells

value: Thymidine treatment 15h, G1 sort


title: MOC2 cells, Control CRISPR, Sample 1

description:
Library name: MOC2_Ctrl_KO_S1
bulk RNA-Seq

value: HPV negative HNSCC


title: TTchemSeq Untreated (h2o2) with 1hour OGG1i replicate 1 exp5

description: Library name: TT5_unt_ogg1i_r1


title: Rex1-EmGFPd2 Tbcc gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_43_Tbcc_5_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
16_Tbcc_mean_w200ks40k.bedGraph

tag: strain

tag: genetic modification

value: EmGFPd2 knockin at Rex1 locus, Cas9 knockin at Rosa26 locus

value: pU6-Tbcc-gRNA#1-CBA-PuroR transfection


title: Cdc45-mAID G1-Control Thymidine 15h ESCs Replicate 1, Hi-C

description: Library name: Sample254

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Cdc45


title: L-fHP_23

description: Library name: 79036050

value: Female

value: No

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival

value: alive

tag: surv months


title: Merged_Gins4-mAID G1-KD 5-Ph-IAA 15h ESCs Replicate 2, Hi-C

description:
Library name: Sample253
merged file

tag: cell line

tag: cell type

tag: genotype

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA treatment 15h, G1 sort


title: periosteum, day7, grafted, rep2

city: Rochester

first: Jared

last: Mereness

state: New York

address: 204 Robert B. Goergen Hall, Department of Biomedical Engineering, Box 270168

department: Biomedical Engineering

institute: University of Rochester

description: Library name: Sample_S9

library_source: transcriptomic single cell

data_processing:
Samples were demultiplexed using ‘cellranger mkfastq’ within 10× cellranger-8.0.0, using the default parameters
Samples were aligned to 10× provided reference refdata-gex-GRCmm10–2020-A-GFP using ‘cellranger count’ within cellranger-8.0.0 using default parameters
Assembly: 10x refdata-gex-GRCmm10–2020-A-GFP
Supplementary files format and content: barcodes.tsv.gz MEX barcodes
Supplementary files format and content: features.tsv.gz MEX features
Supplementary files format and content: matrix.mtx.gz MEX matrix

source_name: Periosteum

extract_protocol:
Femurs were harvested, and ends were cut. Bone marrow was flushed and incubated with red blood cell lysis buffer for 5 min at room temperature, followed by digestion in 1 mg/mL collagenase type IV (Sigma), 2 mg/mL dispase (Sigma), and 10 U/mL DNase (Thermo Scientific) for 45 min at 37 °C. Bone tissue was crushed into small pieces and digested in 0.7 mg/mL collagenase type I (Sigma) for 1.5 h.  Both bone marrow and bone-associated cells were passed through 100 μm cell strainers (Fisher) to form single-cell suspensions and combined for analyses. Cell suspensions (N=2–3, n=1 per sample) were stained with 10 μg/ml of DAPI for 3–5 min. Cells were sorted using a BD Symphony S6 cell sorter. Cells negative for DAPI were considered viable and were retained for bulk RNA sequencing. Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA).
150 pg of cDNA was used to generate Illumina-compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols

tag: tissue

value: Periosteum

tag: treatment

value: grafted


title: L-fHP_22

description: Library name: 79033150

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

tag: Sex

value: Male

tag: age blood_draw

tag: smoking history

tag: cigyears

value: White

value: deadtx


title: TTchemSeq Untreated (h2o2) with 1hour olaparib replicate 2 exp5

description: Library name: TT5_unt_parp_r2

value: HEK293 Flp-in T-Rex


title: TTchemSeq Untreated (h2o2) with 1hour olaparib replicate 1 exp5

description: Library name: TT5_unt_parp_r1


title: periosteum, day7, grafted, rep1

description: Library name: Sample_S8


title: L-fHP_21

description: Library name: 79032550

value: L-fHP

value: Yes

tag: race

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

value: venous blood


title: Merged_Gins4-mAID G1-KD 5-Ph-IAA 15h ESCs Replicate 1, Hi-C

description:
Library name: Sample252
merged file

value: embryonic stem cells


title: TTchemSeq Untreated replicate 2 exp5

description: Library name: TT5_unt_dmso_r2


title: L-fHP_20

description: Library name: 79031750

value: Female

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival


title: periosteum, day7, control, rep1

description: Library name: Sample_S7

value: control


title: periosteum, day14, grafted, rep2

description: Library name: Sample_S6


title: Merged_Gins4-mAID G1-Control Thymidine 15h ESCs Replicate 2, Hi-C

description:
Library name: Sample251
merged file

tag: cell line

tag: cell type

tag: genotype

value: Thymidine treatment 15h, G1 sort


title: TTchemSeq Untreated replicate 1 exp5

description: Library name: TT5_unt_dmso_r1


title: L-fHP_19

description: Library name: 79030750

tag: diagnosis

value: No

value: alive

tag: surv months

tag: tissue


title: L-fHP_18

description: Library name: 79029550

tag: endotype

tag: Sex

tag: age blood_draw


title: TTchemSeq 1 hour recovery after h2o2 in XRCC1 KO8 with olaparib replicate 2 exp4

description: Library name: TT4_min60_xrcc1_8_olaparib

source_name: HEK293 Flp-in T-Rex XRCC1 KO#8

value: HEK293 Flp-in T-Rex XRCC1 KO#8


title: periosteum, day14, grafted, rep1

description: Library name: Sample_S5

value: Periosteum

tag: treatment

value: grafted


title: Merged_Gins4-mAID G1-Control Thymidine 15h ESCs Replicate 1, Hi-C

description:
Library name: Sample250
merged file

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 16

description: Library name: Sample349

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 genome. As mESCs tend to have karyotype abnormality on chr 8 and chr 11, these chromosomed were removed from the reference genome.
Duplicated reads were filtered out.
For quality control of scRepli-seq data, we applied median-absolute-deviation (MAD) score evaluation to filter out cells with problematic RT (MAD scores = 0 or >1.0).
For generating log2[(mappability-corrected S-phase reads)/median] scores (log2median RT score) to obtain single-cell RT profiles using cells that passed MAD score evaluation, we counted the reads in sliding windows of 200-kb at 40-kb intervals after normalizing S-phase data with AneuFinder’s correctMappability command based on G1 control without karyotype defects in each strain. (Miura et al., 2020).
The binarization for each 80-kb was performing find CNVs command in AneuFinder (Miura et al., 2020). We applied the 1-somy mode for early S-phase cells. Repliscore as a percentage of replicated bins in the total number of replicated and unreplicated bins was calculated from binarized scRepli-seq data (Miura et al., 2020).
Assembly: mm9
Supplementary files format and content: Binarized bedGraph
Supplementary files format and content: Log2median bedGraph

extract_protocol:
We followed the scRepli-seq protocol as described (Miura et al., 2020). Early-S phase cell population were sorted by a Sony SH800 cell sorter (thymidine/5-Ph-IAA removed cells: ultra-purity mode, G1/early-S cells: single-cell mode). Thymidine/5-Ph-IAA removed cells were manually collected after EdU signal observation and cells were transferred into lysis buffer using mouth pipette. G1/early-S cells were directly sorted into lysis buffer.
Extracted gDNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed WGA DNA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions.

treatment_protocol: Cells were synchronized at the G1/S boundary by treating with 2.5 mM thymidine for 12 hours. After thymidine release, late-replicating DNA was pulse-labeled with EdU, followed by mitotic arrest using 50 ng/ml nocodazole. Nocodazole was replaced with 5-Ph-IAA solution, and cells were cultured for 15 hours, then switched to normal medium for an additional 4 hours. EdU and DNA were stained using Click-iT Plus EdU Alexa Fluor 594 Imaging Kit (Invitrogen) and  FxCycle™ Violet Stain (Invitrogen), respectively, then early-S phase cells were sorted, and EdU signals were observed. Selected cells were manually picked for library preparation using mouth pipette under the microscopy.

value: EarlyS sort


title: periosteum, day14, control, rep1

description: Library name: Sample_S4


title: TTchemSeq 1 hour recovery after h2o2 in XRCC1 KO3 with olaparib replicate 1 exp4

description: Library name: TT4_min60_xrcc1_2_olaparib

source_name: HEK293 Flp-in T-Rex XRCC1 KO#3

value: HEK293 Flp-in T-Rex XRCC1 KO#3


title: L-fHP_17

description: Library name: 79029450

value: whole blood cells

value: Fibrotic hypersensitivity pneumonitis

value: Male

tag: smoking history

tag: cigyears

tag: race

value: Asian

tag: fvc pred


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 15

description: Library name: Sample348


title: periosteum, day1, grafted, rep2

description: Library name: Sample_S3


title: TTchemSeq 1 hour recovery after h2o2 in XRCC1 KO8 replicate 2 exp4

description: Library name: TT4_min60_xrcc1_8


title: L-fHP_16

description: Library name: 79028750

value: L-fHP

value: White

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: venous blood


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 14

description: Library name: Sample347

tag: cell line

tag: cell type

value: embryonic stem cells


title: periosteum, day1, grafted, rep1

description: Library name: Sample_S2


title: TTchemSeq 1 hour recovery after h2o2 in XRCC1 KO3 replicate 1 exp4

description: Library name: TT4_min60_xrcc1_2


title: L-fHP_15

description: Library name: 79026651

tag: diagnosis

value: Female

tag: medical center

tag: transplant free_survival


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 13

description: Library name: Sample346

tag: genotype


title: TTchemSeq 1 hour recovery after h2o2 with olaparib replicate 2 exp4

description: Library name: TT4_min60_olaparib-r2

value: HEK293 Flp-in T-Rex


title: periosteum, day1, control, rep1

description: Library name: Sample_S1

tag: tissue

value: control


title: L-fHP_14

description: Library name: 79026450

tag: endotype

tag: Sex

tag: age blood_draw

value: Yes

value: alive

tag: surv months


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 11

description: Library name: Sample345

tag: treatment


title: S 3

city: Xi'an

first: xiao

last: yu

state: Shaanxi

address: Innovation Harbor Campus, Xi'an Jiaotong University, Chang'an District

country: China

institute: Xi'an Jiaotong University

description:
Library name: Sample 6
low-input RNA-seq(Smart-seq2)

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: FPKM, count values for each Sample

source_name: bone marrow

extract_protocol:
100 bone marrow hematopoietic stem cells (HSCs)  were sorted into 96-well plates containing low-input lysis buffer (0.1% Triton X-100, 40 U/μL RNase inhibitor) and stored at -80°C. Total RNA was extracted using the RNeasy Micro Kit (Qiagen) following the manufacturer’s low-input RNA extraction protocol. RNA quantity was measured with the Qubit RNA HS Assay Kit (Thermo Fisher), with RNA input ≥10 pg per sample.
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribe™ Reverse Transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5’ end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand,indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

value: bone marrow

value: sorted HSC

value: Piezo1 cKO


title: TTchemSeq 1 hour recovery after h2o2 with  olaparib replicate 1 exp4

description: Library name: TT4_min60_olaparib-r1


title: L-fHP_13

description: Library name: 79026150

tag: smoking history

tag: cigyears

tag: race

tag: fvc pred

value: deadtx


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 10

description: Library name: Sample344

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: EarlyS sort


title: S 2

description:
Library name: Sample 5
low-input RNA-seq(Smart-seq2)


title: TTchemSeq 1 hour recovery after h2o2 replicate 2 exp4

description: Library name: TT4_min60_dmso_r2


title: L-fHP_12

description: Library name: 79024250

value: whole blood cells

value: Fibrotic hypersensitivity pneumonitis

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: S 1

description:
Library name: Sample 4
low-input RNA-seq(Smart-seq2)

tag: cell type


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 09

description: Library name: Sample343

tag: cell line


title: TTchemSeq 1 hour recovery after h2o2 replicate 1 exp4

description: Library name: TT4_min60_dmso_r1


title: L-fHP_11

description: Library name: 79023250

tag: diagnosis

value: L-fHP

value: Male

tag: medical center

tag: transplant free_survival


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 08

description: Library name: Sample342

tag: genotype


title: WT 3

description:
Library name: Sample 3
low-input RNA-seq(Smart-seq2)

tag: tissue

value: WT


title: KDM2B-mAID_J2_7_DMSO_3

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description:
Library name: KDM2B-mAID_J2_7_DMSO_3
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx

data_processing:
Single-end reads obtained from treated cells were analyzed with Strand Avadis NGS (v3.0) software (Strand Life Sciences Pvt. Ltd). The STAR aligner was used in two-pass mode with default settings to map the obtained paired-end reads from treated cells to the hg38 reference genome. Alternatively, raw reads were trimmed using TrimGalore v.0.6.7. Using the DESeq2 package, the data was normalized and differentially expressed genes (DEGs) were found. Genes with an adjusted p-value < 0.05 and log2FoldChanges > < 0.585 were found to be differentially expressed and were used in further analysis.
Assembly: hg38
Supplementary files format and content: RNAseqcount text file which includes expression values for each sample fo each gene

extract_protocol:
For RNA sequencing total RNA was extracted from cells, using the RNeasy Mini Kit from Qiagen (Venlo, The Netherlands) according to the manufacturer’s recommendations.
RNA samples were qualified by automated gel electrophoresis on the 2200 TapeStation System (Agilent Technologies). Using KAPA RNA HyperPrep kit with riboErase (HMR) from Roche Sequencing and Life Sciences, cDNAs were synthesized from fragmented RNA and the sequences library were generated, according to the manufacturer’s recommendations. These libraries were then sequenced on an Illumina NextSeq500 using standard settings and the single-end reads obtained from treated cells were analyzed with Strand Avadis NGS (v3.0) software (Strand Life Sciences Pvt. Ltd). The STAR aligner was used in two-pass mode with default settings to map the obtained paired-end reads from treated cells to the hg38 reference genome. Alternatively, RNA-seq libraries were prepared using the Smart-3SEQ protocol from 100 ng of total RNA input, as previously described at IPsomics (https://ipsomics.com/). Next, libraries were pooled and sequenced using an Illumina NovaSeqX plus 150PE at Novogene (10B flow cell). Raw reads were trimmed using TrimGalore v.0.6.7. Using the DESeq2 package, the data was normalized and differentially expressed genes (DEGs) were found. Genes with an adjusted p-value < 0.05 and log2FoldChanges > < 0.585 were found to be differentially expressed and were used in further analysis.

value: DMSO


title: TTchemSeq 30min recovery after h2o2 in XRCC1 KO8 with olaparib replicate 2 exp4

description: Library name: TT4_min30_xrcc1_8_olaparib

value: HEK293 Flp-in T-Rex XRCC1 KO#8


title: L-fHP_10

description: Library name: 79020550

tag: endotype

tag: Sex

value: Female

tag: age blood_draw

value: White

tag: surv months

value: venous blood


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 04

description: Library name: Sample341

value: embryonic stem cells

tag: treatment


title: WT 2

description:
Library name: Sample 2
low-input RNA-seq(Smart-seq2)

value: bone marrow


title: TTchemSeq 30min recovery after h2o2 in XRCC1 KO3 with olaparib replicate 1 exp4

description: Library name: TT4_min30_xrcc1_2_olaparib

value: HEK293 Flp-in T-Rex XRCC1 KO#3


title: L-fHP_9

description: Library name: 79011750

tag: smoking history

value: Yes

tag: cigyears

tag: race

tag: fvc pred

value: alive


title: WT 1

description:
Library name: Sample 1
low-input RNA-seq(Smart-seq2)

value: sorted HSC


title: L-fHP_8

description: Library name: 79011151

value: No

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 02

description: Library name: Sample339

tag: cell line

tag: cell type

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: EarlyS sort


title: TTchemSeq 30min recovery after h2o2 in XRCC1 KO8 replicate 2 exp4

description: Library name: TT4_min30_xrcc1_8


title: Gins4-mAID asy earlyS-sorted ESCs scRepli-seq 03

description: Library name: Sample340

tag: genotype


title: NPC3

description: Library name: Sample 9

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: counts, FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

tag: tissue

value: NPC


title: L-fHP_7

description: Library name: 79003950

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: L-fHP

value: Male

value: Asian

tag: medical center

tag: transplant free_survival

value: deadtx


title: TTchemSeq 30min recovery after h2o2 in XRCC1 KO3 replicate 1 exp4

description: Library name: TT4_min30_xrcc1_2


title: Gins4-mAID asy G1-sorted control ESCs scRepli-seq 04

description: Library name: Sample338

tag: treatment

value: G1 sort


title: NPC2

description: Library name: Sample 8


title: TTchemSeq 30min recovery after h2o2 with olaparib replicate 2 exp4

description: Library name: TT4_min30_olaparib-r2

value: HEK293 Flp-in T-Rex


title: L-fHP_6

description: Library name: 77905343

tag: Sex

tag: age blood_draw

tag: smoking history

value: White

tag: surv months

value: venous blood


title: NPC1

description: Library name: Sample 7

value: bone marrow


title: Gins4-mAID asy G1-sorted control ESCs scRepli-seq 02

description: Library name: Sample337

value: embryonic stem cells


title: TTchemSeq 30min recovery after h2o2 with olaparib replicate 1 exp4

description: Library name: TT4_min30_olaparib-r1


title: L-fHP_5

description: Library name: 77903593

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

value: alive


title: Gins4-mAID asy G1-sorted control ESCs scRepli-seq 01

description: Library name: Sample336


title: NC3

description: Library name: Sample 6

value: NC


title: TTchemSeq 30min recovery after h2o2 replicate 2 exp4

description: Library name: TT4_min30_dmso_r2


title: L-fHP_4

description: Library name: 77903543

value: No

tag: race

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 33

description: Library name: Sample335

tag: cell line

tag: cell type

tag: genotype

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: NC2

description: Library name: Sample 5

tag: tissue


title: L-fHP_3

description: Library name: 77902143

value: whole blood cells

tag: diagnosis

tag: endotype

value: Female

tag: medical center

tag: transplant free_survival


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 32

description: Library name: Sample334

tag: treatment


title: WT3

description: Library name: Sample 3

value: WT


title: L-fHP_2

description: Library name: 77901343

value: Fibrotic hypersensitivity pneumonitis

value: L-fHP

tag: Sex

tag: age blood_draw

tag: smoking history

value: Yes

tag: surv months


title: TTchemSeq 15min recovery after h2o2 in XRCC1 KO8 with olaparib replicate 2 exp4

description: Library name: TT4_min15_xrcc1_8_olaparib

value: HEK293 Flp-in T-Rex XRCC1 KO#8


title: TTchemSeq 30min recovery after h2o2 replicate 1 exp4

description: Library name: TT4_min30_dmso_r1

value: HEK293 Flp-in T-Rex


title: TTchemSeq 15min recovery after h2o2 in XRCC1 KO3 with olaparib replicate 1 exp4

description: Library name: TT4_min15_xrcc1_2_olaparib

value: HEK293 Flp-in T-Rex XRCC1 KO#3


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 30

description: Library name: Sample333


title: NC1

description: Library name: Sample 4


title: L-fHP_1

description: Library name: 77901093

value: Male

tag: cigyears

tag: race

value: White

tag: fvc pred

tag: fvc+pred pct

value: venous blood


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 29

description: Library name: Sample332

tag: cell line

value: embryonic stem cells


title: WT2

description: Library name: Sample 2

value: bone marrow


title: N-fHP_38

description: Library name: 79118350

tag: cell type

value: N-fHP

value: No

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: deadtx


title: TTchemSeq 15min recovery after h2o2 in XRCC1 KO8 replicate 2 exp4

description: Library name: TT4_min15_xrcc1_8


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 28

description: Library name: Sample331

tag: genotype

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: WT1

description: Library name: Sample 1

tag: tissue

value: WT


title: TTchemSeq 15min recovery after h2o2 in XRCC1 KO3 replicate 1 exp4

description: Library name: TT4_min15_xrcc1_2


title: N-fHP_37

description: Library name: 79112450

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: Female

tag: medical center

tag: transplant free_survival


title: TTchemSeq 15min recovery after h2o2 with olaparib replicate 2 exp4

description: Library name: TT4_min15_olaparib-r2


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 27

description: Library name: Sample330

tag: treatment


title: TTchemSeq 15min recovery after h2o2 with olaparib replicate 1 exp4

description: Library name: TT4_min15_olaparib-r1


title: Viseral adipose tissue NM1 KO, Replicate 3

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

description: Library name: Sample 6

data_processing:
Subsequent analysis, including quality trimming, was executed using the BioSAILs workflow execution system. Trimmomatic (version 0.36) was used for quality trimming of the raw reads to get rid of low-quality bases, systematic base-calling errors and sequencing adapter contamination(Bolger et al., 2014). The quality of the sequenced reads pre/post quality trimming was assessed by FastQC and only the reads that passed quality trimming in pairs were selected for downstream analysis (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The quality-trimmed RNA-Seq reads were aligned to the Mus musculus GRCm38 (mm10) genome using HISAT2 (version 2.0.4)(Kim et al., 2015). The conversion and sorting of SAM alignment files for each sequenced sample to BAM format were done by using SAMtools (version 0.1.19)(Li et al., 2009). The BAM alignment files were processed using HTseq-count, using the reference annotation file to produce raw counts for each sample.
Assembly: GRCm38 (mm10)
Supplementary files format and content: txt files (.txt)

source_name: Viseral adipose tissue

growth_protocol: Wild type and NM1 KO C57/Bl6 mice (18 months old) were used for the analysis. The mice were housed in a pathogen-free sterile ventilation system supplied with sterile woodchip and ad libitum feed and water supply. Mice were kept in a room maintained at a temperature of 21-24 °C on a schedule of 12 h light/dark cycle. All animal experiments were performed after approval by the NYUAD-IACUC (Protocol 20-004).

extract_protocol:
Adipose was isolated from euthanized mice and cleaned from surrounding connective tissue. Approximately 5mm3 of tissue from the tip of the viseral adipose tissue from abdominal region was merged in RNAzol and homogenized in bead mill homogenizer followed by standard RNA isolation protocol. The final RNA concentration was measured by the Qubit RNA BR Assay Kit.
Three replicates were prepared for each genotype. 500ng of total RNA was used for the RNA-Seq library preparation by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with the NextSeq 500/550 sequencing platform (performed at the NYUAD Sequencing Center).

value: Viseral adipose tissue

value: NM1 KO

value: no treatment


title: N-fHP_36

description: Library name: 79112050

tag: Sex

value: Male

tag: age blood_draw

tag: smoking history

value: Asian

value: alive

tag: surv months


title: Viseral adipose tissue NM1 KO, Replicate 2

description: Library name: Sample 5


title: N-fHP_35

description: Library name: 79109850

tag: cigyears

tag: race

value: White

tag: fvc pred

tag: fvc+pred pct

value: venous blood


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 24

description: Library name: Sample328

tag: cell line

tag: cell type

value: embryonic stem cells


title: Viseral adipose tissue NM1 KO, Replicate 1

description: Library name: Sample 4

tag: genotype


title: TTchemSeq 15min recovery after h2o2 replicate 2 exp4

description: Library name: TT4_min15_dmso_r2

value: HEK293 Flp-in T-Rex


title: N-fHP_34

description: Library name: 79106550

value: N-fHP

value: No

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: tissue


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 23

description: Library name: Sample327

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: Viseral adipose tissue  WT, Replicate 3

description: Library name: Sample 3

value: WT


title: TTchemSeq 15min recovery after h2o2 replicate 1 exp4

description: Library name: TT4_min15_dmso_r1


title: N-fHP_33

description: Library name: 79102650

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: Yes

tag: medical center

tag: transplant free_survival

value: deadtx


title: TTchemSeq treated (h2o2) in XRCC1 KO8 with 1hour olaparib replicate 2 exp4

description: Library name: TT4_treated_xrcc1_8_olaparib

value: HEK293 Flp-in T-Rex XRCC1 KO#8


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 22

description: Library name: Sample326

tag: treatment


title: N-fHP_32

description: Library name: 79098950

tag: Sex

value: Female

tag: age blood_draw

tag: smoking history

tag: surv months


title: Viseral adipose tissue WT, Replicate 2

description: Library name: Sample 2

value: Viseral adipose tissue

value: no treatment


title: Viseral adipose tissue WT, Replicate 1

description: Library name: Sample 1


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 21

description: Library name: Sample325


title: TTchemSeq treated (h2o2) in XRCC1 KO3 with 1hour olaparib replicate 1 exp4

description: Library name: TT4_treated_xrcc1_2_olaparib

value: HEK293 Flp-in T-Rex XRCC1 KO#3


title: N-fHP_31

description: Library name: 79098250

tag: cigyears

tag: race

value: White

tag: fvc pred

tag: fvc+pred pct

value: alive

value: venous blood


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 20

description: Library name: Sample324

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype


title: TTchemSeq treated in XRCC1 KO8 replicate 2 exp4

description: Library name: TT4_treated_xrcc1_8


title: Con TAC M #5

city: Birmingham

first: Samuel

middle: F

last: Chang

state: Alabama

institute: University of Alabama Heersink School of Medicine

description: Library name: dnOGAh-F40-08

data_processing:
Quality control of fastq files assessed via FastQC (0.11.7-Java-1.8.0_74) and MultiQC (0.8)
Reads were aligned to the mouse genome (GRCm39) via STAR (2.7.3a-GCC-6.4.0-2.28) and Salmon Quantification (1.8.0-gompi-2020b)
Performed quality control on all output files from STAR and Salmon via MultiQC (0.8)
Using R software (v4.3.1) on R-studio (2024.12.0+467), DESeq2 perform differential gene expression based on a negative binomial generalized linear model.
Assembly: GRCm39
Supplementary files format and content: Excel spreadsheet file includes normalized counts as given by DESeq2 for each sample and gene

source_name: Left ventricle

extract_protocol:
RNA was extracted usinhg RNAeasy Fibrous Tissue Minikit (Qiagen) according to manufacturer protocol
"NGS Stranded RNA Library Prep" performed by the UAB Heflin Center for Genomic Sciences, Genomics Core Lab

treatment_protocol: Left Ventricle tissue was harvested from Control or dnOGAh mice following 2 weeks of Doxycycline food treatment then switch back to standard chow diet; 2 weeks after switch back to standard chow, mice recieved either transverse aortic constriction (TAC) or sham surgery. Mice were under TAC or sham for 9 weeks.

tag: tissue

value: Left ventricle

tag: strain

value: FVB/NJ

value: M

value: Con

value: TAC


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 17

description: Library name: Sample323

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: N-fHP_30

description: Library name: 79090550

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: N-fHP

value: Male

value: Yes

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: deadtx


title: Con Sham M #5

description: Library name: dnOGAh-F38-57

tag: Sex

tag: treatment

value: Sham


title: TTchemSeq treated in XRCC1 KO3 replicate 1 exp4

description: Library name: TT4_treated_xrcc1_2

value: HEK293 Flp-in T-Rex XRCC1 KO#3


title: N-fHP_29

description: Library name: 79090250

tag: age blood_draw

tag: smoking history

value: No

value: White

tag: medical center

tag: transplant free_survival

tag: surv months

value: venous blood


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 16

description: Library name: Sample322

tag: cell line

value: embryonic stem cells


title: ONOFF Sham M #5

description: Library name: dnOGAh-F38-56

value: Left ventricle

value: FVB/NJ

value: M

value: ONOFF


title: N-fHP_28

description: Library name: 79088950

tag: cell type

value: Female

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct


title: TTchemSeq treated (h2o2) with 1hour olaparib replicate 2 exp4

description: Library name: TT4_treated_olaparib-r2

value: HEK293 Flp-in T-Rex


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 15

description: Library name: Sample321

tag: genotype

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: TTchemSeq treated (h2o2) with 1hour olaparib replicate 1 exp4

description: Library name: TT4_treated_olaparib-r1


title: Con TAC F #5

description: Library name: dnOGAh-F38-30

tag: tissue

tag: strain

value: F

value: Con

value: TAC


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 14

description: Library name: Sample320


title: N-fHP_27

description: Library name: 79086950

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: N-fHP

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: deadtx


title: Con Sham F #5

description: Library name: dnOGAh-F38-28

tag: Sex

tag: treatment

value: Sham


title: TTchemSeq treated replicate 2 exp4

description: Library name: TT4_treated_dmso_r2


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 13

description: Library name: Sample319

value: embryonic stem cells


title: N-fHP_26

description: Library name: 79085750

value: Male

tag: age blood_draw

tag: smoking history

value: No

value: White

tag: medical center

tag: transplant free_survival

value: alive

tag: surv months

value: venous blood


title: ONOFF Sham F #5

description: Library name: dnOGAh-F38-27

value: Left ventricle

value: FVB/NJ

value: ONOFF


title: TTchemSeq treated replicate 1 exp4

description: Library name: TT4_treated_dmso_r1

tag: cell line

value: HEK293 Flp-in T-Rex


title: ONOFF TAC M #5

description: Library name: dnOGAh-F38-08

value: M


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 12

description: Library name: Sample318

tag: cell type

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: N-fHP_24

description: Library name: 79081650

value: whole blood cells

value: Fibrotic hypersensitivity pneumonitis

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct


title: TTchemSeq Untreated (h2o2) in XRCC1 KO8 with 1hour olaparib replicate 2 exp4

description: Library name: TT4_unt_xrcc1_8_olaparib

value: HEK293 Flp-in T-Rex XRCC1 KO#8


title: N-fHP_25

description: Library name: 79082550

tag: diagnosis

tag: endotype

value: N-fHP

value: Female

value: deadtx

tag: tissue


title: ONOFF Sham M #4

description: Library name: dnOGAh-F38-06

tag: strain

tag: genotype

value: Sham


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 11

description: Library name: Sample317

value: embryonic stem cells

tag: treatment


title: N-fHP_23

description: Library name: 79074150

tag: Sex

value: Male

tag: age blood_draw

value: Yes

value: Asian

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: alive


title: TTchemSeq Untreated (h2o2) in XRCC1 KO3 with 1hour olaparib replicate 1 exp4

description: Library name: TT4_unt_xrcc1_2_olaparib

tag: cell line

value: HEK293 Flp-in T-Rex XRCC1 KO#3


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 09

description: Library name: Sample316

tag: cell type


title: ONOFF TAC F #5

description: Library name: dnOGAh-F37-37

value: Left ventricle

value: FVB/NJ

value: F

value: ONOFF

value: TAC


title: N-fHP_22

description: Library name: 79071751

value: whole blood cells

value: Fibrotic hypersensitivity pneumonitis

tag: smoking history

value: No

tag: cigyears

value: White

tag: medical center

tag: transplant free_survival

tag: surv months

value: venous blood


title: TTchemSeq Untreated in XRCC1 KO8 replicate 2 exp4

description: Library name: TT4_unt_xrcc1_8

value: HEK293 Flp-in T-Rex XRCC1 KO#8


title: Con Sham F #4

description: Library name: dnOGAh-F37-35

value: Con

value: Sham


title: TTchemSeq Untreated in XRCC1 KO3 replicate 1 exp4

description: Library name: TT4_unt_xrcc1_2


title: Con TAC M #4

description: Library name: dnOGAh-F36-14

value: M


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 07

description: Library name: Sample315

value: embryonic stem cells

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: TTchemSeq Untreated (h2o2) with 1hour olaparib replicate 2 exp4

description: Library name: TT4_unt_olaparib-r2

value: HEK293 Flp-in T-Rex


title: N-fHP_20

description: Library name: 79064950

tag: diagnosis

tag: endotype

value: N-fHP

value: Female

value: Yes

tag: race

tag: fvc pred

tag: fvc+pred pct

value: alive


title: N-fHP_21

description: Library name: 79070750

value: whole blood cells

tag: Sex

value: Male

tag: tissue


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 06

description: Library name: Sample314

tag: genotype

tag: treatment


title: Con TAC M #3

description: Library name: dnOGAh-F36-13

value: Left ventricle

tag: strain

value: FVB/NJ

value: TAC


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 05

description: Library name: Sample313

tag: cell line


title: TTchemSeq Untreated (h2o2) with 1hour olaparib replicate 1 exp4

description: Library name: TT4_unt_olaparib-r1


title: N-fHP_19

description: Library name: 79059450

tag: cell type

value: Fibrotic hypersensitivity pneumonitis

tag: age blood_draw

value: White

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: deadtx

value: venous blood


title: 41461_5_EV_5_Ph_IAA_A14

description: Library name: 41461_5_EV_5_Ph_IAA_A14

data_processing:
Single-end reads obtained from treated cells were analyzed with Strand Avadis NGS (v3.0) software (Strand Life Sciences Pvt. Ltd). The STAR aligner was used in two-pass mode with default settings to map the obtained paired-end reads from treated cells to the hg38 reference genome. Using the DESeq2 package, the data was normalized and differentially expressed genes (DEGs) were found. Genes with an adjusted p-value < 0.05 and log2FoldChanges > < 0.585 were found to be differentially expressed and were used in further analysis.
Assembly: hg38
Supplementary files format and content: RNAseqcount text file which includes expression values for each sample fo each gene

extract_protocol:
For RNA sequencing total RNA was extracted from cells, using the RNeasy Mini Kit from Qiagen (Venlo, The Netherlands) according to the manufacturer’s recommendations.
RNA samples were qualified by automated gel electrophoresis on the 2200 TapeStation System (Agilent Technologies). Using KAPA RNA HyperPrep kit with riboErase (HMR) from Roche Sequencing and Life Sciences, cDNAs were synthesized from fragmented RNA and the sequences library were generated, according to the manufacturer’s recommendations. These libraries were then sequenced on an Illumina NextSeq500 using standard settings and the single-end reads obtained from treated cells were analyzed with Strand Avadis NGS (v3.0) software (Strand Life Sciences Pvt. Ltd). The STAR aligner was used in two-pass mode with default settings to map the obtained paired-end reads from treated cells to the hg38 reference genome. Using the DESeq2 package, the data was normalized and differentially expressed genes (DEGs) were found. Genes with an adjusted p-value < 0.05 and log2FoldChanges > < 0.585 were found to be differentially expressed and were used in further analysis.


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 04

description: Library name: Sample312

value: embryonic stem cells


title: TTchemSeq Untreated replicate 2 exp4

description: Library name: TT4_unt_ctrl_r2


title: N-fHP_18

description: Library name: 79059150

tag: smoking history

value: No

tag: cigyears

tag: medical center

tag: transplant free_survival

tag: surv months


title: ONOFF Sham M #3

description: Library name: dnOGAh-F36-12

value: M

value: ONOFF

value: Sham


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 03

description: Library name: Sample311

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA removed 4h, earlyS sort


title: Con Sham M #4

description: Library name: dnOGAh-F36-10

value: Con


title: TTchemSeq Untreated replicate 1 exp4

description: Library name: TT4_unt_ctrl_r1

value: HEK293 Flp-in T-Rex


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 02

description: Library name: Sample310


title: Con TAC M #2

description: Library name: dnOGAh-F31-32


title: TTchemSeq 1 hour recovery from h2h2 with DRB replicate 2 exp3

description: Library name: TT3_1hrd_2


title: N-fHP_16

description: Library name: 79042550

value: whole blood cells

tag: diagnosis

tag: endotype

value: N-fHP

value: Female

value: Yes

tag: race

tag: fvc pred

tag: fvc+pred pct


title: N-fHP_17

description: Library name: 79050750

value: Fibrotic hypersensitivity pneumonitis

tag: Sex

value: Male

tag: tissue


title: Con Sham M #3

description: Library name: dnOGAh-F31-31

value: Left ventricle

tag: strain

value: FVB/NJ

tag: genotype

tag: treatment


title: TTchemSeq 1 hour recovery from h2h2 with DRB replicate 1 exp3

description: Library name: TT3_1hrd_1

tag: cell line


title: Gins4-mAID 5-Ph-IAA removed 4h earlyS-sorted ESCs scRepli-seq 01

description: Library name: Sample309

tag: cell type

value: embryonic stem cells


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 17

description: Library name: Sample308

value: Thymidine removed 4h, earlyS sort


title: N-fHP_15

description: Library name: 79042350

tag: age blood_draw

tag: smoking history

value: White

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: alive

value: venous blood


title: N-fHP_14

description: Library name: 79040950

tag: diagnosis

value: No

tag: cigyears

tag: medical center

tag: transplant free_survival

tag: surv months


title: TTchemSeq 1 hour recovery from h2h2 replicate 2 exp3

description: Library name: TT3_1hr_2


title: Con TAC M #1

description: Library name: dnOGAh-F24-08

tag: Sex

value: M

value: TAC


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 12

description: Library name: Sample307

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4


title: ONOFF TAC M #4

description: Library name: dnOGAh-F24-05

tag: tissue

value: ONOFF


title: TTchemSeq 1 hour recovery from h2h2 replicate 1 exp3

description: Library name: TT3_1hr_1

value: HEK293 Flp-in T-Rex


title: N-fHP_13

description: Library name: 79039050

value: whole blood cells

tag: endotype

value: N-fHP

value: Female

tag: race

tag: fvc pred

tag: fvc+pred pct

value: deadtx


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 11

description: Library name: Sample306

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Con Sham F #3

description: Library name: dnOGAh-F24-01

value: Left ventricle

tag: strain

value: F

value: Con

value: Sham


title: TTchemSeq treated with DRB replicate 2 exp3

description: Library name: TT3_nod_2


title: N-fHP_12

description: Library name: 79037150

value: Fibrotic hypersensitivity pneumonitis

value: Male

tag: age blood_draw

tag: smoking history

value: Yes

value: White

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 10

description: Library name: Sample305

value: embryonic stem cells

value: Thymidine removed 4h, earlyS sort


title: TTchemSeq treated with DRB replicate 1 exp3

description: Library name: TT3_nod_1


title: Con TAC F #4

description: Library name: dnOGAh-F23-02

value: FVB/NJ

value: TAC


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 09

description: Library name: Sample304

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4


title: N-fHP_11

description: Library name: 79036650

value: whole blood cells

tag: diagnosis

tag: cigyears

tag: medical center

tag: transplant free_survival

tag: surv months

value: venous blood


title: TTchemSeq treated replicate 2 exp3

description: Library name: TT3_no_2

value: HEK293 Flp-in T-Rex


title: ONOFF TAC M #3

description: Library name: dnOGAh-F22-03

tag: tissue

tag: Sex

value: M

value: ONOFF


title: N-fHP_10

description: Library name: 79032150

tag: endotype

value: N-fHP

tag: race

tag: fvc pred

tag: fvc+pred pct

value: alive


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 08

description: Library name: Sample303

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ONOFF TAC M #2

description: Library name: dnOGAh-F21-01

value: Left ventricle

tag: strain


title: TTchemSeq treated replicate 1 exp3

description: Library name: TT3_no_1


title: N-fHP_9

description: Library name: 79030950

value: Fibrotic hypersensitivity pneumonitis

value: Female

tag: age blood_draw

tag: smoking history

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: ONOFF Sham M #2

description: Library name: dnOGAh-F20-20

value: Sham


title: N-fHP_8

description: Library name: 79026550

tag: diagnosis

value: Male

value: No

tag: cigyears

value: White

tag: medical center

tag: transplant free_survival

tag: surv months


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 03

description: Library name: Sample302

value: embryonic stem cells

value: Thymidine removed 4h, earlyS sort


title: TTchemSeq  DRB release 30min with 15min DRB re-inhibition and h2o2 treatment replicate 2 exp3

description: Library name: TT3_R30DH_2


title: ONOFF Sham F #4

description: Library name: dnOGAh-F20-15

tag: tissue

value: FVB/NJ

tag: Sex

value: F


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 02

description: Library name: Sample301

tag: cell line

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4


title: TTchemSeq  DRB release 30min with 15min DRB re-inhibition and h2o2 treatment replicate 1 exp3

description: Library name: TT3_R30DH_1

value: HEK293 Flp-in T-Rex


title: N-fHP_7

description: Library name: 79024050

tag: cell type

value: whole blood cells

tag: endotype

tag: race

tag: fvc pred

tag: fvc+pred pct

value: venous blood


title: Gins4-mAID thymidine removed 4h earlyS-sorted ESCs scRepli-seq 01

description: Library name: Sample300

tag: genotype

tag: treatment


title: Con TAC F #3

description: Library name: dnOGAh-F17-47

tag: strain

value: Con

value: TAC


title: N-fHP_6

description: Library name: 79020950

value: N-fHP

tag: age blood_draw

tag: smoking history

value: Yes

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

value: alive


title: Gins4-mAID 5-Ph-IAA 15h, 5-Ph-IAA removed 6h earlyS-sorted ESCs Replicate 2, Hi-C

description: Library name: Sample249

treatment_protocol: (1) Nocodazole treatment: nocodazole was added to the culture medium at a final concentration of 50 ng/ml for 7-10 hours, then G2/M cell population was sorted by cell sorter based on the relative levels of Propidium iodide. (2) Thymidine treatment: after nocodazole treatment, cells were released to G1 phase with thymidine at a final concentration of 2.5 mM for certain time, then G1 population was sorted. (3) 5-Ph-IAA treatment: after nocodazole treatment, cells were released to G1 phase with 5-Ph-IAA at a final concentration of 1 µM for certain time, then G1 population was sorted. (4) INK-128 treatment: INK-128 (MedChemExpress, HY-13328) was added to the culture medium at a final concentration of 1 µM for more than 50 hours, then G1 cell population was sorted. (5) 5-Ph-IAA removed: after nocodazole treatment, cells were released into G1 phase with 5-Ph-IAA at a final concentration of 1 µM for 15 hours. The medium was then replaced with normal culture medium after washing the cells twice with 1xPBS. Early S cell population was sorted after 6 hours.

value: 5-Ph-IAA treatment 15h, 5-Ph-IAA removed 6h, earlyS sort


title: N-fHP_5

description: Library name: 79014650

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

value: Female

tag: cigyears

tag: medical center

tag: transplant free_survival

value: deadtx

tag: surv months


title: TTchemSeq  DRB release 30min with 15min DRB re-inhibition replicate 1 exp3

description: Library name: TT3_R30D_1

tag: cell line


title: TTchemSeq  DRB release 30min with 15min DRB re-inhibition replicate 2 exp3

description: Library name: TT3_R30D_2


title: Con Sham F #2

description: Library name: dnOGAh-F17-46

tag: tissue

value: Left ventricle

tag: Sex

value: Sham


title: ONOFF Sham M #1

description: Library name: dnOGAh-F17-27

value: FVB/NJ

value: M

value: ONOFF


title: TTchemSeq  DRB release 30min treated with h2o2 replicate 2 exp3

description: Library name: TT3_R30H_2

value: HEK293 Flp-in T-Rex


title: Gins4-mAID 5-Ph-IAA 15h, 5-Ph-IAA removed 6h earlyS-sorted ESCs Replicate 1, Hi-C

description: Library name: Sample248

tag: cell type

value: embryonic stem cells

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4


title: N-fHP_4

description: Library name: 79013750

value: whole blood cells

tag: endotype

value: Male

tag: race

value: White

tag: fvc pred

tag: fvc+pred pct

value: venous blood


title: Gins4-mAID G1-KD 5-Ph-IAA 15h woNocodazole ESCs Replicate 2, Hi-C

description: Library name: Sample247

tag: genotype

tag: treatment

value: 5-Ph-IAA treatment 15h woNocodazole, G1 sort


title: Con Sham M #2

description: Library name: dnOGAh-F17-25

tag: strain

value: Con


title: TTchemSeq  DRB release 30min treated with h2o2 replicate 1 exp3

description: Library name: TT3_R30H_1


title: N-fHP_3

description: Library name: 79009250

value: Fibrotic hypersensitivity pneumonitis

value: N-fHP

tag: age blood_draw

tag: smoking history

value: No

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr


title: Gins4-mAID G1-KD 5-Ph-IAA 15h woNocodazole ESCs Replicate 1, Hi-C

description: Library name: Sample246


title: ONOFF Sham F #3

description: Library name: dnOGAh-F17-22

value: Left ventricle

value: F


title: TTchemSeq  DRB release 30min replicate 2 exp3

description: Library name: TT3_R30_2


title: Con Sham M #1

description: Library name: dnOGAh-F16-43

value: FVB/NJ

value: Sham


title: N-fHP_2

description: Library name: 77902243

tag: diagnosis

value: Yes

tag: cigyears

tag: medical center

tag: transplant free_survival

value: deadtx

tag: surv months


title: Gins4-mAID G1-KD 5-Ph-IAA 9h woNocodazole ESCs Replicate 2, Hi-C

description: Library name: Sample245

tag: cell line

tag: cell type

value: embryonic stem cells

value: 5-Ph-IAA treatment 9h woNocodazole, G1 sort


title: N-fHP_1

description: Library name: 77900793

value: whole blood cells

tag: endotype

tag: Sex

value: Female

tag: race

tag: fvc pred

value: alive

tag: tissue


title: Gins4-mAID G1-KD 5-Ph-IAA 9h woNocodazole ESCs Replicate 1, Hi-C

description: Library name: Sample244

tag: genotype

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

tag: treatment


title: ONOFF TAC M #1

description: Library name: dnOGAh-F15-45

tag: strain

value: M

value: ONOFF

value: TAC


title: TTchemSeq  DRB release 30min replicate 1 exp3

description: Library name: TT3_R30_1

value: HEK293 Flp-in T-Rex


title: TTchemSeq  DRB release 15min replicate 2 exp3

description: Library name: TT3_R15_2


title: WU1227-Edge2

description:
Library name: TWKI-WU1227-Edge2
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE

data_processing:
Demultiplexing, image and transcript alignment, and transcript quantification was performed using the Spaceranger pipeline (10x Genomics, v1.2, GRCh38 reference)
Assembly: GRCh38
Supplementary files format and content: Filtered feature matrices output from spaceranger
Supplementary files format and content: fiducial images and json files from spaceranger
Library strategy: Spatial Transcriptomics

extract_protocol:
Using image-guided surgical biopsies and 5-aminolevulinic acid (5-ALA) fluorescence, we collected 22 samples from tumor regions ranging from the core to the margin in nine patients with IDHWT GBM undergoing surgical resection of radiographic, primary high-grade glioma. Each section (i.e. sample) was preserved, stained with hematoxylin and eosin (H&E), imaged, and processed to generate a spatial transcriptomic library. The first 13 samples were fresh-frozen and OCT-embedded, and cDNA libraries were constructed according to the Visium Spatial 3’ Gene Expression User Guide Rev. D. The next nine samples were preserved in FFPE, and cDNA libraries were generated according to the Visium Spatial Gene Expression for FFPE User Guide Rev. E.
All libraries were sequenced on an Illumina Novaseq S2 flow cell to a target depth of 50,000 reads/spot and yielded high quality transcriptome data (median values: 2300 spots under tissue, 55917 mean reads under tissue spot, 2275 panel genes per spot, 4544 median panel UMIs/spot, and 22508 (OCT) or 16334 (FFPE) total genes detected)

value: Brain tumor section (IDH wildtype Glioblastoma)

tag: batch


title: ONOFF TAC F #4

description: Library name: dnOGAh-F15-42

value: Left ventricle


title: Gins4-mAID G1-KD 5-Ph-IAA 3h woNocodazole ESCs Replicate 2, Hi-C

description: Library name: Sample243

value: 5-Ph-IAA treatment 3h woNocodazole, G1 sort


title: TTchemSeq  DRB release 15min replicate 1 exp3

description: Library name: TT3_R15_1


title: WU1227-Core5

description:
Library name: TWKI-WU1227-Core5
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE


title: Gins4-mAID G1-KD 5-Ph-IAA 3h woNocodazole ESCs Replicate 1, Hi-C

description: Library name: Sample242


title: ONOFF TAC F #3

description: Library name: dnOGAh-F15-04

value: FVB/NJ

value: F


title: TTchemSeq  DRB inhibition for 3.5hours replicate 2 exp3

description: Library name: TT3_unR-2


title: WU1221-Edge1

description:
Library name: TWKI-WU1221-Edge1
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE


title: Gins4-mAID INK128 5-Ph-IAA G1-sorted ESCs Replicate 2, Hi-C

description: Library name: Sample241

value: INK-128, 5-Ph-IAA treatment, G1 sort


title: ONOFF TAC F #2

description: Library name: dnOGAh-F15-02


title: TTchemSeq  DRB inhibition for 3.5hours replicate 1 exp3

description: Library name: TT3_unR-1


title: WU1221-Core2

description:
Library name: TWKI-WU1221-Core2
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE


title: Con Sham F #1

description: Library name: dnOGAh-F11-33

value: Con

value: Sham


title: TTchemSeq Untreated replicate 2 exp3

description: Library name: TT3_unt_2_1


title: Gins4-mAID INK128 5-Ph-IAA G1-sorted ESCs Replicate 1, Hi-C

description: Library name: Sample240

value: embryonic stem cells


title: WU1220-03

description:
Library name: TWKI-WU1220-3
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE


title: ONOFF Sham F #2

description: Library name: dnOGAh-F10-32


title: Gins4-mAID INK128 G1-sorted ESCs Replicate 2, Hi-C

description: Library name: Sample239

value: INK-128 treatment, G1 sort


title: TTchemSeq Untreated replicate 1 exp3

description: Library name: TT3_unt_1_1


title: WU1220-02

description:
Library name: TWKI-WU1220-2
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE


title: Gins4-mAID INK128 G1-sorted ESCs Replicate 1, Hi-C

description: Library name: Sample238


title: TTchemSeq 2 hours recovery after Menadione replicate 2 exp2

description: Library name: TT2_m120_MND_2


title: ONOFF TAC F #1

description: Library name: dnOGAh-F08-56


title: WU1220-01

description:
Library name: TWKI-WU1220-1
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE


title: Gins4-mAID Asy earlyS-sorted ESCs Replicate 2, Hi-C

description: Library name: Sample237

value: EarlyS sort


title: Con TAC F #2

description: Library name: dnOGAh-F08-55


title: Gins4-mAID Asy earlyS-sorted ESCs Replicate 1, Hi-C

description: Library name: Sample236


title: TTchemSeq 2 hours recovery after Menadione replicate 1 exp2

description: Library name: TT2_m120_MND_1


title: Con TAC F #1

description: Library name: dnOGAh-F08-54


title: TTchemSeq 1 hour recovery after Menadione replicate 2 exp2

description: Library name: TT2_m60_MND_2


title: ONOFF Sham F #1

description: Library name: dnOGAh-F08-53


title: ST073021-04

description:
Library name: TWBK-ST073021-4
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE


title: Gins4-mAID Asy G1-sorted ESCs Replicate 2, Hi-C

description: Library name: Sample235

value: G1 sort


title: B186-04

description:
Library name: TWBK-B186-04
Spatial transcriptomics of glioblastoma using 10x Visium (V1) OCT


title: ST073021-02

description:
Library name: TWBK-ST073021-2
Spatial transcriptomics of glioblastoma using 10x Visium (V1) FFPE