title: Patient P021 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P021_CRANI1_TUMOR_EPIC

data_processing:
Sequencing reads were processed to generate fragment-level methylation profiles.
Assembly: Sequencing libraries included lambda phage DNA as a spike-in control. Reads were processed relative to the human reference genome GRCh37 (hg19).
Supplementary files format and content: Differentially methylated fragments (DMFs) were quantified and aggregated into matrices for downstream analysis.

extract_protocol:
Cell-free DNA (cfDNA) was extracted from plasma and cerebrospinal fluid using standard protocols. Tumor genomic DNA was extracted from FFPE tissue sections.
Libraries were prepared using the PredicineEPIC platform for genome-wide methylation profiling.


title: E280_rep1

status: Public on Jun 12 2026

type: SRA

city: Xianyang City

first: Guanghui

last: Tan

address: No.22, Xinong Road, Yangling Demonstration Zone, Yangling District, Xianyang City

country: China

institute: Northwest A&F University

description: Library name: TP_C4_2_rep1

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed and processed with Cell Ranger (v7.1.0) against the ARS-UCD2.0 bovine reference genome.
Assembly: Bovine reference genome ARS-UCD2.0 (Ensembl release) was used for read alignment and downstream analyses.
Supplementary files format and content: Processed expression matrices are provided in Matrix Market format (MTX) along with barcodes and feature annotation files. Additional processed data are provided as Seurat R objects (RDS format) containing metadata, normalized counts, dimensionality reduction coordinates, and cell type annotations.

molecule: nuclear RNA

organism: Bos taurus

source_name: placenta

growth_protocol: All experimental animals were healthy Holstein heifers (Bos taurus) with normal estrous cycles. Estrus synchronization was performed by hormone treatment, followed by embryo transfer on day 7 after estrus as previously described (Moraes et al., 2018). Pregnant animals were humanely euthanized at different gestational stages (E60, E85, E110, E180, E240, and E280) for placenta collection.

extract_protocol:
Frozen placental tissues were minced into 2 mm pieces and homogenized in EZ lysis buffer supplemented with protease and RNase inhibitors using a Dounce homogenizer. The nuclear fraction was isolated by filtration and centrifugation steps, stained with 7-AAD, and sorted by FACS to remove debris and doublets. Nuclei were resuspended at 700–1200 nuclei/μl in PBS + 0.07% BSA + RNase inhibitor before loading.
Single-nucleus suspensions were processed using the Chromium Single Cell 3' v3 Reagent Kit (10x Genomics) according to the manufacturer’s instructions. Libraries were quality checked and sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp).

tag: tissue

value: placenta

tag: characteristics [gestation_stage]


title: E240_rep4

description: Library name: TP_C3_1_rep4


title: Patient P020 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

city: New Haven

first: Darin

last: Dolezal

address: 310 Cedar Street

department: Pathology

country: USA

institute: Yale School of Medicine

description: Library name: P020_CRANI1_TUMOR_EPIC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Human brain metastasis tissue

value: Human brain metastasis tissue

tag: cell type

value: Non-small cell lung carcinoma


title: Rex1-EmGFPd2 Pfn1 gRNA#1 mESCs, BrdU-IP Late

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_085_07_Pfn1_153_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
11_Pfn1_mean_w200ks40k.bedGraph

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

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

value: embryonic stem cells

tag: strain

tag: genetic modification

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

tag: treatment

value: pU6-Pfn1-gRNA#1-CBA-PuroR transfection


title: E240_rep3

description: Library name: TP_C3_1_rep3


title: Rex1-EmGFPd2 Pfn1 gRNA#1 mESCs, BrdU-IP Early


title: Patient P019 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P019_CRANI1_TUMOR_EPIC


title: E240_rep1

description: Library name: TP_C3_1_rep1


title: Rex1-EmGFPd2 Ddx39b gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_085_05_Ddx39b_59_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
04_Ddx39b_mean_w200ks40k.bedGraph


title: E180_rep4

description: Library name: TP_6_4_rep4


title: E180_rep3

description: Library name: TP_6_4_rep3


title: Rex1-EmGFPd2 Ddx39b gRNA#2 mESCs, BrdU-IP Early


title: E180_rep2

description: Library name: TP_6_4_rep2


title: Patient P017 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P017_CRANI1_TUMOR_EPIC


title: DSS Proximal, replicate 5, RNA_seq

status: Public on Jun 13 2026

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

description: Library name: DP5

library_source: transcriptomic

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

molecule: total RNA

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon


title: E180_rep1

description: Library name: TP_6_4_rep1


title: Rex1-EmGFPd2 Ddx39b gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_085_03_Ddx39b_57_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
04_Ddx39b_mean_w200ks40k.bedGraph


title: E60_rep2

description: Library name: TP_4_1_rep2


title: E60_rep3

description: Library name: TP_4_1_rep3


title: Rex1-EmGFPd2 Ddx39b gRNA#1 mESCs, BrdU-IP Early


title: Patient P018 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P018_CRANI1_TUMOR_EPIC


title: E60_rep1

description: Library name: TP_4_1_rep1


title: E240_rep2

description: Library name: TP_C3_1_rep2


title: mAID-Mcm6 5-Ph-IAA ESCs Replicate 1, BrdU-IP Early

description: 04_DEP_01_117_7_Mcm6_IAA_IP_w200ks40k_Percent_q0.05.bedGraph

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at N-terminus of Mcm6

value: 5-Ph-IAA treatment


title: Z3_K562BCO_72h5phIAA_A40_S15

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description: Library name: Z3_K562BCO_72h5phIAA_A40_S15

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: Z2_K562BCO_72h5phIAA_A39_S14

description: Library name: Z2_K562BCO_72h5phIAA_A39_S14


title: Y3_K562BCO_24h5phIAA_A36_S2

description: Library name: Y3_K562BCO_24h5phIAA_A36_S2


title: Patient P015 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P015_CRANI1_TUMOR_EPIC


title: E85_rep3

description: Library name: TP_3_1_rep3


title: Rex1-EmGFPd2 Aars2 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_163_3_Aars_47_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
18_Aars_mean_w200ks40k.bedGraph

value: pU6-Aars2-gRNA#2-CBA-PuroR transfection


title: E85_rep2

description: Library name: TP_3_1_rep2


title: E85_rep1

description: Library name: TP_3_1_rep1


title: Patient P032 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P032_CRANI1_TUMOR_EPIC


title: Patient P014 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P014_CRANI1_TUMOR_EPIC


title: Rex1-EmGFPd2 Aars2 gRNA#2 mESCs, BrdU-IP Early


title: Patient P031 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P031_CRANI1_TUMOR_EPIC


title: Patient P013 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P013_CRANI1_TUMOR_EPIC


title: Rex1-EmGFPd2 Aars2 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_63_Aars_45_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
18_Aars_mean_w200ks40k.bedGraph

value: pU6-Aars2-gRNA#1-CBA-PuroR transfection


title: A14_IgG_Positive_Rep2

city: Baltimore

first: Elana

last: Shaw

address: 855 N Wolfe St

institute: Johns Hopkins University

description: Library name: Sample11

data_processing:
Samples were sequenced on NovaSeq X Plus 10B or 25B.
Illumina's bcl2fastq v2.20.0 was used to convert BCL files to FASTQ files.
fastp v0.23.4 was used to trim the reads.
rsem v1.3.3 was used for running the alignments as well as generating gene and transcript expression levels. The data was aligned to the hg38 reference genome.
Differential expression analysis was performed using DeSeq2 with multi-factor design accounting for all experimental groups and experimental batches. Log2 fold change values were then shrunk using lfcShrink with default parameters. Significant differentially expressed genes were defined using a FDR cutoff of <0.05 and log2FC of |0.5|. Gene Set Enrichment Analysis was performed using Reactome pathways.
Assembly: hg38
Supplementary files format and content: Tab delimited file "genes_expected_counts_all_samples.txt"  includes raw counts from each sample

source_name: pancreatic ductal adenocarcinoma

growth_protocol: Cells were grown in RPMI media supplemented with 10% fetal bovine serum and 1% penn-strep

extract_protocol:
After sorting, cell pellets were resuspended in 1 mL of Invitrogen™ TRIzol™ Reagent and stored at -80°C until RNA extraction. The Invitrogen™ PureLink™ RNA Mini Kit was used to extract and purify RNA from TRIzol™ following protocols outlined by the manufacturer. Optional on-column DNase treatment was performed. Purified samples were stored at -80°C until being transported on dry ice to the SKCCC Experimental and Computational Genomics Core for Bioanalyzer to assess RNA quality and bulk RNA sequencing.
RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA with RiboZero Human/Mouse/Rat” kit following the manufacturers instructions.

treatment_protocol: Thawed cells were added to 15 mL of complete RPMI media, centrifuged (5 minutes at 1500 rpm), and the supernatant was aspirated. Cells were resuspended in complete RPMI and added to a V-bottom Corning® 96 Well Clear Polystyrene Microplate for staining. The staining plate was centrifuged (5 minutes at 1500 rpm) and media was aspirated. The cell pellets were resuspended in Stain 1 (1:20 Invitrogen human Fc Receptor block in PBS) and incubated for 30 minutes at 4°C in the dark. The staining plate was centrifuged (5 minutes at 1500 rpm) and media was aspirated. The cell pellets were resuspended in Stain 2 (1:10 ascitic supernatant in eBioscience™ Flow Cytometry Staining Buffer) and incubated for 30 minutes in the dark at room temperature. The staining plate was centrifuged (5 minutes at 1500 rpm) and media was aspirated. Cells were washed 3 times by resuspending the pellet in PBS, centrifugation (5 minutes at 1500 rpm), and aspiration of the media. The cell pellets were resuspended in Stain 3 (1:100 Abcam Goat Anti-Human IgG H&L (DyLight® 488 in eBioscience™ Flow Cytometry Staining Buffer) for 30 minutes in the dark at room temperature. The staining plate was centrifuged (5 minutes at 1500 rpm) and media was aspirated. Cells were washed 3 times by resuspending the pellet in PBS, centrifugation (5 minutes at 1500 rpm), and aspiration of the media. Cells were resuspended in PBS and added to Falcon® 5 mL Round Bottom Polystyrene Test Tube with Cell Strainer Snap Caps. Cells were sorted into 15 mL Falcon tubes using the Sony SH800 Cell Sorter by gating on cells, singlets, and then IgG positive and negative subpopulations by fluorescence in the DyLight® 488 channel using an unstained control as a guide. Cells were centrifuged (5 minutes at 1500 rpm) and the supernatant was aspirated. The cell pellets were used in downstream experiments.

value: pancreatic ductal adenocarcinoma

value: epithelial cell

tag: genotype

value: WT

tag: batch


title: A14_IgG_Positive_Rep1

description: Library name: Sample10


title: Patient P012 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P012_CRANI1_TUMOR_EPIC


title: A14_IgG_Negative_Rep3

description: Library name: Sample9


title: A14_IgG_Positive_Rep3

description: Library name: Sample12


title: A14_IgG_Negative_Rep2

description: Library name: Sample8


title: Rex1-EmGFPd2 Aars2 gRNA#1 mESCs, BrdU-IP Early


title: Ctrl Distal, replicate 2, RNA_seq

description: Library name: CD2


title: KO_Dex_3

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: Library name: KD12

data_processing:
Base-calling was performed using NextSeq Control Software 2.2.0.4 (RTA 2.4.11) and the BCL files were demultiplexed into fastq files using bcl2fast2 v2.20.0.422.
Bulk ATAC-seq data were preprocessed using the ATAC-seq Pipeline (v1.2.0) on Via Foundry (https://www.gcp.viafoundry.com/). Specifically, read quality filtering (phred >= 33) and adaptors trimming were performed using Trimmomatic v0.39, trimmed reads were then aligned to the mm10 mouse genome using Bowtie2 v2.3.5, and duplicated reads were marked and removed by Picard v2.18.27. BAM files were sorted and indexed using Samtools v1.3.
Data were further cleaned up by filtering out the reads that meet any of the following criteria using deepTools v3.5.6: (1) mapped to chrM (mitochondria), chr*_random, chrUn, and chrY (because cells are derived from female mice); (2) mapped to blacklist regions (https://github.com/Boyle-Lab/Blacklist); (3) with low mapping quality (MAPQ < 30); (4) fragment length < 50bp. Peak calling was then performed for all samples together using Genrich v0.6.1 (joint ATAC-seq mode). Peaks were then quantified using featureCounts v2.1.1 from the Subread package.
Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv) files include read counts for every peak (rows)  in every sample (columns)
Supplementary files format and content: BigWig (.bw) files contain the normalized, genome-wide chromatin accessibility signal (read depth) for each sample.

source_name: in vitro; originally from spleen and dLN

extract_protocol:
6,000 cells were sorted by FACS into PBS buffer supplemented with 0.5% BSA.
For library preparation, cells were lysed and tagmented with 9.5uL lysis and transposition mix buffer (10mM TAPS-NaOH pH 8.5, 5mM MgCl2, 10% DMF, 0.02% digitonin) and 0.5uL Tn5 transposase (Diagenode) at 37 °C for 30 min. Tagmentation was terminated by the direct addition of 10 µL stop buffer (100 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.4% SDS, 40 µg/mL proteinase K), followed by incubation at 55 °C overnight. Subsequently, 5 µL of 25% Tween-20 was added directly to the reaction. Libraries were amplified by PCR for 16 cycles under the following conditions: 72 °C for 5 min; 98 °C for 3 min; followed by cycling at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min; with a final extension at 72 °C for 5 min. PCR products were purified using a two-step SPRI beads cleanup (1.5× followed by 0.6×). Library concentration was measured using the Qubit dsDNA HS Assay Kit (Invitrogen), and fragment size distribution was assessed using an Agilent FA5400 Fragment Analyzer. Final libraries were sequenced on an Illumina NextSeq™ 1000/2000 platform using a P2 XLEAP-SBS™ Reagent Kit (100 cycles; Cat. No. 20100987).

value: T cell

value: GR cKO (C57/B6)

value: Dex


title: Adult Distal, replicate 2, RNA_seq

description: Library name: AD2

data_processing:
Raw sequencing reads were assessed for quality and adapter contamination prior to alignment.
Clean reads were aligned to the mouse reference genome (mm10) using Bowtie2.
Reads with low mapping quality, mitochondrial reads, and PCR duplicates were removed before downstream analysis. Accessible chromatin regions were identified using MACS2 peak calling.
Peak annotations and downstream analyses were performed using standard bioinformatic workflows. Genome-wide accessibility tracks were generated in bigWig format for visualization in IGV.
Assembly: All ATAC-seq sequencing reads were aligned to the official mouse reference genome assembly. The Mus musculus GRCm38 (mm10) genome build was used as the standard reference for genome mapping and subsequent bioinformatics analysis (default standard for mouse intestinal epigenetic research).
Supplementary files format and content: Processed data files include BED files containing ATAC-seq peak coordinates, bigWig files containing normalized chromatin accessibility signal tracks, and tab-delimited text files containing peak annotations and differential accessibility results. BED files report genomic coordinates of accessible chromatin regions identified by MACS2, while bigWig files provide genome-wide accessibility profiles for visualization. Differential accessibility files include genomic coordinates, fold changes, statistical significance values, and associated gene annotations.

source_name: colonic epithelial cells

extract_protocol:
Colonic epithelial cells were isolated from mouse tissues and processed immediately for ATAC-seq library preparation. Cells were washed with ice-cold PBS and lysed in a detergent-containing lysis buffer to release intact nuclei. Nuclei were collected by centrifugation, washed, and resuspended in transposition reaction buffer for subsequent tagmentation.
ATAC-seq libraries were prepared using the Novoprotein ATAC Library Prep Kit (Novoprotein, China) according to the manufacturer's instructions. Briefly, purified nuclei were incubated with Tn5 transposase at 37°C for 30 min to simultaneously fragment accessible chromatin and insert sequencing adapters. Following transposition, DNA was purified using magnetic beads and amplified by PCR with indexed primers. Amplified libraries were purified, quantified using Qubit fluorometry, and assessed for fragment size distribution using an Agilent Bioanalyzer. Libraries were sequenced on an Illumina platform with paired-end 150-bp reads (PE150).

value: colonic epithelial cells


title: Patient P016 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P016_CRANI1_TUMOR_EPIC

value: Human brain metastasis tissue


title: Patient P027 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P027_CRANI1_TUMOR_EPIC

value: Non-small cell lung carcinoma


title: Patient P011 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P011_CRANI1_TUMOR_EPIC


title: A14_IgG_Negative_Rep1

description: Library name: Sample7


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

description:
DEP_01_066_61_Hal_32_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
19_Hal_mean_w200ks40k.bedGraph

value: embryonic stem cells

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


title: KO_Ctrl_2

description: Library name: KC8

value: in vitro; originally from spleen and dLN

value: control


title: A1_IgG_Positive_Rep3

description: Library name: Sample6


title: Patient P010 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P010_CRANI1_TUMOR_EPIC


title: A1_IgG_Positive_Rep2

description: Library name: Sample5


title: KO_Ctrl_1

description: Library name: KC7


title: Rex1-EmGFPd2 Hal gRNA#2 mESCs, BrdU-IP Early

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


title: A1_IgG_Positive_Rep1

description: Library name: Sample4


title: Patient P009 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P009_CRANI1_TUMOR_EPIC


title: Patient P008 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P008_CRANI1_TUMOR_EPIC


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

description:
DEP_01_163_1_Hal_37_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
19_Hal_mean_w200ks40k.bedGraph

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


title: A1_IgG_Negative_Rep2

description: Library name: Sample2


title: A1_IgG_Negative_Rep1

description: Library name: Sample1


title: WT_Dex_2

description: Library name: WD5


title: Rex1-EmGFPd2 Hal gRNA#1 mESCs, BrdU-IP Early


title: Patient P007 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P007_CRANI1_TUMOR_EPIC


title: Human PBMCs CITE-seq library, 10X Batch 5, ADT + HTO

city: Parkville

first: Davide

last: Vespasiani

state: VIC

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute

description:
Library name: PBMC_Batch5_ADT_HTO
10x Genomics

data_processing:
Bcl2fastq (v2.20.0; Illumina) was used to convert and demultiplex CITE-seq and VDJ-seq BaseCall files into FASTQ files. Cellranger mkref and cellranger mkvdjref (v8.0.1; 10x Genomics) were used to build the hs1/T2T-CHM13v2.0 reference genome respectively for the CITE-seq and VDJ-seq data using the GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf file downloaded from NCBI https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ and the hs1.fa fasta file was downloaded from https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/. Cellranger multi and cellranger vdj (v8.0.1; 10x Genomics) were respectively used to align the CITE-seq and VDJ-seq libraries to the hs1 reference genome and to generate the cell barcode-gene UMI count matrices. Gene expression count matrices for each sequencing batch were separately processed with Seurat (v.5.4.0) in R (v. 4.4.1). HTODemux (assay = "HTO", positive.quantile = 0.99, kfunc='clara') was used to assign the donor ID and the vaccination timepoint for each single cell based on cell hashtags and to remove both doublets and negative droplets.  High-quality single-cells were identified and processed using Seurat.
Assembly: hs1 (T2T-CHM13v2.0), GCF_009914755.1_T2T-CHM13v2.0
Supplementary files format and content: GEX_matrix.mtx.gz (matrix with gene expression counts, with row names in GEX_features.tsv and column names in GEX_barcodes.tsv)
Supplementary files format and content: ADT_matrix.mtx.gz (matrix with protein expression counts, with row names in ADT_features.tsv and column names in ADT_barcodes.tsv)
Supplementary files format and content: HTO_matrix.mtx.gz (matrix with cell hashtag expression counts, with row names in HTO_features.tsv and column names in HTO_barcodes.tsv)
Supplementary files format and content: TCR_filtered_contig.fastq containing the raw sequence for the assembled VDJ contigs of high-confidence for the T cell receptor with corresponding annotations in TCR_filtered_contig_annotations.csv
Supplementary files format and content: BCR_filtered_contig.fastq containing the raw sequence for the assembled VDJ contigs of high-confidence for the B cell receptor with corresponding annotations in BCR_filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: polyA RNA

source_name: peripheral mononuclear blood cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were separated and cryopreserved from blood samples collected at baseline and 7-days post-vaccination
PBMC samples were collected from 10 patients with SAD, 10 CVID and 10 healthy controls collected before and 7 days after vaccination. All 60 samples were stained with Hash Tag Oligonucleotides (HTOs) and a panel of 130 Antibody-Derived Tags (ADTs) using TotalSeqTM antibodies (BioLegend), pooled and then split into 5 batches (12 samples each). For each batch, GEX, ADT and HTO and VDJ libraries were generateed using the 10X Genomics Chromium single-cell 5′ reagent kit v3 according to manufacturer’s protocol and then sequenced on a NovaSeq X Plus (PE150).

treatment_protocol: A single dose of Vi-polysaccharide vaccine (TYPHIM Vi; Sanofi Pasteur, Lyon France), containing 25mcg of purified Salmonella Typhi capsular Vi-polysaccharide, was administered intramuscularly on day 0 (baseline). Follow up visits were performed at 7 days and 1, 6 and 13 months post-vaccination. Serum samples collected at baseline and 1, 6 and 13 months post-vaccination were stored at -80C prior to analysis. PBMCs were separated and cryopreserved from freshly isolated blood samples collected at baseline and 7-days post-vaccination.

value: peripheral mononuclear blood cells

tag: time

value: Day0 and Day7 post-vaccination

value: Typhim Vi vaccine


title: Rex1-EmGFPd2 Pold2 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_59_Pold2_19_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
12_Pold2_mean_w200ks40k.bedGraph

value: pU6-Pold2-gRNA#2-CBA-PuroR transfection


title: Human PBMCs CITE-seq library, 10X Batch 5, GEX

description:
Library name: PBMC_Batch5_mRNA
10x Genomics


title: Human PBMCs CITE-seq library, 10X Batch 4, ADT + HTO

description:
Library name: PBMC_Batch4_ADT_HTO
10x Genomics


title: Patient P006 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P006_CRANI1_TUMOR_EPIC


title: Human PBMCs CITE-seq library, 10X Batch 4, GEX

description:
Library name: PBMC_Batch4_mRNA
10x Genomics


title: Rex1-EmGFPd2 Pold2 gRNA#2 mESCs, BrdU-IP Early


title: Human PBMCs CITE-seq library, 10X Batch 3, ADT + HTO

description:
Library name: PBMC_Batch3_ADT_HTO
10x Genomics


title: A1_IgG_Negative_Rep3

description: Library name: Sample3

value: pancreatic ductal adenocarcinoma

value: epithelial cell

value: WT


title: Rex1-EmGFPd2 Pold2 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_57_Pold2_17_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
12_Pold2_mean_w200ks40k.bedGraph

value: pU6-Pold2-gRNA#1-CBA-PuroR transfection


title: Human PBMCs CITE-seq library, 10X Batch 3, GEX

description:
Library name: PBMC_Batch3_mRNA
10x Genomics


title: Human PBMCs CITE-seq library, 10X Batch 2, GEX

description:
Library name: PBMC_Batch2_mRNA
10x Genomics


title: Human PBMCs CITE-seq library, 10X Batch 1, ADT + HTO

description:
Library name: PBMC_Batch1_ADT_HTO
10x Genomics


title: Patient P004 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy 1 of 2

description: Library name: P004_CRANI1_TUMOR_EPIC


title: MCOLN3 Y391D #2

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description:
Library name: WR10
column name in RNAseq_counts.tsv: WR10

data_processing:
Reads were aligned to the human transcriptome (Gencode r.28) using kallisto (Bray et al. 2016)
Transcript-level abundance estimates were summarized to gene-level expression values using the lengthScaledTPM method in tximport (Soneson et. al., 2015).
Data was normalized using edgeR’s TMM mormalization
log2CPM values were calculated using voom (from limma)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes raw counts. Samples are identified by the column header.

growth_protocol: Human adrenocortical HAC15 cell line was routinely cultured in growth media consisting of Dulbecco’s modified Eagle’s medium (DMEM)-F12 (Gibco) supplemented with 10 % cosmic calf serum (Hyclone), 1 % ITS (insulin-transferrin-selenium; Corning), and antibiotics, 1 % penicillin/streptomycin (Gibco) and 0.1 % gentamicin (Gibco). Cells were grown at 37 °C in a humidified atmosphere of 5 % CO2.

extract_protocol:
Total RNA was isolated from cells using the RNeasy Plus Mini kit (Qiagen; Cat#: 74134) and eluted in nuclease-free H2O.
Poly(A) Tail RNA Selection 250-300 bp Insert cDNA Library Strand-Specific Preparation by LC Sciences. Library construction and sequencing is described by LCScience.com as: "Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the paired-end 2×150bp sequencing on an Illumina Hiseq 4000 at LC Sciences following the vendor's recommended protocol.

value: Adrenocortical carcinoma cell


title: HCT116 cells, sh_control

city: Hefei

first: yu

middle: xiang

last: dai

address: No.81 Meishan Road Hefei China

institute: Anhui Medical University

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Colorectal cancer

growth_protocol: Normal growth conditions, according to instructions by provider

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.Kit: mirVana™ miRNA ISOlation Kit, Ambion-1561. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: HCT116 cells were transfected with an sh-RNA knockdown system purchased from Sigma-Aldrich, and after 36 or 48 h of incubation, the cells were collected.

value: Colorectal cancer

value: MT


title: Rex1-EmGFPd2 Anapc11 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_55_Anapc11_15_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
02_Anapc11_mean_w200ks40k.bedGraph

value: embryonic stem cells


title: KOLF2.1J CLYBL-NBS9 iPSC R3

first: Beth

last: Stevens

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: Sample 24

data_processing:
In accordance with sharing guidelines by Jackson Laboratory, fastq data files were processed before alignment and deposition to remove Y chromosome reads.
Reads were aligned to the human genome with STAR using Ensembl genome files: ‘Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz’ and ‘Homo_sapiens.GRCh38.115.gtf.gz’. Output BAM files were processed with samtools48 to identify Y chromosome reads. Fastq files were filtered to remove Y chromosome reads using custom shell scripts.
Salmon was used to quantify transcript abundances from filtered fastq files. Salmon index was built using ‘gencode.v48.transcripts.fa.gz’. pytximport was used to process salmon output ‘quant.sf’ files into RNA counts matrix (Table S3).
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz, gencode.v48.transcripts.fa.gz
Supplementary files format and content: Table S1.xlsx sheet name "This study" includes processed counts matrix.

source_name: KOLF2.1J CLYBL-NBS9

growth_protocol: iAstrocytes were cultured in maturation medium until day 21. KOLF2.1J uninduced iPSCs were cultured in E8 medium until near confluency.

extract_protocol:
Cells were lysed in Buffer RLT (Qiagen) with DTT. RNA was isolated using RNAeasy kits (Qiagen).
Bulk RNA-seq was performed using Novogene commercial sequencing service. Directional mRNA libraries were prepared using ultra-low input total RNA directional library preparation. Sequencing was performed using NovaSeq X Plus Series (PE150).

value: KOLF2.1J CLYBL-NBS9

value: iPSC


title: Rex1-EmGFPd2 Anapc11 gRNA#2 mESCs, BrdU-IP Early


title: KOLF2.1J CLYBL-NBS9 iPSC R2

description: Library name: Sample 23


title: KOLF2.1J CLYBL-NBS9 iPSC R1

description: Library name: Sample 22


title: Patient P003 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P003_CRANI1_TUMOR_EPIC

value: Human brain metastasis tissue

value: Non-small cell lung carcinoma


title: Patient P002 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P002_CRANI1_TUMOR_EPIC


title: Rex1-EmGFPd2 Anapc11 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_53_Anapc11_13_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
02_Anapc11_mean_w200ks40k.bedGraph

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


title: FA13.1J CLYBL-AB9 R2

description: Library name: Sample 20

source_name: FA13.1J CLYBL-AB9

value: FA13.1J CLYBL-AB9

value: iAstrocyte


title: Patient P001 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P001_CRANI1_TUMOR_EPIC


title: FA13.1J CLYBL-AB9 R1

description: Library name: Sample 19


title: Rex1-EmGFPd2 Anapc11 gRNA#1 mESCs, BrdU-IP Early


title: FA13.1J CLYBL-NBS9 R3

description: Library name: Sample 18

source_name: FA13.1J CLYBL-NBS9

value: FA13.1J CLYBL-NBS9


title: FA13.1J CLYBL-NBS9 R2

description: Library name: Sample 17


title: L-fHP_88

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: Library name: 79152050

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

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: Yes

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

value: venous blood


title: FA13.1J CLYBL-NBS9 R1

description: Library name: Sample 16

tag: cell line

tag: cell type


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

description:
DEP_01_066_49_Tardbp_11_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
15_Tardbp_mean_w200ks40k.bedGraph

value: embryonic stem cells

tag: strain

tag: genetic modification

tag: treatment


title: KOLF2.1J CLYBL-AB9 R3

description: Library name: Sample 15

source_name: KOLF2.1J CLYBL-AB9

value: KOLF2.1J CLYBL-AB9


title: Rex1-EmGFPd2 Tardbp gRNA#2 mESCs, BrdU-IP Early


title: L-fHP_86

description: Library name: 79148250

tag: diagnosis

tag: endotype

tag: Sex

value: Male

tag: age blood_draw

tag: tissue


title: KOLF2.1J CLYBL-NBS9 R2

description: Library name: Sample 11

value: KOLF2.1J CLYBL-NBS9


title: Rex1-EmGFPd2 Tardbp gRNA#1 mESCs, BrdU-IP Early

description:
DEP_01_066_47_Tardbp_9_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
15_Tardbp_mean_w200ks40k.bedGraph


title: KOLF2.1J CLYBL-NBS9 R1

description: Library name: Sample 10


title: H9 CLYBL-AB9 R3

description: Library name: Sample 9

source_name: H9 CLYBL-AB9

value: H9 CLYBL-AB9


title: L-fHP_84

description: Library name: 79147150

tag: smoking history

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct


title: H9 CLYBL-AB9 R2

description: Library name: Sample 8


title: Empty vector #4

description:
Library name: WR4
column name in RNAseq_counts.tsv: WR4

value: Adrenocortical carcinoma cell


title: Epi-2

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

description: Library name: set2_Gil_CTL_Epi62_H3K27me3

data_processing:
Reads were trimmed with Trim Galore (v0.6.7) and aligned to the human reference genome (hg38) using Bowtie2 (v.2.2.5). Deduplicated reads were removed using samtools (v.1.14). Peaks were identified using a sliding window method to determine genomic regions with >1.5 mapping read enrichment over IgG control and adjusted p < 0.05. The BAM file for each replicate was converted to a TDF file for Integrative Genomics Viewer (IGV) software.
Assembly: hg38
Supplementary files format and content: TDF, tag density file
Library strategy: CUT&RUN

source_name: Skin epidermis

extract_protocol:
Normal human skin samples were washed once in cold 1x PBS, fat layer was removed, and the skin was then incubated in 1.26 U/ml dispase (Gibco) overnight at 4 °C. The epidermis was separated from underlying dermis and kept at liquid nitrogen until use. Human SCC tumor biopsies were freshly collected after surgery and kept at liquid nitrogen until use.   Next, nuclei from frozen human epidermis and SCC tumor samples were isolated. Isolated nuclei were then subjected to CUT&RUN analysis using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNext Multiplex Oligos (NEB) for Illumina following the manufacturer’s instructions. PCR-amplified libraries were purified using 1X ratio of Agencourt AMPure-XP Beads (Beckman) and eluted in 15μl TE buffer. All libraries were sequenced on an Illumina NextSeq using 50 bp paired-end reads.

value: Skin epidermis

value: Epidermal cells


title: L-fHP_83

description: Library name: 79145951

value: No

tag: dlco uncorrected

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival


title: H9 CLYBL-AB9 R1

description: Library name: Sample 7

tag: cell line

tag: cell type

value: iAstrocyte


title: H1 CLYBL-AB9 R2

description: Library name: Sample 5

source_name: H1 CLYBL-AB9

value: H1 CLYBL-AB9


title: L-fHP_81

description: Library name: 79129250

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

value: L-fHP

tag: surv months


title: KOLF2.1J CLYBL-AB9 R2

description: Library name: Sample 14


title: H1 CLYBL-NBS9 R3

description: Library name: Sample 3

source_name: H1 CLYBL-NBS9

value: H1 CLYBL-NBS9


title: H1 CLYBL-NBS9 R1

description: Library name: Sample 1


title: Rex1-EmGFPd2 Orc1 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_41_Orc1_159_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
10_Orc1_mean_w200ks40k.bedGraph

tag: strain

tag: genetic modification

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

tag: treatment

value: pU6-Orc1-gRNA#2-CBA-PuroR transfection


title: CD95F

city: Guangzhou

first: Ren

last: Mao

address: 58 Zhongshan Road 2nd, Guangzhou

institute: The First Affiliated Hospital, Sun Yat-Sen University

description:
Library name: sample8
10× Genomics

data_processing:
Human mesenteric tissue single-nucleus RNA-seq data were processed using Cell Ranger software (v3.1.0; 10x Genomics). Raw sequencing reads were converted to FASTQ files, aligned to the human reference genome, and quantified to generate gene-barcode expression matrices for each sample. Low-quality barcodes and UMIs were filtered out. Reads uniquely mapped to the transcriptome and intersecting exonic regions were counted. UMI sequences were corrected for sequencing errors, and valid cell/nucleus barcodes were identified for downstream matrix generation. Cell-by-gene count matrices were generated by UMI counting and cell barcode calling. The filtered feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, are provided as processed data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Creeping fat of Mesenteric adipose tissue in Crohn's disease

extract_protocol:
The samples were chopped on ice into 1-2 mm³ pieces, transferred to cryovials, snap-frozen in liquid nitrogen for 5 minutes, and then stored in an ultra-low temperature freezer and liquid nitrogen.. Then transfer the tissue from the cryovial to a Dounce homogenizer and add 500 μl of pre-chilled lysis buffer to thaw. Use a small and a tight pestle to press the tissue 15-20 times and 5-10 times, respectively, to create a homogenate. Add 700 μl of nuclear wash buffer, mix, and filter through a 70 μm cell strainer. Add 1 ml of 50% iodixanol to the filtrate, mix gently, and layer onto a gradient solution of 30% and 33% iodixanol. Centrifuge at 10,000×g for 20 minutes at 4°C. Extract the white nuclear layer at the interface, add nuclear wash buffer, mix, and centrifuge at 500×g for 8 minutes at 4°C. Transfer the supernatant, resuspend the nuclei, and repeat the wash. Filter through a 40 μm filter, centrifuge, resuspend the nuclei, and adjust the concentration to 700-1200 nuclei/μl using a microscope.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and equenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.

tag: tissue


title: KDM2B-mAID_J2_7_GSK343_3

description:
Library name: KDM2B-mAID_J2_7_GSK343_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.


title: L-fHP_79

description: Library name: 79118751

tag: endotype

tag: Sex

tag: age blood_draw

tag: smoking history

tag: cigyears

value: White

value: deadtx

value: venous blood


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

description:
DEP_01_066_43_Tbcc_5_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
16_Tbcc_mean_w200ks40k.bedGraph

value: embryonic stem cells

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


title: KDM2B-mAID_J2_7_GSK343_2

description:
Library name: KDM2B-mAID_J2_7_GSK343_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_80

description: Library name: 79119550

value: Female

value: Yes

tag: race

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred

value: alive


title: Rex1-EmGFPd2 Orc1 gRNA#2 mESCs, BrdU-IP Early

tag: cell line

tag: cell type


title: KDM2B-mAID_J2_7_GSK343_1

description:
Library name: KDM2B-mAID_J2_7_GSK343_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: Rex1-EmGFPd2 Orc1 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_39_Orc1_157_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
10_Orc1_mean_w200ks40k.bedGraph

value: pU6-Orc1-gRNA#1-CBA-PuroR transfection


title: WiDr GSK715 RNA-seq replicate 1

city: Nanjing

first: Mu

last: Xu

address: No.32, Gongqingtuan Road,

department: Nanjing First Hospital

institute: Nanjing Medical University

description:
Library name: WiDr_GSK715_1
Total RNA from WiDr cells treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): widr_gene_count_matrix.tsv.gz.

data_processing:
Short-read RNA-seq: Adapters and low-quality reads were removed with Cutadapt. Clean reads were aligned to GRCh38 using HISAT2, and transcript abundance was quantified as FPKM using StringTie. Differential expression analysis was performed with DESeq2 (adjusted P < 0.05, |log2FC| >= 1).
ONT full-length cDNA sequencing: Raw pod5/fast5 signals were base-called with Dorado (--no-trim) to generate FASTQ reads. Reads passing the basecalling quality filter (Q >= 10) were retained as clean reads. Full-length cDNA reads were identified, oriented and trimmed using Pychopper (-Q 7 -z 50), followed by additional filtering with NanoFilt (-q 7 -l 50). Filtered full-length reads were aligned to GRCh38 using minimap2 (-ax splice -uf -k14). Consensus transcript sets were constructed using Pinfish, and transcript reconstruction and merging were performed with StringTie. Transcript abundance was quantified as TPM using Salmon. Differentially expressed transcripts and genes were identified using DESeq2 (P < 0.05 and |log2FoldChange| > 2). Poly(A) sites were identified, clustered and annotated using QuantifyPoly(A) to analyze 3'-end heterogeneity.
Processed matrices prepared for GEO: hct116_gene_count_matrix.tsv.gz; widr_gene_count_matrix.tsv.gz; ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.
Assembly: GRCh38
Supplementary files format and content: hct116_gene_count_matrix.tsv.gz and widr_gene_count_matrix.tsv.gz are gzip-compressed tab-delimited gene-level count matrices for short-read RNA-seq samples.
Supplementary files format and content: ont_widr_gene_counts_matrix.tsv.gz is a gzip-compressed tab-delimited gene-level count matrix for ONT full-length cDNA sequencing samples; ont_widr_full_length_stats.tsv.gz contains full-length read summary statistics.

growth_protocol: HCT116 and WiDr cells were cultured under standard mammalian cell culture conditions before treatment.

extract_protocol:
Total RNA was extracted from treated cells and assessed for quality before library construction.
Total RNA from WiDr and HCT-116 cells treated with DMSO, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor) for 96 h was subjected to poly(A)-enriched library construction by Lianchuan Biotechnology (Hangzhou) and paired-end sequencing on an Illumina NovaSeq 6000. WiDr cells treated with DMSO or 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h were subjected to Oxford Nanopore Technologies (ONT) full-length cDNA sequencing on a PromethION platform by Benagen (Wuhan).

treatment_protocol: Cells were treated for 96 h with DMSO vehicle control, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor), as applicable.

value: colon

value: WiDr

value: colorectal carcinoma cell line

tag: batch

value: short-read RNA-seq


title: KDM2B-mAID_J2_7_DMSO_2

description:
Library name: KDM2B-mAID_J2_7_DMSO_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx

value: DMSO


title: L-fHP_77

description: Library name: 79114650

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

value: L-fHP

value: No

tag: pctdlcouncorr

tag: medical center


title: Rex1-EmGFPd2 Orc1 gRNA#1 mESCs, BrdU-IP Early

tag: strain

tag: genetic modification

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

tag: treatment


title: KDM2B-mAID_J2_7_5PhIAA_GSK343_3

description:
Library name: KDM2B-mAID_J2_7_5PhIAA_GSK343_3
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: H1 CLYBL-NBS9 R2

description: Library name: Sample 2

value: H1 CLYBL-NBS9

value: iAstrocyte


title: KDM2B-mAID_J2_7_5PhIAA_GSK343_2

description:
Library name: KDM2B-mAID_J2_7_5PhIAA_GSK343_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: Rex1-EmGFPd2 Mcm6 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_35_Mcm6_43_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
09_Mcm6_mean_w200ks40k.bedGraph

value: embryonic stem cells

value: pU6-Mcm6-gRNA#2-CBA-PuroR transfection


title: KDM2B-mAID_J2_7_5PhIAA_GSK343_1

description:
Library name: KDM2B-mAID_J2_7_5PhIAA_GSK343_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_75

description: Library name: 79103950

tag: endotype

tag: Sex

value: Female

tag: age blood_draw

value: Yes

value: White

tag: transplant free_survival

tag: surv months

tag: tissue

value: venous blood


title: KDM2B-mAID_J2_7_5PhIAA_3

description:
Library name: KDM2B-mAID_J2_7_5PhIAA_3
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: Rex1-EmGFPd2 Mcm6 gRNA#2 mESCs, BrdU-IP Early


title: L-fHP_78

description: Library name: 79115350

value: Male

tag: smoking history

tag: cigyears

tag: race

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

value: deadtx


title: L-fHP_74

description: Library name: 79103050

tag: cell type

tag: diagnosis

tag: dlco pred

tag: pctdlcouncorr


title: KDM2B-mAID_J2_7_5PhIAA_1

description:
Library name: KDM2B-mAID_J2_7_5PhIAA_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx

tag: cell line

tag: treatment


title: KDM2B-mAID_J2_7_DMSO_1

description:
Library name: KDM2B-mAID_J2_7_DMSO_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: Rex1-EmGFPd2 Mcm6 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_33_Mcm6_41_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
09_Mcm6_mean_w200ks40k.bedGraph

tag: strain

tag: genetic modification

value: pU6-Mcm6-gRNA#1-CBA-PuroR transfection


title: KDM2B-mAID_GSK343_3

description:
Library name: KDM2B-mAID_GSK343_3
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_73

description: Library name: 79102750

tag: endotype

tag: Sex

tag: age blood_draw

tag: medical center

tag: transplant free_survival


title: L-fHP_76

description: Library name: 79107850

tag: smoking history

tag: cigyears

tag: race

value: alive

tag: surv months

tag: tissue


title: KDM2B-mAID_GSK343_2

description:
Library name: KDM2B-mAID_GSK343_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: Rex1-EmGFPd2 Mcm6 gRNA#1 mESCs, BrdU-IP Early

tag: cell type


title: KDM2B-mAID_GSK343_1

description:
Library name: KDM2B-mAID_GSK343_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: Patient P005 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P005_CRANI1_TUMOR_EPIC

data_processing:
Sequencing reads were processed to generate fragment-level methylation profiles.
Assembly: Sequencing libraries included lambda phage DNA as a spike-in control. Reads were processed relative to the human reference genome GRCh37 (hg19).
Supplementary files format and content: Differentially methylated fragments (DMFs) were quantified and aggregated into matrices for downstream analysis.

source_name: Human brain metastasis tissue

extract_protocol:
Cell-free DNA (cfDNA) was extracted from plasma and cerebrospinal fluid using standard protocols. Tumor genomic DNA was extracted from FFPE tissue sections.
Libraries were prepared using the PredicineEPIC platform for genome-wide methylation profiling.

value: Human brain metastasis tissue

value: Non-small cell lung carcinoma


title: L-fHP_72

description: Library name: 79100050

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

value: L-fHP

tag: fvc pred

tag: fvc+pred pct

tag: dlco uncorrected

tag: dlco pred


title: Human PBMCs CITE-seq library, 10X Batch 2, ADT + HTO

description:
Library name: PBMC_Batch2_ADT_HTO
10x Genomics

value: peripheral mononuclear blood cells

tag: time

value: Day0 and Day7 post-vaccination

tag: treatment

value: Typhim Vi vaccine

tag: batch


title: Patient P004 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy 2 of 2

description: Library name: P004_CRANI2_TUMOR_EPIC


title: Rex1-EmGFPd2 Pold2 gRNA#1 mESCs, BrdU-IP Early

description:
DEP_01_066_57_Pold2_17_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
12_Pold2_mean_w200ks40k.bedGraph

tag: cell line

value: embryonic stem cells

tag: strain

tag: genetic modification

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

value: pU6-Pold2-gRNA#1-CBA-PuroR transfection


title: Human PBMCs CITE-seq library, 10X Batch 1, GEX

description:
Library name: PBMC_Batch1_mRNA
10x Genomics


title: KDM2B-mAID_DMSO_3

description:
Library name: KDM2B-mAID_DMSO_3
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx

value: DMSO


title: Rex1-EmGFPd2 Topbp1 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_31_Topbp1_35_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
17_Topbp1_mean_w200ks40k.bedGraph


title: KDM2B-mAID_DMSO_2

description:
Library name: KDM2B-mAID_DMSO_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_71

description: Library name: 79099850

tag: endotype

tag: Sex

tag: age blood_draw

tag: smoking history

value: Yes

value: White

tag: pctdlcouncorr

tag: medical center

tag: transplant free_survival

value: venous blood


title: FA13.1J CLYBL-AB9 R3

description: Library name: Sample 21

value: FA13.1J CLYBL-AB9

tag: cell type

value: iAstrocyte


title: Rex1-EmGFPd2 Topbp1 gRNA#2 mESCs, BrdU-IP Early


title: KDM2B-mAID_DMSO_1

description:
Library name: KDM2B-mAID_DMSO_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: KDM2B-mAID_5PhIAA_GSK343_3

description:
Library name: KDM2B-mAID_5PhIAA_GSK343_3
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: KDM2B-mAID_5PhIAA_GSK343_2

description:
Library name: KDM2B-mAID_5PhIAA_GSK343_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_70

description: Library name: 79099250

tag: diagnosis

value: Female

value: No

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

value: deadtx

tag: surv months

tag: tissue


title: Rex1-EmGFPd2 Topbp1 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_29_Topbp1_33_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
17_Topbp1_mean_w200ks40k.bedGraph

tag: cell line

tag: treatment


title: KDM2B-mAID_5PhIAA_GSK343_1

description:
Library name: KDM2B-mAID_5PhIAA_GSK343_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_69

description: Library name: 79098650

value: whole blood cells

value: Fibrotic hypersensitivity pneumonitis

value: Male

tag: race

tag: dlco uncorrected

tag: dlco pred

value: alive


title: KDM2B-mAID_5PhIAA_3

description:
Library name: KDM2B-mAID_5PhIAA_3
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_87

description: Library name: 79148450

tag: endotype

value: L-fHP

tag: Sex

tag: age blood_draw


title: L-fHP_68

description: Library name: 79097650

tag: smoking history

tag: pctdlcouncorr

tag: medical center


title: KDM2B-mAID_5PhIAA_1

description:
Library name: KDM2B-mAID_5PhIAA_1
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: KDM2B-mAID_5PhIAA_2

description:
Library name: KDM2B-mAID_5PhIAA_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_67

description: Library name: 79096950

tag: cell type

tag: diagnosis

tag: transplant free_survival


title: Cancer tissue, coculture with hepatic tissue, bio rep 4

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

description: Library name: H6

data_processing:
Read alignment, counting, differential expression analysis, gene ontology (GO), Reactome, and gene set enrichment analysis (GSEA) were performed in-house at Novogene Corporation Inc. Briefly, Hisat2 (v2.2.1) was used to build the index of, and align cleaned reads to, the reference genome (GRCh38). Mapped reads were counted using featureCounts (v2.0.6) then converted to FPKM. The DESeq2 R package (v1.42.0) was used for differential expression analysis. FDR < 0.05 (Benjamini-Hochberg corrected) was considered significant. The clusterProfiler R package (v4.8.1) was used for downstream biological enrichment analyses with gene length bias corrected, including GO enrichment analysis and Reactome pathway analysis (FDR < 0.05 considered significant for each). For each pairwise GO enrichment comparison between groups, the top 10 most significant upregulated GO terms (Biological Process, Cellular Component, Molecular Factor, FDR < 0.05) were displayed and dimmed if they were not significant (FDR > 0.05) in the list of downregulated GO terms (and vice versa). The Broad Institute web-based tool (v.4.3.2) was used for GSEA (https://www.gsea-msigdb.org/gsea/index.jsp; Accessed May 2025) of the GO and Reactome datasets (FDR < 0.25 considered significant). Principal component analysis of raw counts (from featureCounts) was performed using PCAGO (normalization using DESeq2 rlog transformation) and plotted using GraphPad Prism. Heatmaps were generated using SRPlot using rlog normalized counts from DESeq2 analysis performed on the Galaxy platform, with complete Euclidean clustering of rows.
Assembly: GRCh38
Supplementary files format and content: text file listing raw gene counts for each sample

extract_protocol:
RNA extraction and isolation of the tissues cultured in AngioPlate was performed using the PicoPure™ RNA Isolation Kit (Applied Biosystems, KIT0204) according to manufacturer’s protocol. Briefly, the cancer tissue in the middle well of the AngioPlate was removed and placed in a RNase-free microtube, followed by adding 100 µL of extraction buffer, incubating at 42ºC for 30 minutes, and centrifuging at 3000g for 2 minutes to collect the supernatant containing RNA. The RNA extract from each sample was mixed with equal volume of 70% ethanol by pipetting several times until a uniform mixture was formed. The mixture was then run through a preconditioned column to have RNA bound to the column, followed by 3-4  washes according to the manufacturer's instructions. Lastly, 12 µL of elution buffer was used to elute the RNA from the column. Quantification of isolated RNA was performed using a NanoDrop spectrophotometer. Isolated RNA was stored at -80ºC before sequencing.
Non strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Human Breast Cancer


title: Rex1-EmGFPd2 Ddb1 gRNA#2 mESCs, BrdU-IP Early

description:
DEP_01_066_27_Ddb1_27_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
03_Ddb1_mean_w200ks40k.bedGraph

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

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

value: embryonic stem cells

tag: strain

tag: genetic modification

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

value: pU6-Ddb1-gRNA#2-CBA-PuroR transfection


title: Cancer tissue, coculture with hepatic tissue, bio rep 3

description: Library name: H4


title: Cancer tissue, coculture with hepatic tissue, bio rep 2

description: Library name: H3


title: L-fHP_66

description: Library name: 79095250

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

tag: surv months

tag: tissue


title: Cancer tissue, coculture with cardiac tissue, bio rep 4

description: Library name: CM6

tag: cell line


title: L-fHP_65

description: Library name: 79093450

tag: endotype

value: Yes

tag: race

tag: dlco uncorrected

tag: dlco pred


title: Cancer tissue, coculture with cardiac tissue, bio rep 3

description: Library name: CM5


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

description:
DEP_01_066_25_Ddb1_25_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
03_Ddb1_mean_w200ks40k.bedGraph

tag: treatment

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


title: Cancer tissue, coculture with cardiac tissue, bio rep 2

description: Library name: CM2


title: Cancer tissue, coculture with cardiac tissue, bio rep 1

description: Library name: CM1


title: Rex1-EmGFPd2 Prim1 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_23_Prim1_3_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
13_Prim1_mean_w200ks40k.bedGraph

value: pU6-Prim1-gRNA#2-CBA-PuroR transfection


title: Cancer tissue, monoculture, bio rep 4

description: Library name: C6


title: L-fHP_63

description: Library name: 79090150

tag: Sex

tag: age blood_draw

tag: smoking history

value: White

tag: pctdlcouncorr

tag: medical center

value: venous blood


title: Cancer tissue, monoculture, bio rep 3

description: Library name: C4

tag: cell type


title: Rex1-EmGFPd2 Prim1 gRNA#2 mESCs, BrdU-IP Early

tag: strain

tag: genetic modification


title: Cancer tissue, monoculture, bio rep 2

description: Library name: C3


title: L-fHP_62

description: Library name: 79084750

tag: diagnosis

tag: cigyears

value: Black

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival


title: Cancer tissue, monoculture, bio rep 1

description: Library name: C2

tag: cell line


title: Sample 6

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

description: Library name: 24-227B

data_processing:
Transcriptomic maps of single-end reads were generated using STAR v2.7 against the hg38 reference genome.
Transcript counts were assessed by TETranscripts using the default settings and counts were assigned to Ensembl gene ids. TEs were removed from count files.
Assembly: Hg38
Supplementary files format and content: Count data in CSV format

source_name: Endometrial biopsy

growth_protocol: Primary endometrial stromal cells were maintained in DMEM/F12 supplemented with 10% dextran-coated charcoal-striped fetal bovine serum (DCC-FBS), 1% antibiotic/antimycotic, 1 nM 17β-estradiol (Merck Life Sciences UK Ltd) and 2 μg/mL insuline (Merck Life Sciences UK Ltd) in a humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
RNA was harvested using RNeasy plus mini kit (Qiagen, UK). The purified RNA (>10ng/uL) was then sent to Novogene Co., Ltd for sequencing service.
Libraries were quality checked and quantified before sequencing. Paired-end sequencing (150 bp reads) was carried out on an Illumina NovaSeq X Plus platform, generating approximately 6 Gb of raw data per sample.

treatment_protocol: After confluence (designated as day 0), decidualization was induced by a eight-day treatment with 0.5 mM cAMP (Merck Life Sciences UK Ltd) and 1 μM medroxyprogesterone (Merck Life Sciences UK Ltd) (C+M), concurrently with 2 μM CBG (PhytoLab GmbH, Germany)

tag: tissue

value: Endometrial biopsy

value: endometrial stromal cells

value: C+M+CBG


title: Sample 5

description: Library name: 24-227A

value: C+M


title: L-fHP_61

description: Library name: 79084150

value: whole blood cells

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: Female

tag: race

tag: dlco uncorrected

tag: dlco pred

tag: surv months


title: Rex1-EmGFPd2 Prim1 gRNA#1 mESCs, BrdU-IP Early

description:
DEP_01_066_21_Prim1_1_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
13_Prim1_mean_w200ks40k.bedGraph

tag: treatment

value: pU6-Prim1-gRNA#1-CBA-PuroR transfection


title: Sample 4

description: Library name: 24-226B


title: L-fHP_60

description: Library name: 79084050

value: L-fHP

tag: Sex

tag: age blood_draw

tag: smoking history

value: No

tag: pctdlcouncorr

tag: medical center

value: deadtx


title: Sample 2

description: Library name: 24-225B

tag: cell type


title: Rex1-EmGFPd2 Gins4 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_17_Gins4_31_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
07_Gins4_mean_w200ks40k.bedGraph

value: embryonic stem cells

tag: strain

tag: genetic modification

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

value: pU6-Gins4-gRNA#2-CBA-PuroR transfection


title: L-fHP_59

description: Library name: 79083850

tag: diagnosis

tag: cigyears

value: White

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival

value: alive


title: Sample 1

description: Library name: 24-225A

tag: tissue


title: Rex1-EmGFPd2 Gins4 gRNA#2 mESCs, BrdU-IP Early

tag: cell line


title: L-fHP_58

description: Library name: 79082350

tag: endotype

tag: race

tag: dlco uncorrected

tag: dlco pred

tag: surv months

value: venous blood


title: TTchemSeq 1 hour recovery after h2o2 with OGG1i and Olaparib 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_60_double_r2

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

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: Triticum aestivum water infected RNA bio rep 3

city: Columbus

first: Jonathan

last: Jacobs

state: OH

address: 2021 Coffey Rd

department: Plant Pathology

institute: Ohio State University

description: Library name: mockR3

data_processing:
Trimmomatic - fastq trimming and pairing
STAR - mapping the reads to a reference genome
Htseq - counting the reads mapped
DEseq2 - the differential expression analysis
Assembly: Taestivumcv_ChineseSpring_725_v2.1
Supplementary files format and content: non-normalized gene count files

organism: Triticum aestivum

source_name: Leaf

extract_protocol:
TRIzol
16s and plant ribosomal depletion

value: Leaf

tag: genotype

value: Triticum aestivum 'Chinese Spring'

tag: treatment

value: water mock


title: Rex1-EmGFPd2 Gins4 gRNA#1 mESCs, BrdU-IP Late

first: Ichiro

last: Hiratani

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

institute: RIKEN

description:
DEP_01_066_15_Gins4_29_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
07_Gins4_mean_w200ks40k.bedGraph

tag: cell type

value: pU6-Gins4-gRNA#1-CBA-PuroR transfection


title: TTchemSeq 1 hour recovery after h2o2 with OGG1i and Olaparib replicate 1 exp5

description: Library name: TT5_60_double_r1


title: L-fHP_57

description: Library name: 79081250

value: whole blood cells

value: Fibrotic hypersensitivity pneumonitis

tag: Sex

value: Male

tag: age blood_draw

tag: smoking history

tag: pctdlcouncorr

tag: medical center


title: Triticum aestivum water infected RNA bio rep 2

description: Library name: mockR2


title: Rex1-EmGFPd2 Gins4 gRNA#1 mESCs, BrdU-IP Early

tag: strain

tag: genetic modification


title: TTchemSeq 1 hour recovery after h2o2 with OGG1i replicate 2 exp5

description: Library name: TT5_60_ogg1i_r2


title: L-fHP_56

description: Library name: 79079850

tag: diagnosis

value: L-fHP

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival

tag: tissue


title: Triticum aestivum water infected RNA bio rep 1

description: Library name: mockR1


title: Rex1-EmGFPd2 Gins3 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_13_Gins3_55_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
06_Gins3_mean_w200ks40k.bedGraph

tag: cell line

value: pU6-Gins3-gRNA#2-CBA-PuroR transfection


title: TTchemSeq 1 hour recovery after h2o2 with OGG1i replicate 1 exp5

description: Library name: TT5_60_ogg1i_r1


title: L-fHP_55

description: Library name: 79072750

tag: endotype

value: Female

value: No

tag: race

tag: dlco uncorrected

tag: dlco pred

tag: surv months


title: Rex1-EmGFPd2 Prim1 gRNA#1 mESCs, BrdU-IP Late

tag: cell type

value: embryonic stem cells

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

tag: treatment

value: pU6-Prim1-gRNA#1-CBA-PuroR transfection


title: Triticum aestivum Xanthomonas translucens pv. undulosa with xopAL1 genomic inserion infected RNA bio rep 3

description: Library name: XtuxopAL1R3

tag: genotype

value: Xanthomonas translucens pv undulosa


title: Rex1-EmGFPd2 Gins3 gRNA#2 mESCs, BrdU-IP Early

tag: strain


title: TTchemSeq 1 hour recovery after h2o2 with olaparib replicate 2 exp5

description: Library name: TT5_60_olaparib_r2


title: L-fHP_54

description: Library name: 79072650

tag: Sex

tag: age blood_draw

tag: smoking history

value: White

tag: pctdlcouncorr

tag: medical center

value: alive

value: venous blood


title: Triticum aestivum Xanthomonas translucens pv. undulosa with xopAL1 genomic inserion infected RNA bio rep 2

description: Library name: XtuxopAL1R2

value: Leaf

value: Triticum aestivum 'Chinese Spring'


title: Rex1-EmGFPd2 Gins3 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_11_Gins3_53_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
06_Gins3_mean_w200ks40k.bedGraph

tag: genetic modification

value: pU6-Gins3-gRNA#1-CBA-PuroR transfection


title: TTchemSeq 1 hour recovery after h2o2 with olaparib replicate 1 exp5

description: Library name: TT5_60_olaparib_r1

value: HEK293 Flp-in T-Rex


title: Sample 3

description: Library name: 24-226A

tag: tissue

value: Endometrial biopsy

value: endometrial stromal cells

value: C+M


title: L-fHP_53

description: Library name: 79071850

value: whole blood cells

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

value: L-fHP

value: Male

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival


title: Triticum aestivum Xanthomonas translucens pv. undulosa with xopAL1 genomic inserion infected RNA bio rep 1

description: Library name: XtuxopAL1R1


title: Rex1-EmGFPd2 Gins3 gRNA#1 mESCs, BrdU-IP Early

tag: cell line

value: embryonic stem cells

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


title: L-fHP_52

description: Library name: 79069550

tag: cell type

tag: endotype

value: No

tag: race

tag: dlco uncorrected

tag: dlco pred


title: Triticum aestivum Xanthomonas translucens pv. undulosa infected RNA bio rep 3

description: Library name: XtuR3

tag: genotype

tag: treatment

value: Xanthomonas translucens pv undulosa


title: TTchemSeq 1 hour recovery after h2o2 replicate 2 exp5

description: Library name: TT5_60_dmso_r2


title: Rex1-EmGFPd2 Gins1 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_066_05_Gins1_23_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
05_Gins1_mean_w200ks40k.bedGraph

tag: strain

value: pU6-Gins1-gRNA#2-CBA-PuroR transfection


title: TTchemSeq 1 hour recovery after h2o2 replicate 1 exp5

description: Library name: TT5_60_dmso_r1


title: KDM2B-mAID_J2_7_5PhIAA_2

description:
Library name: KDM2B-mAID_J2_7_5PhIAA_2
processed data file: KDM2B-mAID_JARID2_AEBP2_DKO_and_wt_counts.xlsx


title: L-fHP_51

description: Library name: 79068050

tag: Sex

value: Female

tag: age blood_draw

tag: smoking history

value: White

tag: pctdlcouncorr

tag: medical center

value: alive

tag: surv months

value: venous blood


title: Triticum aestivum Xanthomonas translucens pv. undulosa infected RNA bio rep 2

description: Library name: XtuR2

tag: tissue

value: Leaf

value: Triticum aestivum 'Chinese Spring'


title: Rex1-EmGFPd2 Gins1 gRNA#2 mESCs, BrdU-IP Early

tag: genetic modification


title: TTchemSeq 30min recovery after h2o2 with OGG1i and Olaparib replicate 2 exp5

description: Library name: TT5_30_double_r2

tag: cell line

value: HEK293 Flp-in T-Rex


title: Triticum aestivum Xanthomonas translucens pv. undulosa infected RNA bio rep 1

description: Library name: XtuR1


title: Rex1-EmGFPd2 Gins1 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_066_03_Gins1_21_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
05_Gins1_mean_w200ks40k.bedGraph

tag: cell type

value: pU6-Gins1-gRNA#1-CBA-PuroR transfection


title: TTchemSeq 30min recovery after h2o2 with OGG1i and Olaparib replicate 1 exp5

description: Library name: TT5_30_double_r1


title: L-fHP_50

description: Library name: 79067650

value: whole blood cells

tag: diagnosis

tag: endotype

value: Yes

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival


title: L-fHP_49

description: Library name: 79067250

value: Fibrotic hypersensitivity pneumonitis

value: L-fHP

tag: race

tag: dlco uncorrected

tag: dlco pred


title: Rex1-EmGFPd2 Gins1 gRNA#1 mESCs, BrdU-IP Early

value: embryonic stem cells

tag: strain

tag: treatment


title: TTchemSeq 30min recovery after h2o2 with OGG1i replicate 2 exp5

description: Library name: TT5_30_ogg1i_r2


title: Triticum aestivum Xanthomonas translucens pv. translucens with xopAL1 deletion infected RNA bio rep 3

description: Library name: XttDxopAL1R3

tag: genotype

value: Xanthomonas translucens pv translucens


title: L-fHP_48

description: Library name: 79066050

tag: Sex

tag: age blood_draw

tag: smoking history

value: No

value: Black

tag: pctdlcouncorr

tag: medical center

value: deadtx

tag: surv months


title: Triticum aestivum Xanthomonas translucens pv. translucens with xopAL1 deletion infected RNA bio rep 2

description: Library name: XttDxopAL1R2

tag: tissue


title: TTchemSeq 30min recovery after h2o2 with OGG1i replicate 1 exp5

description: Library name: TT5_30_ogg1i_r1

tag: cell line


title: Rex1-EmGFPd2 Control mESCs Replicate 5, BrdU-IP Late

description:
DEP_01_085_15_vector_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
01_vec_mean_w200ks40k.bedGraph

tag: cell type

tag: genetic modification

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

value: pU6-sgRNAscaff-CBA-PuroR transfection


title: L-fHP_47

description: Library name: 79064750

tag: diagnosis

tag: endotype

value: Male

tag: cigyears

value: White

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival


title: Rex1-EmGFPd2 Control mESCs Replicate 5, BrdU-IP Early

tag: strain

tag: treatment


title: Triticum aestivum Xanthomonas translucens pv. translucens with xopAL1 deletion infected RNA bio rep 1

description: Library name: XttDxopAL1R1

value: Leaf

tag: genotype


title: TTchemSeq 30min recovery after h2o2 with olaparib replicate 2 exp5

description: Library name: TT5_30_olaparib_r2


title: Rex1-EmGFPd2 Control mESCs Replicate 4, BrdU-IP Late

description:
DEP_01_085_01_vector_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
01_vec_mean_w200ks40k.bedGraph


title: Triticum aestivum Xanthomonas translucens pv. translucens infected RNA bio rep 3

description: Library name: XttR3

value: Triticum aestivum 'Chinese Spring'


title: L-fHP_46

description: Library name: 79062150

tag: Sex

tag: age blood_draw

tag: smoking history

tag: race

tag: dlco uncorrected

tag: dlco pred

value: alive

value: venous blood


title: TTchemSeq 30min recovery after h2o2 with olaparib replicate 1 exp5

description: Library name: TT5_30_olaparib_r1

tag: cell line

value: HEK293 Flp-in T-Rex


title: L-fHP_45

description: Library name: 79060750

tag: cell type

value: whole blood cells

value: Female

tag: pctdlcouncorr

tag: medical center

tag: surv months

tag: tissue


title: Triticum aestivum Xanthomonas translucens pv. translucens infected RNA bio rep 2

description: Library name: XttR2


title: Rex1-EmGFPd2 Control mESCs Replicate 4, BrdU-IP Early

tag: genetic modification


title: TTchemSeq 30min recovery after h2o2 replicate 2 exp5

description: Library name: TT5_30_dmso_r2


title: L-fHP_44

description: Library name: 79060150

tag: diagnosis

value: Fibrotic hypersensitivity pneumonitis

tag: endotype

value: L-fHP

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival


title: Triticum aestivum Xanthomonas translucens pv. translucens infected RNA bio rep 1

description: Library name: XttR1

tag: genotype

tag: treatment

value: Xanthomonas translucens pv translucens


title: TTchemSeq 30min recovery after h2o2 replicate 1 exp5

description: Library name: TT5_30_dmso_r1


title: L-fHP_43

description: Library name: 79059050

tag: Sex

tag: age blood_draw

tag: smoking history

value: No

tag: race

tag: dlco uncorrected


title: Rex1-EmGFPd2 Control mESCs Replicate 3, BrdU-IP Late

description:
DEP_01_066_37_vector_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
01_vec_mean_w200ks40k.bedGraph

tag: cell line

tag: cell type

value: embryonic stem cells

tag: strain


title: Rex1-EmGFPd2 Topbp1 gRNA#1 mESCs, BrdU-IP Early

description:
DEP_01_066_29_Topbp1_33_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
17_Topbp1_mean_w200ks40k.bedGraph

tag: genetic modification


title: Rex1-EmGFPd2 Ddb1 gRNA#2 mESCs, BrdU-IP Late

value: pU6-Ddb1-gRNA#2-CBA-PuroR transfection


title: Rex1-EmGFPd2 Control mESCs Replicate 3, BrdU-IP Early

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


title: Scramble-nanopore

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

institute: University of Manitoba

description:
Library name: Sample 10
Nanopore_Direct_RNA-seq

data_processing:
FASTQ files were aligned against Ensembl release 102 Mus musculus genome GRCm38 using hisat2 v2.2.0 with the --dta option
For calculating gene/transcript abundances Stringtie v2.2.1 was used with -G -A -B -e -x parameters. For gene/transcript annotation we used the ensemble release 102 version of the Mus Musculus genome in conjunction with transcriptome gtf’s of the same release.
For calculating editrate tables, samples are aligned against the sequences of unique B2 with bwa aln v0.7.19 using options -n 10. The sense-aligning fraction of the bam files was extracted using samtools v1.21 with options -F 16. The sense aligning component was run with reditools v1.2.1 REDItoolDenovo script with options -c 1 -q 1 -m 1 -O 0 -V 1 -n 0. Edit rate was computed using custom method as detailed in the assocaited with this GSE series published manuscript.
Nanopore samples were concatonated group-wise and aligned against Ensembl release 102 GRCm38 mouse genome using Minimap2 v2.24 with the options -ax sr -uf --secondary=yes. Nanopore samples were additionally aligned against the sequences of unique B2 elements (>=125 bp in length) using Minimap2 v2.24 with the same options. The first alignment (on genome) was used with nanopolish v0.14.0 to produce eventalign files, which were then intersected with the coordinates of known B2 mm1a using bedtools v2.31.1. The second alignment (on unique B2ome) was used with nanopolish v0.14.0 and xpore v2.0 to produce the xpore tables.
Assembly: GRCm38
Supplementary files format and content: Normalized abundance measurements generated from stringtie in a tab delimited format depicting FPKM and TMP for  genes/transcripts in the annotation file.
Supplementary files format and content: Editrate tables generated from reditools in a tab delimited format with additional columns added as described in publication. Nanopolish and xpore tables are generated from their respective programs and stored in a tab delimited format. Nanopolish tables contain additional columns representing the B2 loci which they intersected with.

growth_protocol: The HT-22 hippocampal cell line was grown as a monolayer up to 70% confluency in DMEM, 1%pen/strep, 10%Calf Serum (heat inactivated)

extract_protocol:
Trizol RNA extraction: 1mL trizol added to pelleted cells, dissolved 5min. 200uL chloroform added to trizol treated cells, incubate 2min. Centrifuged at 12 000xg 4C. Aqueous layer treated with 500uL isopropanol, incubate -20C 1hour, centrifuged at 12 000xg 10min 4C, pellet washed with 75% ethanol and centrifuged at 7 500xg 5min 4C. Pellet dried 1min, resuspended in 30uL pure H2O. For the Nanopore direct RNA-seq RNA experiment of the HT-22 anti Adar treatment, samples were pooled from n=4 biological replicates prior to library preparation.
Illumina_RNA-seq: Libraries for directional RNA-seq were prepared according to manufacturer's instructions with a size enrichment for longer RNAs >100nt by MiRvana size selection kit preceeding the library construction using NEBNext rRNA depletion kit and NEBNext Ultra RNA Library Prep Kit for Illumina (E7530). Nanopore_Direct_RNA-seq: The libraries were prepared using the vendor recommended protocol for the SQK_RNA002 direct RNA sequencing kit from 1ug of starting material. Briefly, 9.5uL of RNA was mixed with 1uL RTA adaptor (Nanopore), 1.5uL T4 DNA ligase (NEB, M0202M) and 3uL NEBNext quick ligation buffer (NEB, B6058S), and incubated for 15min at room temperature. The first-strand synthesis reaction was constructed from the ligation product by adding 9uL H2O, 2uL dNTP mix (NEB, N0447S), 8uL FS buffer (Invitrogen, 18080093), 4uL 0.1M DTT (Invitrogen, 18080093) and 2uL Superscript III reverse transcriptase (Invitrogen, 18080093) and incubated at 50C for 50min, 70C for 10min, then placed immediately on ice. The sample was then subjected to a 1.8X bead clean up using the vendor recommended protocol with Mag-Bind TotalPure NGS beads (Omega Bio-Tek, M1378), eluting in 23uL H2O. 6uL of the RMX adaptor (Nanopore), 8uL of the NEBNext quick ligation buffer and 3uL of T4 DNA ligase were added to the eluted RNA:DNA hybrid and incubated for another 15min at room temperature, concluded by a 1X bead cleaning reaction. The prepared libraries were loaded and sequenced on a R9.4.1 PromethION flow cell using a PromethION 24 Beta instrument as per manufacturer suggestions.

treatment_protocol: Anti-Adar 1 and 2 siRNA treatment: A pool of siRNAs  targeting Adar1 and Adar 2 (Anti-ADAR) or a control scramble siRNA with no known targets (scramble) were transfected to  500 000 cells for 36h. siRNA was transfected using the Qiagen hiperfect transfecting reagent, according to manufacturers instructions. siRNA incubation occurred at a final concentration of 10nM. siRNA and hiperfect were incubated for 20min before being added to the culture media dropwise. Cells grown in 6 well plates (1mL growth media).

tag: tissue

value: Hippocampal cell line

value: Scramble siRNA


title: L-fHP_42

description: Library name: 79058050

tag: diagnosis

tag: endotype

value: White

tag: dlco pred

tag: pctdlcouncorr

tag: medical center

tag: surv months


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

description: Library name: TT5_15_double_r2


title: AntiAdar-nanopore

description:
Library name: Sample 9
Nanopore_Direct_RNA-seq

tag: treatment

value: Adar1&Adar2 siRNA knockdown


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

city: Kobe

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 and Olaparib replicate 1 exp5

description: Library name: TT5_15_double_r1


title: L-fHP_41

description: Library name: 79054350

tag: Sex

value: Male

value: Yes

tag: cigyears

tag: fvc pred

tag: fvc+pred pct

tag: transplant free_survival

value: alive


title: Cancer tissue, coculture with hepatic tissue, bio rep 1

description: Library name: H2

tag: cell line

value: Human Breast Cancer