title: Recovery, 5h, KO, rep2

status: Public on Jul 26 2025

type: SRA

city: Minneapolis

first: Colin

last: Campbell

state: MN

address: 3-130 Nils Hasselmo Hall

department: Pharmacology

country: USA

institute: University of Minnesota

library_source: genomic

data_processing:
High-throughput sequencing was performed on prepared libraries Azenta/Genewiz (South Plainfield, NJ) using HiSeq platforms with 150 paired-end (PE) at ~30M reads per library. Adaptor sequences were removed with Trim galore (v 0.6.6). Trimmed reads were then mapped onto the human genome (hg38) using the default settings of BWA MEM (v 0.7.17). Exclusion regions for hg38 were downloaded from (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and were removed with Bedtools (v 2.29.2) along with the mitochondrial chromosome. PCR duplicates were removed with Picard MarkDuplicates (v 2.25.6). Reads were quality filtered (-bq 55), sorted and indexed using SAMtools (v 1.9).
MACS2 (v 2.2.8) was used to identify peaks in formaldehyde-treated samples compared to untreated controls using the following parameter (--nomodel --nolambda –broad). For untreated control samples, no control file was used to identify the peaks. Randomized peak lists were generated by randomly selecting three sets of peaks that have the average length and width of T0 and T5 peak lists using R (v 4.2.2).
OverlapEnrichment command from ChromHMM was used to calculate the fold enrichment of each chromatin state to control, treatment, and recovery peak lists generated by MACS2 and for randomized peaklists.  The fold enrichment is computed as: (number of bases in the state and peak list /number of bases in the state)/number of bases in the peak list /number of bases in the genome))
All samples were normalized as counts per million mapped reads (CPM) using deepTools (v 3.5.2) command bamCoverage with the following parameters (--binSize 10 --normalizeUsing CPM --ignoreForNormalization chrM --extendReads).
To generate gene expression quintiles, FPKM of HT1080 polyA plus RNA-seq (accession number ENCFF691EGO) was used to divide gene expression into four quintiles (Q1-Q4) with a threshold of FPKM = 0.1 for Q1.  Q0 was generated by sampling genes that has FPKM = 0. Heatmaps were plotted using EnrichedHeatmap (v 3.17).
Assembly: hg38
Supplementary files format and content: bigWig (bw) and broadPeak
Library strategy: DPC seq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HT1080 cells were cultured in Eagle’s Minimum Essential Media (MEM) supplemented with 9% fetal bovine serum (FBS). Cells were maintained in 5%  CO2 humidified incubator at 37 C.

extract_protocol:
Briefly, media was gently aspirated, and cells were lysed with MB buffer prewarmed at 55℃  (5.6 M guanidine thiocyanate 10 mM Tris–HCl (pH 6.5), 20 mM EDTA, 4% Triton X-100, 1% Sarkosyl, and 1% DTT). After scraping, the viscous lysate was passed through 1mL pipette tip six times, then transferred into 1.5 mL Eppendorf tube. The lysate was further sheared by passing it through a 19-gauge needle for six times, then equal volume of pre-chilled 100% ethanol was added to precipitate free and protein-linked DNA. After a full speed sedimentation at 4℃ for 20 min, the supernatant was carefully removed and the pellet was washed with a 50% ethanol wash buffer (20 mM Tris–HCl pH 6.5, 150 mM NaCl and 50% ethanol). The wash buffer was carefully aspirated and the remaining sedimented material was saved at -80℃ with no air-drying. The next day, precipitated DNA was resuspended in 1 mL 1% SDS buffer containing 20 mM Tris-HCl (pH 7.4), sheared by passing through a 21-guage needle six times, transferred to 1 mL Covaris milliTUBE, and subjected to ultrasonication for 12-14 minutes in a Covaris S-220 instrument following the manufacturer’s protocol to generate DNA fragments in the 200-500bp size range. Following ultrasonication, KCl-SDS precipitation was used as previously described with some modifications. Briefly, 1M KCl and 1M Tris-HCl (pH 7.4) were added to a final concentration of 100 mM and 20mM; respectively, to precipitate protein-linked DNA. Samples were chilled on ice for 5 min then spun at full speed, 4℃, for 5 min. The precipitated protein-linked DNA was then washed with 1.5 mL of 100mM KCl buffer containing 20mM Tris-HCl (pH 7.4), heated at 55℃, chilled on ice, then spun again. The last wash was repeated one more time. The final pellet containing protein-linked DNA was then resuspended in a 100mM KCl buffer containing 20 mM Tris-HCl (pH 7.4), 10mM EDTA, and 0.2mg/ml proteinase K, and incubated overnight at 55℃ to digest DPCs and reverse the crosslink. The next day, samples were chilled on ice for 5 min, and supernatant was carefully collected after a full speed centrifuge at 4℃ for 10 min. Samples were then purified with Qiagen PCR purification column, and amount of purified DNA was measured with Qubit dsDNA High Sensitivity Assay kit following the manufacturer’s guidelines (Fig. S2). Then, equal amounts of protein-linked DNA precipitated from each group were used to prepare DNA libraries for next-generation sequencing.
DNA libraries were prepared using the NEBNext Ultra II DNA Prep Kit for Illumina following the manufacturer’s protocol. Libraries with 200-500 bp were selected using the E-Gel Ex 2% agarose gel ran at 35v for 1.5 hour. Size-selected libraries were then purified using the MinElute Gel extraction kit and quantified with the Qubit. For library QC, libraries were diluted to 1 pM and amplified with kapa primers (kapa forward: AATGATACGGCGACCACCGA; kapa reverse: CAAGCAGAAGACGGCATACGA), where similar Ct values were expected. Then, libraries were pooled with equimolar ratio.

treatment_protocol: Cells were treated with +/- 400uM formaldehyde for two hours in serum-free medium

tag: cell line

tag: cell type

value: Human fibrosarcoma

tag: genotype

value: XPA-KO

tag: treatment

value: 400uM formaldehyde, 2h, followed by 5h recovery


title: Recovery, 5h, KO, rep1


title: initial untreated, KO, rep2

value: 400uM formaldehyde, 2h


title: Recovery, 5h, WT, rep2

value: WT


title: initial untreated, WT, rep1


title: initial untreated, KO, rep1


title: untreated, KO, rep2

value: no treatment


title: untreated, WT, rep2


title: untreated, KO, rep1


title: initial untreated, WT, rep2


title: untreated, WT, rep1


title: Recovery, 5h, rep2

description: 5h_merged_CPM_deeptools_normalized.unique.bw


title: Recovery, 5h, rep3


title: Initial treatment, rep3

description: T0_merged_CPM_deeptools_normalized.unique.bw


title: Recovery, 5h, rep1


title: untreated, rep3


title: Initial treatment, rep2


title: untreated, rep2


title: Hatchling_IV

status: Public on Jun 30 2025

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

library_source: transcriptomic

data_processing:
Alignment with STAR aligner
Assembly: GCF_003073045.1
Supplementary files format and content: devel_star_count.csv.gz contains read counts from STAR aligner for all samples.

molecule: polyA RNA

organism: Pomacea canaliculata

source_name: Whole Animal

extract_protocol:
Trizol Extraction of whole embryos extracted from eggs at each stage
PoylA selected RNA

tag: tissue

value: Whole Animal

tag: developmental stage

value: Hatchling


title: Hatchling_II


title: Hatchling_I


title: Recovery, 5h, WT, rep1


title: Stage-10_II


title: Stage-10_III


title: Stage-9_III


title: Stage-10_I


title: Stage-9_IV


title: Initial treatment, rep1


title: Stage-9_II


title: Stage-8_IV


title: untreated, rep1


title: Stage-8_II


title: Stage-8_I


title: Stage-8_III


title: Stage-7_I


title: Stage-7_II


title: Stage-10_IV


title: Stage-9_I


title: Stage-7_III


title: Hatchling_III


title: Stage-6_III


title: Stage-6_II


title: Stage-6_I


title: Stage-5_III


title: Stage-5_II


title: Stage-5_I


title: Stage-4_III


title: Stage-4_II


title: Stage-4_I


title: Stage-3_III


title: Stage-3_II


title: Stage-2_III


title: Stage-3_I


title: Stage-2_I


title: Stage-2_II


title: pht1-V85A-input-2

city: Vienna

first: Zachary

middle: Hugh

last: Harvey

state: Vienna

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

data_processing:
Alignments, quality control, and initial processing of the raw fastq files from the sequencing run were performed using the dev version of the nf-core/chipseq pipeline (https://github.com/nf-core/chipseq) with default parameters.
Input-normalized bigWig files were subsequently generated using Deeptools (v3.3.1)
Assembly: ASM294v2
Supplementary files format and content: Provided are bigWig files representing the read-depth normalized ChIP-seq of myc-tagged Spt6 and input control for each sample. Additionally, input-normalized bigWig files for each sample are also provided.

organism: Schizosaccharomyces pombe

growth_protocol: Cells were revived from frozen (-70 ºC) stocks on YES plates at 32 ºC. Cells were then grown to saturation in YES at 32 ºC, subcultured and grown to mid-log (OD600 ~ 0.5) before being harvested.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis with beads via a Precellys homogenizer, chromatin was sonicated with a E220 focused ultra-sonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext Ultra II library preparation kit for Illumina complemented with custom synthesized barcoded sequencing adapters provided by the Vienna BioCenter Core Facilities Next Generation Sequencing Facility. PCR was performed as a 50 µl reaction using the Q5 polymerase (NEB). Samples were PCR-amplified to the beginning of the logarithmic phase, as determined using a small-scale qPCR reaction run in parallel (typically around 8-10 cycles). Following quality control by Agilent Fragment Analyzer and quantification by RT-qPCR using a Kapa Library Quantification Kit, libraries were sequenced at the Vienna BioCenter Core Facilities Next Generation Sequencing Core Facility on an Illumina NovaSeq X.

treatment_protocol: No treatment was used.

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 V85A-hygMX spt6-13xMyc-kanMX

tag: chip antibody


title: pht1-V85A-input-1


title: pht1-K84H-input-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 K84H-hygMX spt6-13xMyc-kanMX


title: pht1-L83G-input-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 L83G-hygMX spt6-13xMyc-kanMX


title: pht1-L83N-input-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 L83N-hygMX spt6-13xMyc-kanMX


title: pht1-L83N-input-1


title: pht1-L83G-input-1


title: pht1-L83F-input-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 L83F-hygMX spt6-13xMyc-kanMX


title: pht1-L83M-input-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 L83M-hygMX spt6-13xMyc-kanMX


title: pht1-A80S-input-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 A80S-hygMX spt6-13xMyc-kanMX


title: pht1-A80S-input-1


title: pht1-K84H-input-1


title: pht1-input-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::hygroMX spt6-13xMyc-kanMX


title: pht1-L83M-input-1


title: pht1-input-1


title: pht1-L83F-input-1


title: wt-input-2

value: h- ade6-M216 ura4-D18 leu1-32 spt6-13xMyc-kanMX


title: pht1-V85A-spt6-1

value: anti-Myc 9E10


title: wt-input-1


title: pht1-L83N-spt6-2


title: pht1-V85A-spt6-2


title: pht1-L83N-spt6-1


title: pht1-K84H-spt6-2


title: pht1-A80S-spt6-1


title: pht1-L83F-spt6-1


title: pht1-L83F-spt6-2


title: pht1-L83G-spt6-2


title: pht1-L83M-spt6-1


title: pht1-L83M-spt6-2


title: wt-spt6-2


title: H3K27me3, KMS11, plumKD, ctrl, rep1

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Processed using ENCODE ChIP-seq pipeline
Reads aligned to hg38 using bowtie2 and filtered for duplicates, poor quality and blacklisted regions
Coverage across 20 bp windows quantified by BAMscale
Peaks called by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, fragment coverage across 20 bp windows
Supplementary files format and content: narrowPeak, MACS2 peak calls

source_name: Haematopoietic and Lymphoid

growth_protocol: Cells were cultured in RPMI 1640 media with 2.05 mM L-Glutamine (SH30027.01; Hyclone).

extract_protocol:
Cells were fixed in 1% formaldehyde for 12 minutes, swelled in 0.5% SDS buffer then lysed in 0.5% SDS + 5% Triton buffer (2:1). Genomic DNA was sheared to 200-500bp by sonication.
ChIP libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Cells were transduced with shRNA-PLUM targeting virus and selected with 0.1 µg/ml puromycin for 48h followed by recovery of 3 days. Following recovery, cells were harvested/seeded for RNA-seq, ChIP-seq and other functional assays.

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

tag: Sex

value: Female

value: control


title: EZH2, KMS11, endogenous, ctrl, rep1

value: EZH2 (491043; Life technologies)

value: untreated


title: pht1-L83G-spt6-1


title: EZH2, KMS11, endogenous, ctrl, rep2


title: EZH2, KMS11, endogenous, ctrl, rep3


title: wt-spt6-1


title: pht1-spt6-1


title: Day 12 microfluidic SCLS

city: Ann Arbor

first: Jeyoon

last: Bok

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering Department

institute: University of Michigan

description: Library name: Sample 1

library_source: transcriptomic single cell

data_processing:
Illumina NovaSeqXPlus for basecalling
Assembly: GRCh38-2020-A
Supplementary files format and content: TSV and MTX files are generated by Cell Ranger pipeline, including barcodes, features and matrix.

source_name: H9 hESC

extract_protocol:
Microfluidic spinal cord-like structures were dissociated into single cells using accutase. Dissociated cells were then lysed and barcoded with 10x Chromium Controller Instrument (10x Genomics).
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Single Cell 3' v3)

value: H9 hESC

value: WT

value: spinal cord differentiation


title: H3K27me3, KMS11, plumKD, ctrl, rep2


title: pht1-A80S-spt6-2


title: PBMC_SK_pooled

city: Gwangju

first: Wooje

last: Lee

email: wjlee@wikim.re.kr, ntinamu001@gmail.com

address: 86, Kimchi-ro, Nam-gu

country: South Korea

institute: World Institute of Kimchi

description:
Library name: PBMC_SK_pooled
BD Rhapsody HT Xpress; Whole transcriptome amplification (WTA) pooled library

data_processing:
Assembly: GRCh38 / hg38
Raw FASTQ files were processed using the BD Rhapsody WTA Analysis Pipeline v2.2.1 (BD Biosciences). Reads were demultiplexed based on sample tag barcodes, quality-filtered, and aligned to the human GRCh38 reference genome. Unique molecular identifiers (UMIs) were deduplicated, and gene-by-cell UMI count matrices were generated.
Processed data include three files per library: (1) barcodes.tsv.gz containing cell barcode sequences, (2) features.tsv.gz containing Ensembl gene IDs and gene names, and (3) matrix.mtx.gz in Matrix Market sparse format containing the gene-by-cell UMI count matrix.
Assembly: GRCh38 / hg38
Supplementary files format and content: Processed data include three files per GEX library: (1) barcodes.tsv.gz containing cell barcode sequences, (2) features.tsv.gz containing Ensembl gene IDs and gene names, and (3) matrix.mtx.gz in Matrix Market sparse format containing the gene-by-cell UMI count matrix.
Supplementary files format and content: Processed data include three files per HTO library: (1) barcodes.tsv.gz containing cell barcode sequences, (2) features.tsv.gz containing sample tag IDs and names, and (3) matrix.mtx.gz in Matrix Market sparse format containing the sample tag-by-cell count matrix.

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: PBMC samples were collected at baseline (randomization) and at the 12-week visit according to the RCT schedule. No additional collection windows.

extract_protocol:
PBMC-derived cells were thawed in 10% FBS/DMEM at 37°C, washed twice with cold calcium/magnesium-free 0.04% BSA/PBS, and resuspended in cold Stain Buffer (BD Biosciences). Cell viability and concentration were assessed using a LUNA-FX7™ cell counter (Logos Biosystems) with AO/PI staining.
Each sample was labeled with antibody-conjugated DNA barcodes and incubated for 20 min at room temperature. Cells were washed three times with Stain Buffer and resuspended in cold Sample Buffer (BD Biosciences) before pooling and recounting. Single-cell capture was performed using the BD Rhapsody HT Xpress system and 8-lane cartridge (BD Biosciences). Cell lysis, mRNA capture on barcoded beads, cDNA synthesis, and Exonuclease I treatment were conducted per BD protocol using BD cDNA Kit (Cat# 633773). Whole transcriptome libraries were constructed using BD Rhapsody WTA Amplification Kit (Cat# 633801) through RPE and index PCR. Sample tag libraries were generated via nested PCR and indexing.

treatment_protocol: Participants received daily oral capsules for 12 weeks (equivalent to 30 g fresh kimchi): placebo (n = 4), spontaneously fermented kimchi powder S-K (n = 5), or starter-fermented kimchi powder LMS-K (Leuconostoc mesenteroides KCKM0828; n = 4) in a randomized, double-blind design. Baseline (pre-intervention) samples were collected prior to any treatment administration. (Cell isolation protocol) Blood was drawn into K₂EDTA vacutainer tubes and processed within 2 hours. PBMCs were isolated using SepMate-50 tubes with Ficoll-Paque PLUS, washed twice with PBS, then centrifuged at 250 × g for 10 min. Cell concentration and viability were assessed.

value: Peripheral Blood Mononuclear Cells

value: pooled male and female

tag: age

value: pooled

tag: library type

value: GEX


title: PBMC_Placebo_pooled

description:
Library name: PBMC_Placebo_pooled
BD Rhapsody HT Xpress; Whole transcriptome amplification (WTA) pooled library

value: Placebo pooled


title: PBMC_LMSK_pooled

description:
Library name: PBMC_LMSK_pooled
BD Rhapsody HT Xpress; Whole transcriptome amplification (WTA) pooled library


title: H3K27me3, KMS11, plumKD, ctrl, rep3


title: pht1-K84H-spt6-1

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 K84H-hygMX spt6-13xMyc-kanMX


title: H3K27me3, KMS11, plumKD, trgt, rep3

value: PLUM KD


title: control volunteer 010 (RRBS)

city: Nanjing

first: Qiong

state: Jiangsu

address: Dingjiaqiao Road 87#

country: China

institute: Southeast University

data_processing:
After passing the library inspection, different libraries were pooled according to the required effective concentration and target offline data volume for Illumina HiSeq sequencing. Data analysis used R package
Assembly: hg19
Supplementary files format and content: chr = chromosome; start/end = start/end site; id = identification number of DNA methylation region

source_name: blood

extract_protocol:
Use a DNA extraction kit to extract DNA, use agarose gel electrophoresis to analyze the degree of DNA degradation and whether there is RNA contamination, and use Qubit to accurately quantify the DNA concentration.
After the sample passes the testing, it is first digested with the methylation-insensitive restriction enzyme, MspI; The digested DNA fragments undergo end repair, A-tailing, and ligation with sequencing adapters that have all cytosines methylated; The gel is cut to select DNA fragments between 150-300bp in length; Bisulfite treatment is then carried out using the EZ DNA Methylation Gold Kit (Zymo Research). Through this treatment, unmethylated Cs turn into U (becoming T after PCR amplification), while methylated Cs remain unchanged. Finally, PCR amplification is conducted to generate the final DNA library.
After the library construction is completed, Qubit 2.0 is used for preliminary quantification, diluting the library to 1ng/µ l. Then, Agilent 2100 is used to detect the length of the inserted fragments in the library. After meeting expectations, Q-PCR is used to accurately quantify the effective concentration of the library (effective concentration>2nM) to ensure the quality of the library.

value: blood

tag: subject status

value: control volunteer


title: control volunteer 009 (RRBS)


title: pht1-spt6-2

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::hygroMX spt6-13xMyc-kanMX

value: anti-Myc 9E10


title: H3K27me3, KMS11, plumKD, trgt, rep2

value: Haematopoietic and Lymphoid

value: Plasma Cell Myeloma

value: Female


title: control volunteer 007 (RRBS)


title: control volunteer 003 (RRBS)


title: control volunteer 002 (RRBS)


title: HAPE patient 010 (RRBS)

value: HAPE patient


title: control volunteer 001 (RRBS)


title: HAPE patient 009 (RRBS)


title: H3K27me3, KMS11, plumKD, trgt, rep1


title: HAPE patient 008 (RRBS)


title: HAPE patient 006 (RRBS)


title: HAPE patient 005 (RRBS)


title: HAPE patient 003 (RRBS)


title: HAPE patient 004 (RRBS)


title: HAPE patient 002 (RRBS)


title: HAPE patient 007 (RRBS)


title: HAPE patient 001 (RRBS)


title: T.globosa_H2A.Z-3

data_processing:
fastQC (v0.11.8) used to check read quality.
trimmomatic (v0.38) used to remoe potential adapter content using TruSeq3-PE adapters as reference.
Read quantification is performed using kallisto (v0.46.0) against S. pombe reference genome downloaded from Ensembl (ASM294v2)
Assembly: ASM294v2
Supplementary files format and content: tab-delimited file of counts for each CDS

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::H2A.Z(T. globoso)-hygMX

extract_protocol:
Total RNA was extracted from yeast strains grown to mid-exponential phase (OD600 ~0.5) using a standard hot acid phenol protocol. Briefly, cell pellets (10 ml) were collected by centrifugation at 4 ºC, washed briefly with 400 µl of sterile, DEPC-treated water, then resuspended in 400 µl TES (TE + 0.5% SDS). 400 µl of acid phenol (pH 4.3) were then added, and samples were vortexed vigorously, then boiled in a thermomixer for 1 hr at 65 ºC, vortexing occaisionally. Samples were then centrifuged at max speed 4 ºC for 10 min to separate aqueous and organic phases, then the aqueous phase was washed with chloroform before being subjected to ethanol precipitation. Precipitated RNA was stored at -70 ºC until use.
Libraries were then prepared by polyA-tail enrichment using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB Cat. No. E7760L) with the polyA selection module (NEB Cat. No. E7490L). Size selection steps and final library cleanup were performed using the NA clean-up bead solution provided by the VBC core facilities, which is adapted from DeAngelis et al. 1995 (DeAngelis et al., 1995) using carboxylate-modified Sera-Mag Speed beads (Cytiva). Library quality control was performed using the Advanced Analytical Fragment Analyzer using the HS NGS fragment analysis kit (Agilent Cat. No. DNF-474) as well as qPCR using reagents produced by the Molecular Biology Service in conjunction with commercial DNA standards (Roche Cat. No KK4903). Data were collected on a Thermo Scientific QuantStudio5 instrument.

treatment_protocol: No treatment was used

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::H2A.Z(T. globoso)-hygMX


title: control volunteer 008 (RRBS)


title: T.globosa_H2A.Z-1


title: C.membranifera_H2A.Z-2

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::H2A.Z(C. membranifera)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::H2A.Z(C. membranifera)-hygMX


title: control volunteer 005 (RRBS)


title: control volunteer 006 (RRBS)


title: P.yezoensis_H2A.Z-1

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::H2A.Z(P. yezoensis)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::H2A.Z(P. yezoensis)-hygMX


title: P.yezoensis_H2A.Z-2


title: P.yezoensis_H2A.Z-3


title: control volunteer 004 (RRBS)


title: P.marinus_H2A.Z-3

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::H2A.Z(P. marinus)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::H2A.Z(P. marinus)-hygMX


title: Choanocystis_H2A.Z-3

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::H2A.Z(Choanocystis)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::H2A.Z(Choanocystis)-hygMX


title: P.marinus_H2A.Z-2


title: P.marinus_H2A.Z-1


title: human dental pulp stem cells, GATA4-OE, rep3

city: Wuhan

first: Yan

last: Zhang

address: Luoyu Road 237

institute: Wuhan University

data_processing:
For analysis of RNA-Seq data, the DEGseq software package was used to identify the differentially expressed genes (DEGs) and DEGs were defined as | log2 (fold change) | >1 and Q value <0.05. Gene Ontology (GO) enrichment analyses were performed using the Dr. Tom system from BGI to annotate the functions of DEGs.
Assembly: hg38
Supplementary files format and content: gene_expression.txt (fpkm, tpm, read_count)
Supplementary files format and content: rna_expression.txt (fpkm, tpm, read_count)

molecule: total RNA

source_name: tooth

growth_protocol: Human dental pulp stem cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS)and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from the normal cultured HDPSCs and those treated with GATA4 overexpression lentivirus using TRIzol reagent. Three biological replicates were set for each sample.
RNA libraries for RNA-seq were preparded using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Odontogenic differentiation was induced in odontogenic medium containing 50 mg/mL ascorbic acid, 10 mM β-glycerophosphate, and 10 nM dexamethasone with 10% FBS in DMEM

value: tooth

value: mesenchymal stem cells

value: GATA4 overexpression

value: odontogenic differentiation


title: human dental pulp stem cells, GATA4-OE, rep1


title: Choanocystis_H2A.Z-1


title: human dental pulp stem cells, GATA4-OE, rep2


title: human dental pulp stem cells, Con, rep3

value: WT


title: T.globosa_H2A.Z-2


title: U2OS_Noco

city: Heidelberg

first: Fabricio

last: Loayza-Puch

state: non-US Resident

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Data was demultiplexed and UMI-sequences were extracted.
rRNA depletion was performed based on custom human rRNA reference files
Genomic bam files were obtained using STAR v2.5.3a (Dobin et al., 2013) to hg19 with --outSAMtype BAM Unsorted --readFilesCommand zcat  --quantMode TranscriptomeSAM GeneCounts --outSAMmapqUnique 0
Count tables were created with featureCounts v1.5.1 with -g gene_id
Assembly: hg19
Supplementary files format and content: featureCounts
Library strategy: Ribo-Seq

extract_protocol:
Cytoplasmic RNA from ribosome protected fragments (RPFs) were isolated from RNaseI-treated, purified monosomes using TRIzol reagent.
Libraries were constructed according to McGlincy NJ and Ingolia NT.  Methods. 2017

value: Nocodazole


title: U87 cells,  Rad18 siRNA, 72 hrs [exon]

type: RNA

city: Montpellier

first: Domenico

last: Maiorano

address: 141, rue de la cardonille

country: France

institute: CNRS

description: gene expression data from U87 cells treated with a control siRNA for 72 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  HuGene2.1 ST array strip (Affymetrix).  Strips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymetrix microarrays were processed at the Microarray Core Facility of the Institute of Regenerative Medicine and Biotherapy, CHU-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/

label: biotin

source_name: U87 cells siRNA Rad18 72 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in Dulbecco’s modified eagle’s medium (DMEM) supplemented with 10 % (v/v) fetal bovine serum, 2 mM glutamine and antibiotics in a humidified atmosphere of 5 % CO2 at 37 °C.

extract_protocol: Total RNA was isolated from U87 cells in which Rad18 was downregulated or not by siRNA using the RNeasy kit according to the manufacturer's instructions (Qiagen). Residual DNA was removed by DNAseI digestion.

treatment_protocol: For siRNA treatment, cells were transfected either with siRNA Rad18 or siRNA Luciferase (Ctrl) as a control as previously described (Kermi et al., Developmetal Cell 2015). Twenty-four hours after transfection, cells were trypsinized and seeded in 12 wells plates at a density of 104 cells/well. For shRNA treatment, cells were transduced with lentiviral particles expressing SMART vectors doxycyclin-inducible shRNA (Dharmacon).

tag: disease state

value: glioblastoma stage 4


title: A.godoyi_H2A.Z-2

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::H2A.Z(A. godoyi)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::H2A.Z(A. godoyi)-hygMX


title: C.membranifera_H2A.Z-3


title: U87 cells,  control siRNA, 72 hrs [exon]

source_name: U87 cells control siRNA 72 hours


title: human dental pulp stem cells, Con, rep2


title: C.membranifera_H2A.Z-1


title: U87  cells, shRad18, Day7 [exon]

description: gene expression data from U87 cells expressing a Rad18 shRNA for 7 days

source_name: U87  cells, shRad18, Day7


title: A.thaliana_H2A.Z9-2

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::HTA9(A. thaliana)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::HTA9(A. thaliana)-hygMX


title: A.thaliana_H2A.Z9-1


title: A.godoyi_H2A.Z-1


title: Choanocystis_H2A.Z-2


title: A.thaliana_H2A.Z9-3


title: U87 cells, control shRNA, Day 7 [exon]

description: gene expression data from U87 cells expressing a control shRNA for 7 days

source_name: U87 cells shRNAcontrol day 7


title: H.sapiens_H2A.Z.1-2

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::H2A.Z1(H. sapiens)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::H2A.Z1(H. sapiens)-hygMX


title: E9-YS-m2-161118-CD31Kit-2

city: Freiburg

first: Nina

last: Peltokangas

address: Stübeweg 51

data_processing:
Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 or 2.20.0.422
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Assembly: ENCODE VM9
Supplementary files format and content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

organism: Mus musculus

source_name: Yolk sac

growth_protocol: Mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

extract_protocol:
Endothelial and hematopoietic cells were isolated from E8.5-E9.5 yolk sac, E9.5-E11.5 AGM, E11.5-E13.5 placenta and E12.5-E14.5 fetal liver. For AGM we used the method described by (Boisset et al., 2010), in which the head and the tail of the embryo are cut and a buffer containing antibodies (CD31, Kit) is injected into the aorta allowing the simultaneous removal of blood and staining of the inner wall of the aorta. After staining, the AGM was dissected from the trunk. The corresponding tissues were pooled together for further processing. For single-cell suspension, yolk sac was digested with TrypLE for 5-10 min at 37˚C, while AGM and minced placenta were digested in 1.2 mg/ml collagenase I at 37˚C for 1-1.5h. Fetal livers were either grinded or digested with 1.2 mg/ml or 3 mg/ml collagenase I for 5-10 min at 37˚C. The samples were then filtered (YS, placenta = 40 µm; AGM = 35 µm; fetal liver = 30, 40 and 70 µm). Contaminating red blood cells were removed from the single-cell suspension of placenta and fetal liver samples by density gradient centrifugation (Ficoll).
As described in CEL-Seq2 protocol (Hashimshony et al. 2016) and its modified version (Herman et al., 2018).
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: No treatment was performed

value: Yolk sac


title: E9-YS-m2-141218-Kit-11

institute: Max Planck Institute of Immunobiology and Epigenetics


title: human dental pulp stem cells, Con, rep1


title: Tetrahymena_H2A.Z-2

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::HTA3(T. thermophilis)-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::HTA3(T. thermophilis)-hygMX


title: H.sapiens_H2A.Z.1-1


title: E9-YS-m2-141218-CD31Kit-7


title: E9-YS-m2-161118-CD31Kit-1


title: pht1-2

source_name: h- ade6-M210 ura4-D18 leu1-32 pht1∆::hygMX

value: h- ade6-M210 ura4-D18 leu1-32 pht1delta::hygMX


title: E9-YS-m2-141218-CD31Kit-6


title: H.sapiens_H2A.Z.1-3


title: pht1-3


title: E9-YS-m2-141218-Kit-9


title: Tetrahymena_H2A.Z-1


title: E9-YS-m2-141218-Kit-12


title: pht1-1


title: E9-YS-Kit-m2-161118-3


title: E9-YS-m2-141218-Kit-10


title: wt-3


title: E9-YS-m2-141218-CD31Kit-5


title: E9-YS-CD31-m2-161118-2


title: Tetrahymena_H2A.Z-3


title: E9-YS-CD31-m2-161118-1


title: wt-1


title: wt-2


title: E9-YS-m2-141218-CD31Kit-8


title: E9_AGM_CD31_280218_9

source_name: AGM

value: AGM


title: E9_AGM_CD31_280218_12


title: E8-YS-m2-121218-Kit-4


title: Mouse liver ChIP IgG control biol rep 3

city: Dallas

first: Gabriella

last: Quinn

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: Mouse Liver ChIP-seq (IgG) rep 3

data_processing:
Raw fastq files were trimmed via Trim Galore with automatic adapter detection and a phred score cut off of 33
Trimmed fastq files were aligned to mm9 reference mouse genome with Bowtie2 v2.4.2
PCR duplicates were removed from Bowtie2 aligned bam files with Samtools rmdup
Peaks were called and BigWig files were generated using MACS v2.1.2 callpeak function
Assembly: mm9
Supplementary files format and content: bigwig

source_name: liver

growth_protocol: H2.35 cells were cultured with complete DMEM supplemented with 4% FBS, 200 nM dexamethasone, and 1x Penicillin/Streptavidin.

extract_protocol:
Mouse livers were perfused and tissue was digested into a single cell suspensions. ChIP-sequencing DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina for the library prep (NEB E7645). For CUT&RUN DNA preparation, low passage number cell lines were harvested, and genomic binding sites were isolated according to the manufacturer’s protocol (Epicypher 14-1048).
NGS libraries were prepared according to the manufacturer’s protocol (Epicypher 14-1001). Samples were sequenced with 50 bp paired end flow cells using an Illumina NextSeq2000 system

treatment_protocol: H2.35 mouse hepatocyte cells (ATCC CRL-1995) were infected with lentivirus expressing a V5-TBX3. Cells were selected with 10 μg/ml blasticidin for at least 6 days before experiments. In mice, 3e10 GC AAV expressing Tbx3 were injected into WT C57BL6 mice. One week after injection, mice were started on WD or maintained on NC for the remainder of the study.

value: liver

value: 3e10 GC AAV expressing Ty1 tagged TBX3 driven by a TBG promoter were injected into a WT C57BL6 mouse


title: Mouse liver ChIP IgG control biol rep 2

description: Library name: Mouse Liver ChIP-seq (IgG) rep 2


title: H2.35 mouse cell line CUT&RUN IgG control

description: Library name: H2.35 CUT_RUN (IgG)

data_processing:
Raw fastq files were trimmed via Trim Galore with automatic adapter detection and a phred score cut off of 33
Trimmed fastq files were aligned to mm9 reference mouse genome with Bowtie2 v2.4.2
PCR duplicates were removed from Bowtie2 aligned bam files with Samtools rmdup
Peaks were called and BigWig files were generated using MACS v2.1.2 callpeak function
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Run

value: hepatocyte

value: Lentiviral expression plasmids with V5 tagged Tbx3 driven by a CMV promoter


title: Mouse liver ChIP IgG control biol rep 4

description: Library name: Mouse Liver ChIP-seq (IgG) rep 4


title: H2.35 mouse cell line CUT&RUN (Tbx3-V5) biol rep 1

description: Library name: H2.35 CUT_RUN (Tbx3-V5) rep 1


title: E9-YS-Kit-m2-161118-4


title: H2.35 mouse cell line CUT&RUN (Tbx3-V5) biol rep 2

description: Library name: H2.35 CUT_RUN (Tbx3-V5) rep 2


title: E8-YS-m2-121218-Kit-8


title: Mouse liver ChIP IgG control biol rep 1

description: Library name: Mouse Liver ChIP-seq (IgG) rep 1


title: E8-YS-m2-121218-Kit-3


title: E8-YS-m2-121218-CD31Kit-6


title: Mouse liver ChIP TBX3 biol rep 3

description: Library name: Mouse Liver ChIP-seq (TBX3-Ty1) rep 3


title: Mouse liver ChIP TBX3 biol rep 2

description: Library name: Mouse Liver ChIP-seq (TBX3-Ty1) rep 2


title: E8-YS-m2-121218-CD31Kit-2


title: E8-YS-m2-121218-CD31Kit-5


title: H2.35 mouse cell line CUT&RUN (Tbx3-V5) biol rep 3

description: Library name: H2.35 CUT_RUN (Tbx3-V5) rep 3


title: E8-YS-m2-121218-CD31Kit-1


title: E9_AGM_CD31_280218_11


title: E9_AGM_CD31_280218_10


title: E8-YS-m1-121218-CD31Kit-16


title: AM, GATA2 -/-, IL33, 24 hour, Rep1

city: Pittsburgh

first: Rachel

last: Gottschalk

state: PA

address: 200 Lothrop St., W1047 BST

department: Center for System Immunology

institute: University of Pittsburgh

description: Library name: Sample 11

data_processing:
Sequencing data was demultiplexed by the on-board Illumina DRAGEN FASTQ Generation software (v3.10.12).
Sequencing reads were aligned to the reference genome using the STAR aligner. Gene-level raw counts were generated using featureCounts from the Subread package, and data normalization and differential expression analysis were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: csv file contains raw counts

source_name: Bronchoalveolar lavages

extract_protocol:
RNA was extracted with the Direct-zol RNA MicroPrep Kit (Zymo Research).
Libraries were generated with the Illumina Stranded mRNA Library Prep kit according to the manufacturer’s instructions. Following adapter ligation, 15 cycles of indexing PCR were completed, using IDT for Illumina RNA UD Indexes. Libraries were normalized and pooled to 2 nM by calculating the concentration based off the fragment size (base pairs) and the concentration of the libraries. Sequencing was performed on an Illumina NextSeq 2000, using a P3 200 flow cell. The pooled library was loaded at 750 pM and sequencing was carried out with read lengths of 2x58 bp, with a target of 25 million reads per sample.

value: Bronchoalveolar lavages

value: Alveolar Macrophages

value: GATA2 -/-

tag: time

value: 24 hour


title: E8-YS-m2-121218-Kit-7


title: AM, GATA2 -/-, IL33, 24 hour, Rep4

description: Library name: Sample 14


title: E8-YS-m1-121218-Kit-3


title: AM, GATA2 -/-, IL33, 24 hour, Rep2

description: Library name: Sample 12


title: AM, GATA2 -/-, IL33, 24 hour, Rep3

description: Library name: Sample 13


title: Mouse liver ChIP TBX3 biol rep 4

description: Library name: Mouse Liver ChIP-seq (TBX3-Ty1) rep 4


title: AM, GATA2 -/-, PBS, 0 hour, Rep3

description: Library name: Sample 8

value: PBS

value: 0 hour


title: E8-YS-m1-121218-CD31Kit-13


title: E8-YS-m1-121218-CD31-2


title: AM, GATA2 -/-, PBS, 0 hour, Rep2

description: Library name: Sample 7


title: E8-YS-m1-121218-CD31Kit-14


title: AM, GATA2 fl/fl, IL33, 24 hour, Rep1

description: Library name: Sample 9

value: GATA2 fl/fl


title: E8-YS-m1-121218-CD31Kit-15


title: E8-YS-150319-CD31Kit-6


title: AM, GATA2 fl/fl, PBS, 0 hour, Rep5

description: Library name: Sample 5


title: AM, GATA2 -/-, PBS, 0 hour, Rep1

description: Library name: Sample 6


title: AM, GATA2 fl/fl, IL33, 24 hour, Rep2

description: Library name: Sample 10


title: Mouse liver ChIP TBX3 biol rep 1

description: Library name: Mouse Liver ChIP-seq (TBX3-Ty1) rep 1


title: AM, GATA2 fl/fl, PBS, 0 hour, Rep4

description: Library name: Sample 4


title: E8-YS-150319-CD31Kit-5


title: E8-YS-m1-121218-CD31-1


title: AM, GATA2 fl/fl, PBS, 0 hour, Rep3

description: Library name: Sample 3


title: E8-YS-150319-CD31Kit-2


title: AM, GATA2 fl/fl, PBS, 0 hour, Rep1

description: Library name: Sample 1


title: E8-YS-m1-121218-Kit-4


title: AM, GATA2 fl/fl, PBS, 0 hour, Rep2

description: Library name: Sample 2


title: E8-YS-150319-CD31Kit-4


title: E14-FL-H9

source_name: Fetal liver

value: Fetal liver

value: Lin-Kit+


title: E8-YS-150319-CD31Kit-3

value: Yolk sac


title: E14-FL-H12


title: E8-YS-150319-CD31Kit-1


title: Liver, Acly knockout

city: Hamilton

first: DONGDONG

last: WANG

state: Ontario

address: 1200 Main Street West

country: Canada

institute: McMaster University

description:
Library name: Sam22
FFPE Spatial transcriptome sequencing

data_processing:
The spatial transcriptomics (ST) data analysis in this paper includes raw data pre-processing and downstream data analysis. Raw data pre-processing consists of alignment of images, mapping, generation of gene-spot matrix and interpretation of outputs. Downstream data analysis includes quality control (QC), normalization, linear dimensional reduction, determination of principal components (PC), clustering, non-linear dimensional reduction (UMAP/t-SNE), identification of biomarkers, differentially expressed gene (DEG) analysis, spatially variable genes (SVGs), cell type annotations, integrative analysis, pseudobulk analysis, cell-cell communication, and metabolic activity analysis.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: aligned_tissue_image.jpg: A registered and aligned tissue image used for spatial mapping
Supplementary files format and content: cytassist_image.tiff: A high-resolution image captured during the CytAssist workflow
Supplementary files format and content: spatial_enrichment.csv: A CSV file with spatial enrichment scores
Library strategy: Spatial Transcriptomics

extract_protocol:
Liver tissues were collected and fixed with 10% neutral-buffered formalin for 36–48 h. After fixation, the samples were immersed in a 70% alcohol solution. The liver tissues were then processed, paraffin-embedded, and sectioned. RNA quality of formalin-fixed & paraffin-embedded (FFPE) tissues was tested by TapeStation system with DV200 > 30%. Slides with 5 µm of tissue sections were processed with deparaffinization, H&E staining, imaging, decrosslinking, hybridization, ligation, probe extension, pre-amplification and probe-based library construction to generate gene expression libraries for each tissue for following sequencing. Images were taken using the Nikon 90i Eclipse upright microscope. RNA-seq was performed using the Illumina NextSeq 2000 (P2 Flow cell, 2 × 50 bp configuration) system. Sequence data from FFPE tissues were analyzed using the Space Ranger count pipeline from 10X genomics for raw data processing and quality control.
After confirming RNA quality of FFPE tissues (DV200 > 30%), slides with 5 µm of tissue sections were processed with deparaffinization, H&E staining, imaging and decrosslinking (Figure 1). Gene expression probes were then added to the tissues to target the whole transcriptome, enabling hybridization and ligation of each probe pair.  Probes were then released from the tissue upon Visium CytAssist Spatial Gene Expression Slide surface, which contains capture areas with barcoded spots that include oligonucleotides to capture gene expression probes. Visium CytAssist slides were removed from CytAssist for probe extension, pre-amplification and probe-based library construction to generate gene expression libraries for each tissue for following sequencing.

value: Acly KO

value: non treatment


title: Liver, control

description:
Library name: Sam77
FFPE Spatial transcriptome sequencing

value: WT

value: Control


title: E14-FL-H11


title: Liver, wild type

description:
Library name: Sam19
FFPE Spatial transcriptome sequencing

value: liver


title: E14-FL-EC-m2-p1-211118-6


title: Liver, EVT0185

description:
Library name: Sam56
FFPE Spatial transcriptome sequencing


title: E14-FL-EC-m2-p1-211118-7


title: PLV and BV (GEX)

city: Boston

first: Guillermo

last: Arroyo Ataz

address: 670 Albany Street

institute: Boston University

description:
HTO_details_README.txt
Hashed_barcodes.tsv
Hashed_features.tsv
Hashed_matrix.mtx

data_processing:
Creation of FASTQ files were performed using BaseSpace. For hashed samples, cells were demultiplexed using the HTODemux function in Seurat, tdTomato sequence was incorporated into the mouse genome reference (ENSEMBL, GRCm38) and single-cell sequencing reads subjected to preprocessing using Cell Ranger analysis pipeline. Expression matrices were imported into R and analyzed using the Seurat Package
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Popliteal lymphatic and blood vessels

extract_protocol:
To obtain single cell suspensions from PLVs and BVs, adult WT1xAi9 mice were anesthetized with K/X (0.2 mL/20g) and administered 4% Evans blue dye footpad injections. Popliteal vessels were then exposed, and we used a previously described method to generate single cell suspensions of the vessels. Briefly, minced vessels were incubated for 60 minutes at 37ºC with agitation in an enzymatic cocktail consisting of 1 mg/ml collagenase I (Worthington, LS004196), 1 mg/ml Dispase II (Gibco, 17105041). The resulting cell suspension was then filtered through a 70 µm nylon filter (Fisher Scientific, 22363548) and digestion enzymes were inactivated by adding FBS. In total, we performed this protocol on one set of two mice. Once we extracted and digested the BVs and PLVs, the samples were hashed with TotalSeq™-A0306 anti-mouse Hashtag 6 Antibody (Biolegend, 155811) and TotalSeq™-A0305 anti-mouse Hashtag 5 Antibody (Biolegend, 155809) according to the manufacturer’s instructions.
Our scRNA-seq library was made using the Next GEM Single Cell 3’ Reagent Kit (10X Genomics) following the manufacturer's instructions

value: Popliteal lymphatic and blood vessels

tag: strain

value: WT1GFPCre [STOCK Wt1tm1(EGFP/cre)Wtp/J, Stock number 010911 crossed with Ai9-tdT [B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J, Stock number 007909

value: Vascular cells


title: E14-FL-EC-m1-p1-211118-4


title: E14-FL-EC-m2-p1-211118-5


title: adult mouse epicardium, biol rep 1

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: Library name: Ti25_A1_S7

data_processing:
Illumina bcl2fastq (v2.20) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v4.6) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.5.1), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v2.0.5) were perfomed for counting reads with the GENCODE (version M23) annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: epicardium

extract_protocol:
miRNeasy micro kit (Qiagen)
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: epicardium

value: primary epicardial cells


title: E14-FL-H10


title: E14-FL-EC-m2-p1-211118-8


title: PLV Biological replicate 1

data_processing:
Creation of FASTQ files were performed using BaseSpace. tdTomato sequence was incorporated into the mouse genome reference (ENSEMBL, GRCm38) and single-cell sequencing reads subjected to preprocessing using Cell Ranger analysis pipeline. Expression matrices were imported into R and analyzed using the Seurat Package
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Popliteal lymphatic vessels

extract_protocol:
To obtain single cell suspensions from popliteal lymphatic (PLVs), adult WT1xAi9 mice were anesthetized with K/X (0.2 mL/20g) and administered 4% Evans blue dye footpad injections. Popliteal vessels were then exposed, and we used a previously described method to generate single cell suspensions of the vessels. Briefly, minced vessels were incubated for 30 minutes at 37ºC with agitation in an enzymatic cocktail consisting of 1 mg/ml collagenase I (Worthington, LS004196), 1 mg/ml Dispase II (Gibco, 17105041), DNAse (Milipore Sigma, 04716728001) and Liberase (Milipore Sigma, 05401020001). The resulting cell suspension was then filtered through a 70 µm nylon filter (Fisher Scientific, 22363548) and digestion enzymes were inactivated by adding FBS. In total, we performed this protocol on two sets of two mice each.
Our scRNA-seq library was made using the Next GEM Single Cell 3’ Reagent Kit (10X Genomics) following the manufacturer's instructions

value: Popliteal lymphatic vessels


title: PLV and BV (HTO)

data_processing:
Creation of FASTQ files were performed using BaseSpace. For hashed samples, cells were demultiplexed using the HTODemux function in Seurat, tdTomato sequence was incorporated into the mouse genome reference (ENSEMBL, GRCm38) and single-cell sequencing reads subjected to preprocessing using Cell Ranger analysis pipeline. Expression matrices were imported into R and analyzed using the Seurat Package
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: HTO


title: OldD28b , Spatial Transcriptomics

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: 10x Genomics Visium

data_processing:
Alignment of reads from the spatial RNA-seq library and unique molecular identifiers (UMIs) counting were performed with 10X Genomics Space Ranger tool.
The 8 spaceranger pipeline outputs containing both the spot-level gene counts and the histological image of the tissue slice were read as seurat objects.
Young.D14_bis and Young.D28_bis samples appeared unusable because of a very low level of detected molecules per spot (<800 detected genes).
The remaining 6 samples (Young.D14, Old.D14.a, Old.D14.b, Young.D28, Old.D28.a, Old.D28.b) were first normalized with SCTransform().
PCA was run in each sample using the intersection of the top 10000 variable features found in each sample in order to integrate them by reciprocal PCA.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, and repertories of histological images
Library strategy: Spatial Transcriptomics

source_name: Fibrotic lung slice

extract_protocol:
Library preparation was performed according to the Visium Spatial Gene Expression User Guide. Libraries were loaded and sequenced on a NextSeq2000 System (Illumina) as paired-end-dual-indexed, at a sequencing depth of approximately 25 M read-pairs per capture area.
10x Genomics Visium

treatment_protocol:
Lung fibrosis was induced in seven-week (“young”) and 18-month (“old”)-old C57BL/6 male mice (Charles River) using 50-µl bleomycin (1 U/kg), aerosolized in mouse lungs using a MicroSprayer Aerosolizer (Penn-Century, Inc.). Mice were sacrificed 14 or 28 days after instillation.
Tissue preparation and slides processing was performed according to the Visium Tissue Preparation Guide (CG000238 Rev A; CG000239 Rev A; CG000240 Rev A, 10× Genomics). Briefly, lungs of bleomycin-challenged mouse were inflated with diluted Optimal Cutting Temperature (OCT), gently removed from mouse then embedded in OCT on dry ice and stored at -80°C. OCT blocks were cryosectioned at 10µm thickness on capture areas of Visium 10 Genomics slide. Before performing the complete protocol, Visium Spatial Tissue Optimization was performed according to manufacturer’s procedure and using the Axioscan 7 scanner (Zeiss). Thirty minutes was selected as optimal permeabilization time. The experimental samples were fixed, stained with H&E and imaged using Axioscan 7 scanner at 5x magnification.

value: All

value: Fibrotic lung slice

tag: Stage

value: Old

value: 18 months old

value: Bleomycin or PBS


title: E14-FL-EC-m1-p1-211118-3

value: Fetal liver


title: PLV Biological replicate 2


title: E14-FL-EC-m1-p1-211118-2


title: adult mouse epicardium, biol rep 2

description: Library name: Ti26_A2_S8


title: OldD28a , Spatial Transcriptomics

description: 10x Genomics Visium


title: YoungD28bis , Spatial Transcriptomics

description: 10x Genomics Visium

value: Young

value: 7 weeks old


title: E14-FL-EC-m1-p1-211118-1


title: YoungD28 , Spatial Transcriptomics

description: 10x Genomics Visium


title: E14-FL-E15


title: E14-FL-E16


title: E14-FL-E14


title: OldD14b , Spatial Transcriptomics

description: 10x Genomics Visium


title: E14-FL-E13


title: YoungD14bis , Spatial Transcriptomics

description: 10x Genomics Visium


title: E14-FL-291018-EC8


title: OldD14a , Spatial Transcriptomics

description: 10x Genomics Visium


title: YoungD14 , Spatial Transcriptomics

description: 10x Genomics Visium


title: E14-FL-291018-EC7


title: YZH269_Pht11

data_processing:
Analysis was performed using the nf-core/ChIP-seq pipeline
Assembly: ASM294v2
Supplementary files format and content: Provided are bigwig files of read-depth normalized ChIP-seq.

extract_protocol:
S. pombe strains (100 ml) were grown to mid-exponential phase (OD600 ~0.4-0.5) in YES, fixed with 1% formaldehyde for 10 min, quenched with 125 mM glycine for 10 min, then collected by centrifugation. Cells were washed once with ice-cold PBS, then resuspended in lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100, 1X Roche Complete Protease Inhibitors), and then lysed using acid-washed glass beads in a Precellys for 4x20 sec maximum speed, 1 min on ice between rounds. Lysate was then separated from the beads and then chromatin was sheared to a predominant final DNA length of ~150-200 bp in a Covaris E220 ultrasonicator, and then clarified of unlysed cells and debris by centrifugation twice at 16,000 × g for 10 min. Prepared chromatin was then frozen at -70 ºC pending use. Chromatin aliquots were thawed on ice, then normalized based on starting culture density using additional lysis buffer for dilution. 10% of normalized and diluted chromatin were reserved as input controls. Anti-H2A.Z (Pht1) or anti-Myc 9E10 antibody (1µg) was then added to each culture and samples were incubated overnight at 4 ºC with inversion. 25 µl of Protein A Dynabeads (Thermo Fisher Cat. No. 10001D) per sample were prepared by washing twice with PBS with 0.1% tween-20, once with lysis buffer, then resuspending in 100 µl of lysis buffer. Prepared beads were then combined with overnight chromatin samples, and incubated for 4 hrs at 4 ºC with inversion. Beads were then collected using the magnet and washed twice with lysis buffer, twice with high salt lysis buffer (50 mM HEPES-KOH, pH 7.5, 500 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X-100), twice using lithium wash buffer (10 mM Tris-HCl, pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE. Beads were then resuspended in 100 µl of elution buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 0.8% SDS) and transferred to PCR strips. Samples were then boiled for 10 min at 95 ºC, then 65 ºC overnight in a thermocycler. The next morning, proteinase K was added (final concentration 0.2 mg/mL) and incubated at 55 °C for 2 h. Samples were then cleaned up using a commercial kit (Zymo Research Cat. No. D5201). DNA concentration was measured by Nanodrop spectrophotometer.
For library preparations, all samples, including input, were processed using the NEBNext Ultra II library preparation kit for Illumina (NEB Cat. No. E7645L) using custom synthesized barcoded sequencing adapters provided by the Vienna BioCenter Core Facilities Next Generation Sequencing Facility. Following quality control by Agilent Fragment Analyzer and quantification by RT-qPCR using a Kapa Library Quantification Kit (Roche Cat. No. KK4903), libraries were sequenced at the Next Generation Sequencing Facility on an Illumina NovaSeq X. Alignments, quality control, and initial processing were performed using the nf-core/chipseq pipeline (https://github.com/nf-core/chipseq) with default parameters. Input-normalized bigWig files were subsequently generated using Deeptools (v3.3.1) (24).

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 K84H-hygMX


title: E14-FL-291018-EC6


title: YZH267_Pht12

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 A80S-hygMX


title: E14-FL-291018-EC4


title: E14-FL-291018-EC2


title: YZH267_Pht11


title: YZH269_Input1


title: E14-FL-291018-EC5


title: E14-FL-291018-EC1


title: YZH267_Input1


title: YZH264_Pht12

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 L83G-hygMX


title: YZH267_Input2


title: E14-FL-290518-H16

value: Lin-Kit+


title: YZH264_Pht11


title: E14-FL-290518-H15


title: E14-FL-291018-EC3


title: E14-FL-290518-H14


title: YZH264_Input1


title: YZH263_Pht12

value: h- ade6-M216 ura4-D18 leu1-32 pht1{delta}::pht1 L83F-hygMX


title: YZH264_Input2


title: E14-FL-290518-H13


title: E14-FL-290518-E12


title: YZH263_Pht11


title: E14-FL-290518-E9


title: YZH263_Input2


title: YZH263_Input1


title: E14-FL-290518-E11


title: YZH002_Pht12


title: E14-FL-290518-E10


title: E13_PL_CD34cKit_140318_8

source_name: Placenta

value: Placenta

value: Lin-Kit+ and Lin-CD34+


title: YZH002_Pht11


title: E13_PL_CD34cKit_140318_6


title: YZH002_Input2


title: YZH002_Input1


title: E13_PL_CD34cKit_140318_7


title: pht1-K86Q-5

library_source: other

data_processing:
Analysis was performed using a pipeline developed by Judd et al. 2020, which we adapted for parallel processing in the Nextflow environment (https://github.com/Gregor-Mendel-Institute/PROalign).
Assembly: ASM294v2
Supplementary files format and content: Provided are bigwig files representing the stranded (fwd or rev) termination point of run-on transcription.
Library strategy: PRO-seq

molecule: other

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 K86Q-hygMX

extract_protocol:
Cells were resuspended in 10 ml of ice-cold PBS, spun down once more, then resuspended in 10 ml ice-cold yeast permeabilization buffer (0.5% Sarkosyl, 0.5 mM DTT, Roche cOmplete protease inhibitor cocktail, 4U/ml Invitrogen RiboLock RNAse Inhibitor). After 20 min incubation on ice, cells were once again collected by gentle centrifugation, then resuspended in 50 µl storage buffer (10 mM Tris-HCl, pH 8.0, 25% (v/v) glycerol, 5 mM MgCl2, 0.1 mM EDTA, 5 mM DTT). A 2X run-on reaction master mix (40 mM Tris pH 7.7, 64 mM MgCl2, 1 mM DTT, 400 mM KCl, 40 µM Biotin-11-CTP, 40 µM Biotin-11-UTP, 40 µM ATP, 40 µM GTP, 1% sarkosyl) was prepared and preheated to 30 ºC. To each aliquot of permeabilized cells, 50 µl of master mix and 1 µl of RNAse inhibitor were added, then mixed by gently pipetting with wide-bore pipet tips before immediately incubating at 30 ºC for 5 min. To ensure precise timing, samples were done in batches staggered by 30–60 sec. Using the Norgen RNA Extraction Kit (Cat. No. 37500), 350 µL of RL buffer were added to each sample and then vortexed. 240 µl of absolute ethanol were added, then the entire well-mixed solution was applied to the RNA extraction column. The column was spun at 3500 x g for 1 min at 25 ºC, then washed once with 400 µl of wash solution A. This step was repeated a second time, then the column was dried by spinning at high speed for 2 min. RNA was eluted twice in 50 µl of DEPC-treated MonoQ water, the two fractions were pooled and then briefly denatured at 65 ºC for 30 sec. After snap cooling on ice, 25 µl of ice cold 1 M NaOH were added to each sample, which was then incubated for 10 min on ice. Finally, samples were quenched with 125 µl of cold 1 M Tris-HCl pH 6.8, then cleaned up using a standard ethanol precipitation overnight. Samples were resuspended in a small volume of DEPC water (6 µl).
Meanwhile, 10 µl per sample of Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Cat. No. 65001) were prepared by washing once with bead preparation buffer (0.1 M NaOH, 50 mM NaCl), then once in bead binding buffer (10 mM Tris-HCl, pH 7.4, 300 mM NaCl, 0.1% (v/v) Triton X-100, 1 mM EDTA, RNAse inhibitors), then resuspended in 25 µl bead binding buffer.    3’RNA adapter ligation was performed by adding 1 µl 10 µM oligo VRA3 to the resuspended RNA, boiling at 65 ºC for 30 sec, then snap cooling on ice. Ligation reactions were then prepared with T4 RNA Ligase using the provided instructions. After incubating reactions at 25 ºC for 1 hr, ligated RNA was bound to the 25 µl previously prepared streptavidin beads by adding 55 µl bead binding buffer and the entire ligation reaction. Samples were incubated for 20 min at 25 ºC, then washed once with 500 µl high salt wash buffer (50 mM Tris-HCl, pH 7.4, 2 M NaCl, 0.5% (v/v) Triton X-100, 1 mM EDTA, 2 µl/10 ml Ribolock RNAse inhibitor), transferring beads to a clean tube. Beads were then washed once more in the new tube with low salt wash buffer (5 mM Tris-HCl, pH 7.4, 0.1% (v/v) Triton X-100, 1 mM EDTA, 2 µl/10 ml Ribolock RNAse inhibitor), then resuspended in 20 µl T4 PNK reaction mix (1X T4 PNK Buffer, 1 mM ATP, 1 µl T4 PNK, 1 µl RiboLock RNAse inhibitor). Samples were then incubate at 37 ºC for 30 min, then the beads were collected by magnet and resuspended in 20 µl ThermoPol reaction mix (1X ThermoPol buffer, 1 µl RppH, 1 µl RiboLock RNAse inhibitor), then incubated at 37 ºC for 1 hr. Beads were once again collected by magnet, then the 5’ RNA adaptor (REV5) was ligated using T4 RNA ligase, setting up the reaction using the provided manual and incubating at 25 ºC for 1 hr. Beads were then washed once with high salt wash buffer, transferring to a clean tube, then once with low salt buffer, before being resuspended in 300 µl of TRIzol reagent (Ambion). Samples were vortexed for 20 sec, then incubated on ice for 3 min before adding 60 µl of chloroform, vortexing for 15 sec, then incubating on ice for a further 3 min. Samples were then spun at 20,000 x g for 8 min at 4 ºC, then the upper ~180 µl aqueous phase was transferred to a clean tube and precipitated using a standard ethanol precipitation.   Finally, pellets were resuspended in 13.5 µl reverse transcription resuspension mix (8.5 µl DEPC water, 4 µl 10 µM primer RP1, 1 µl 10 mM dNTPs), denaturing at 65 ºC for 5 min, snap cooling on ice. Reverse transcription was then performed using Maxima H Minus RT (Thermo Fisher Cat. No. EP0753) by adding 6.5 µl RT master mix (4 µl 5X RT buffer, 1 µl DEPC water, 0.5 µl RiboLick RNAse inhibitor, 1 µl Maxima H Minus RT), then cycling as follows: 50 ºC for 30 min, 65 ºC for 15 min, 85 ºC for 5 min. 2.5 µl of indexed RPI-n primer (10 µM) were then added to each RT reaction, then PCR was performed as a 100 µl reaction using the Q5 polymerase (NEB) with the included high GC content enhancer. Samples were then PCR-amplified to the beginning of the logarithmic phase, as determined using a small-scale qPCR reaction run in parallel (typically less than 20 cycles).   Libraries were sequenced as described previously at the Vienna BioCenter Core Facilities Next Generation Sequencing Core. The data analysis was performed by adapting available pipelines (Judd et al., 2020). Briefly, we created a Nextflow container (URL/Github) to perform all QC, alignment, and read processing steps, generating strand-specific bigwig files that were subsequently analyzed in R.

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 K86Q-hygMX


title: pht1-V85A-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 V85A-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 V85A-hygMX


title: E13_PL_CD31_140318_4


title: E13_PL_CD31_140318_2


title: E13_PL_CD34cKit_140318_5


title: E13_FL_H_140318_8


title: pht1-K81Q-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 K81Q-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 K81Q-hygMX


title: pht1-A80S-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 A80S-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 A80S-hygMX


title: pht1-K84H-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 K84H-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 K84H-hygMX


title: E13_PL_CD31_140318_3


title: E13_PL_CD31_140318_1


title: E13_FL_H_140318_7


title: pht1-L83Q-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 L83Q-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 L83Q-hygMX


title: pht1-L83G-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 L83G-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 L83G-hygMX


title: E13_FL_H_140318_5

value: Fetal liver


title: E13_FL_H_140318_6


title: E13-FL-EC-m2-p3-191118-16


title: pht1-L83N-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 L83N-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 L83N-hygMX


title: pht1-L83F-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 L83F-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 L83F-hygMX


title: pht1-L83M-5

source_name: h- ade6-M216 ura4-D18 leu1-32 pht1∆::pht1 L83M-hygMX

value: h- ade6-M216 ura4-D18 leu1-32 pht1delta::pht1 L83M-hygMX


title: E13-FL-EC-m2-p3-191118-15


title: E13-FL-EC-m2-p3-191118-13


title: wt-5


title: pht1-4

source_name: h- ade6-M210 ura4-D18 leu1-32 pht1∆::hygMX

value: h- ade6-M210 ura4-D18 leu1-32 pht1delta::hygMX


title: E13-FL-EC-m2-p3-191118-14

source_name: Fetal liver


title: E13-FL-EC-m1-191118-16


title: pht1-K86Q-4


title: pht1-V85A-4


title: E13-FL-EC-m1-191118-14


title: pht1-K81Q-4


title: E13-FL-EC-m1-191118-15


title: pht1-K84H-4


title: pht1-A80S-4


title: pht1-L83N-4


title: E13-FL-EC-m1-191118-13


title: E13_FL_E_140318_4


title: E13_FL_E_140318_2


title: pht1-L83G-4


title: pht1-L83F-4


title: E12-PL-CD31Kit-m2-120419-8


title: E13_FL_E_140318_3


title: pht1-L83Q-4


title: pht1-L83M-4


title: E12-PL-CD31Kit-m2-120419-7


title: wt-4


title: E12-PL-CD31Kit-m2-120419-6


title: E12-PL-CD31Kit-m2-120419-5


title: pht1-K86Q-3


title: pht1-V85A-3


title: E12-PL-CD31Kit-m2-120419-4


title: E12-PL-CD31Kit-m2-120419-3


title: pht1-K84H-3


title: pht1-K81Q-3


title: E12-PL-CD31Kit-m2-120419-2


title: E12-PL-CD31Kit-m2-120419-1


title: pht1-A80S-3


title: E13_FL_E_140318_1


title: E12-PL-CD31Kit-m1-120419-8


title: pht1-L83N-3


title: pht1-L83G-3


title: pht1-L83Q-3


title: E12-PL-CD31Kit-m1-120419-7


title: E12-PL-CD31Kit-m1-120419-5


title: pht1-L83F-3


title: E12-PL-CD31Kit-m1-120419-3


title: E12-PL-CD31Kit-m1-120419-4


title: E12-PL-CD31Kit-m1-120419-6


title: E12-PL-CD31Kit-m1-120419-2


title: pht1-3


title: wt-3


title: E12-PL-CD31Kit-m1-120419-1


title: pht1-K86Q-2


title: E12-PL-230718-H15


title: pht1-2


title: pht1-L83M-3


title: E12-PL-230718-H14


title: pht1-K84H-2


title: wt-2


title: pht1-K86Q-1


title: E12-FL-EC-p2-201118-9


title: E12-PL-230718-H13


title: E12-PL-230718-H16


title: pht1-V85A-2


title: E12-FL-EC-p2-201118-12


title: pht1-K81Q-2


title: pht1-K84H-1


title: E12-FL-EC-p2-201118-11


title: pht1-A80S-2


title: pht1-L83Q-2


title: E12-FL-EC-p2-201118-10


title: E12-FL-EC-201118-8


title: pht1-L83N-2


title: E12-FL-EC-201118-5


title: pht1-L83G-2


title: pht1-L83F-2


title: E12-FL-EC-201118-7


title: pht1-L83M-2


title: E12-FL-EC-201118-6


title: pht1-V85A-1


title: E12-FL-230718-H8


title: E12-FL-230718-H6


title: E12-FL-230718-E9


title: pht1-L83Q-1


title: pht1-K81Q-1


title: E12-FL-230718-H5


title: E12-FL-230718-E4


title: pht1-L83G-1


title: pht1-L83F-1


title: pht1-L83N-1


title: E12-FL-230718-E2


title: E12-FL-230718-E3


title: pht1-L83M-1


title: E12-FL-230718-E12


title: wt-1


title: E12-FL-230718-E11


title: pht1-1


title: E12-FL-230718-E10


title: Md, fmi, 13.5dpc, Md18II1

city: New Haven

first: Gunter

middle: P

last: Wagner

state: CT

address: 165 Prospect Street

department: Ecology & Evolutionary Biology

institute: Yale University

description: 10x Genomics

data_processing:
CellRanger v7.0.0-v8.0.0
Assembly: GRCm39 (M. musculus); cavPor3 (C. porcellus); ASM229v1 (M. domestica); Draft Genome (T. ecaudatus)
Supplementary files format and content: CellRanger tab-separated features and cell barcodes and matrix expression files.
Supplementary files format and content: Raw counts in annotated h5 format with hierarchical cell type annotations, and gene annotations according to ENSEMBL and BLAST to human.

organism: Monodelphis domestica

source_name: uterus + placenta

extract_protocol:
All tissue was processed as follows, with small species-specific modifications as noted. Tissue was minced with a scalpel into ~1 mm3 cubes in 2 mL of digestive solution containing 0.2 mg/mL Liberase TL (05401020001, Sigma). Tissue suspensions were heated at 37°C for 15 minutes and then passed 10 times through a 16-gauge needle attached to a 3-mL syringe. This incubation and needle passage process was repeated two more times, with the substitution of an 18-gauge needle. Finally, 2 mL of charcoal-stripped fetal bovine serum (100-199, Gemini) was added and the suspension was immediately passed through a 70-μm cell strainer then a 40-μm cell strainer. The flowthrough was pelleted by centrifugation at 500 g for 5 minutes and cells were resuspended in 1x ACK red blood cell lysis buffer (A1049201, Thermo-Fisher), incubated at room temperature for 5 minutes, centrifuged again and resuspended in PBS containing 0.04% bovine serum albumen (A9647, Sigma). At this point, cells were examined on a hemocytometer to gauge concentration and check for debris and cell death using trypan blue stain (15250061, ThermoFisher). Mouse tissue was processed as above with the addition of Accumax (Stem Cell Technologies) to the final 0.04% bovine serum albumen solution. Guinea pig tissue was processed as with the mouse with the following modifications: a wide-bore 1 mL pipette tip was substituted for the 16-gauge needle, and 0.2 mg/mL collagenase I (17018029, Thermo-Fisher) was added to the digestion solution. As tenrec and guinea pig tissue showed higher cell death, a fractionated protocol was adopted to reduce exposure of cells to digestive enzymes. For these species, cells which had dislodged following each passage step were separated from intact tissue and immediately passed through a 70-μm cell strainer into 2 mL of charcoal-stripped fetal bovine serum (100-199, Gemini), while remaining intact tissue was allowed to continue with further digestion. Each fraction was centrifuged at 300 rpm for 5 minutes and resuspended in 500 μL ACK red blood cell lysis buffer (A1049201, Thermo-Fisher) for 5 minutes, then centrifuged at 500 rpm for 2 minutes and resuspended in 0.04% bovine serum albumen (A9647, Sigma) and kept on ice until dissociation was complete. Cells were counted on a hemocytometer and recombined in a proportional manner before sequencing. Cells were captured using the 10X Chromium platform (3’ chemistry, version 3)
Libraries were generated according to manufacturer protocols (CG000315: 10x Genomics 3’ chemistry, version 3).

value: uterus + placenta

value: Female

value: 13.5 days post copulation


title: E12-FL-230718-E1


title: E12-FL-230718-H7

value: Lin-Kit+


title: Md, fmi, 13.5dpc, Md18HH2

description: 10x Genomics


title: E11-PL-H8

value: Placenta


title: E11-PL-H7


title: pht1-A80S-1


title: A17,335,3515

city: Urbana

first: Amy

last: Marshall-Colon

state: IL

address: 1201 W Gregory Drive

department: Plant Biology

institute: University of Illinois

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina) and adaptors were trimmed
Salmon (v1.4.0) was used to index the combined Medicago trunculata (mrna + ncrna + rrna files) and Sinorhizobium meliloti (cds + rna files) transcriptomes using the decoy-aware method with the entire M. trunculata + S. meliloti genomes as the decoy sequence
Quasi-mapping was performed to map reads to the combined transcriptomes
Gene-level counts were estimated from transcript-level counts using the “bias corrected counts without an offset” method from the tximport package (v1.20.0) in R (v4.1.0)
Assembly: Medicago truncatula A17 r5.0 reference files were downloaded from the  INRAE/CNRS Medicago Bioinformatics Resources, and Sinorhizobium meliloti 1021 reference files were downloaded from NCBI (assembly GCF_000006965.1 ASM696v1)
Supplementary files format and content: Comma Separated Value (.CSV)  file containing gene-level expression counts for each sample

organism: Medicago truncatula

source_name: Nodule

growth_protocol: Plants were grown in the greenhouse under 16 hr days in Steuwe & Sons ray leach “Cone-tainers” containing auto-clave-sterilized 1:1:1 turface:torpedo sand:field soil

extract_protocol:
RNA extraction: RNeasy Plant Mini kit
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), then pooled, quantitated by qPCR, and sequenced on one S4 lane for 151 cycles from both ends of the fragment on a NovaSeq 6000

treatment_protocol: Treatment: 20 strains of Ensifer meliloti

tag: microbe

value: Ensifer meliloti

value: Nodule


title: A17,89,3514


title: E11-PL-H5


title: E11-PL-H6


title: A17,230,3506


title: DZA,230,3513

value: DZA


title: E11-PL-E4


title: DZA,176A,3504


title: E11-PL-E2


title: A17,746B,3505


title: DZA,335,3503


title: E11-PL-CD31Kit-m2-100419-8


title: A17,89,3502


title: DZA,278,3494


title: E11-PL-CD31Kit-m2-100419-6


title: E11-PL-CD31Kit-m2-100419-5


title: A17,724B,3518


title: E11-PL-CD31Kit-m2-100419-4


title: E11-PL-CD31Kit-m2-100419-3


title: A17,176A,3487


title: DZA,182,3485


title: E11-PL-CD31Kit-m2-100419-2


title: DZA,121,3481


title: DZA,216,3476


title: E11-PL-CD31Kit-m2-100419-1


title: E11-PL-E3


title: E11-PL-CD31Kit-m1-100419-8


title: E11-PL-CD31Kit-m2-100419-7


title: E11-PL-CD31Kit-m1-100419-7


title: DZA,230,3469


title: E11-PL-E1


title: DZA,89,3468


title: E11-PL-CD31Kit-m1-100419-5


title: DZA,335,3462


title: A17,748B,3471


title: E11-PL-CD31Kit-m1-100419-6


title: E11-PL-CD31Kit-m1-100419-2


title: A17,144B,3493


title: A17,748B,3492


title: E11-PL-CD31Kit-m1-100419-1


title: DZA,204,3488


title: DZA,141,3459


title: E11-AGM-040618-EC8

source_name: AGM

value: AGM


title: A17,31,3454


title: DZA,25B,3475


title: DZA,89,3452


title: E11-AGM-040618-EC6


title: E11-AGM-040618-EC5


title: DZA,230,3451


title: E11-PL-CD31Kit-m1-100419-3


title: E11-PL-CD31Kit-m1-100419-4


title: A17,748B,3449


title: DZA,89,3446


title: E11-AGM-040618-EC1


title: DZA,278,3450


title: E11-AGM-040618-EC2


title: E10_AGM_HE_220218_8


title: DZA,216,3461


title: A17,724B,3441


title: A17,230,3440


title: E10_AGM_HE_220218_5


title: DZA,121,3457


title: A17,144B,3437


title: E10_AGM_EC_220218_4


title: A17,282,3438


title: E10_AGM_EC_220218_3


title: E11-AGM-040618-EC7


title: A17,25B,3435


title: DZA,335,3431


title: E11-AGM-040618-EC3


title: DZA,278,3429


title: E11-AGM-040618-EC4


title: E10_AGM_EC_220218_2


title: E10-AGM-010318-HEEC12

value: CD31+ and CD31+Kit+


title: E10_AGM_HE_220218_7


title: A17,121,3426


title: A17,31,3424


title: A17,230,3422


title: DZA,282,3443


title: DZA,31,3444


title: DZA,25B,3420


title: E10-AGM-010318-HEEC10


title: E10_AGM_HE_220218_6


title: E10-AGM-010318-HE15


title: A17,278,3416


title: E10-AGM-010318-EC14


title: DZA,206,3414


title: DZA,282,3413


title: A17,206,3412


title: F, Q111, Mut_ASO, Rep 5

city: Seattle

first: Robert

last: Bragg

state: Washington

address: 300 9th Ave

institute: University of Washington

description:
Library name: CSU6
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta

data_processing:
Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. Reads were aligned to the Mus musculus GRCm38 ERCC reference genome assembly (ENSEMBL) using STAR aligner v.2.5.2b. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Assembly: GRCm38
Supplementary files format and content: Text count files from featureCounts

source_name: Striatum

extract_protocol:
RNA was extracted and prepared using rRNA depletion
PE 2x150bp cDNA libraries were constructed at Azenta (South Plainfield, NJ) using the Illumina TruSeq RNA Sample Prep Kit with ERCC spike-in

value: Striatum

tag: batch


title: F, Q111, Mut_ASO, Rep 4

description:
Library name: CSS6
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: E10_AGM_EC_220218_1


title: E10-AGM-010318-HEEC9


title: A17,89,3411


title: DZA,199,3410


title: F, Q111, Saline, Rep 5

description:
Library name: CSR1
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta

value: Saline


title: E10-AGM-010318-HEEC11


title: A17,89,3409


title: DZA,335,3407


title: A17,204,3421


title: F, WT, Pan_ASO, Rep 4

description:
Library name: CSO5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta

value: WT


title: F, WT, Pan_ASO, Rep 5

description:
Library name: CSO6
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: E10-AGM-010318-HE16


title: DZA,182,3406


title: DZA,230,3400


title: F, WT, Saline, Rep 5

description:
Library name: CSO2
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: DZA,724B,3403


title: DZA,206,3399


title: F, WT, Saline, Rep 4

description:
Library name: CSO1
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: F, WT, Mut_ASO, Rep 5

description:
Library name: CSN5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, WT, Pan_ASO, Rep 3

description:
Library name: CSL5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, WT, Mut_ASO, Rep 2

description:
Library name: CSJ2
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, WT, Mut_ASO, Rep 3

description:
Library name: CSK5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: A17,216,3394


title: A17,121,3393


title: E10-AGM-010318-EC13


title: M, WT, Pan_ASO, Rep 2

description:
Library name: CSI6
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: A17,199,3388


title: DZA,31,3389


title: M, WT, Saline, Rep 3

description:
Library name: CSI4
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: DZA,141,3387


title: M, WT, Saline, Rep 2

description:
Library name: CSI3
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: F, Q111, Pan_ASO, Rep 5

description:
Library name: CSR5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, WT, Pan_ASO, Rep 1

description:
Library name: CSI5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: DZA,746B,3385


title: A17,141,3382


title: M, Q111, Pan_ASO, Rep 3

description:
Library name: CSG5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, Q111, Mut_ASO, Rep 3

description:
Library name: CSH6
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, Q111, Saline, Rep 3

description:
Library name: CSG2
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: A17,141,3386


title: DZA,31,3379


title: M, Q111, Mut_ASO, Rep 2

description:
Library name: CSF3
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: DZA,283,3381


title: M, Q111, Saline, Rep 2

description:
Library name: CSG1
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: A17,121,3373


title: A17,182,3378


title: A17,283,3398


title: DZA,283,3380


title: M, Q111, Pan_ASO, Rep 1

description:
Library name: CSE1
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: A17,144B,3371


title: M, Q111, Pan_ASO, Rep 2

description:
Library name: CSE2
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: F, Q111, Pan_ASO, Rep 4

description:
Library name: CRQ6
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: F, Q111, Saline, Rep 4

description:
Library name: CRQ2
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: DZA,724B,3363


title: A17,182,3361


title: DZA,199,3364


title: M, Q111, Saline, Rep 1

description:
Library name: CQW1
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: DZA,31,3359


title: M, Q111, Mut_ASO, Rep 1

description:
Library name: CQX3
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, WT, Saline, Rep 1

description:
Library name: CQQ2
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: F, WT, Mut_ASO, Rep 4

description:
Library name: CRX5
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: M, WT, Mut_ASO, Rep 1

description:
Library name: CQR2
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: genomic DNA from CD4+ T-cell_VAS98

type: genomic

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

country: Spain

institute: IPBLN-CSIC

hyb_protocol: Five hundred nanograms of each DNA sample was bisulfite-converted with the EZ DNA MethylationTM kit (Zymo Research, Irvine, CA, USA), following the manufacturer's instructions. Samples were hybridized onto an Infinium MethylationEPIC Bead Chip array

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
DNA methylation raw data (IDAT files) were processed using ShinyÉPICo, a graphical pipeline based on minfi and limma R packages.
Samples showing poor bisulfite conversion and those with gender discordance between prediction and demographic information were filtered out from further analyses. In addition, we used the 59 single nucleotide polymorphisms (SNPs) probes included in the array to check for sample duplication. One individual from each pair of duplicates was excluded.
Probes with a detection p-value < 0.01 were removed. To avoid technical and biological bias, we also excluded CpGs from X and Y chromosomes as well as those probes containing either a SNP at the CpG interrogation site or at the single base extension site. Probes were annotated using IlluminaHumanMethylationEPICmanifest v0.4.0
Raw methylation values were normalized using the Noob+Quantile method, and DNA methylation was measured as beta and M values.
To identify associations between DNA methylation levels and GCA disease state or clinical status along the genome, we applied a eBayes moderated t-test with trend and robust options enabled. We used a false discovery rate (FDR) to correct for multiple testing and those probes with a FDR < 0.05 were considered as differentially methylated positions (DMPs).
Sensitivity analyses were realized for each comparison to examine the contribution of all potential confounders (sex, age, slide, array and sample plate). Pearson correlation or Wilcoxon signed-rank test was applied depending on whether the variable of interest was continuous or categorical. Variables with a p-value < 0.05 were considered to significantly contribute to DNA methylation and were therefore included as covariates in the model.

label: Cy5 and Cy3

source_name: SAMPLE_97 genomic DNA from CD4+ T-cell_VAS98

label_protocol: Standard Illumina Protocol

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were first obtained from whole blood by density gradient centrifugation using Ficoll-Paque (Rafer, Zaragoza, Spain). For subsequent CD14 T-cell  isolation, PBMCs were incubated with CD14-PE and CD15-FITC conjugated antibodies (MiltenyiBiotec, Germany) in staining buffer (PBS with 2mM of EDTA and 4% FBS) for 20 minutes in the dark. Pure monocytes were next isolated by positive selection as CD14+CD15- cells using flow cytometry sorting and were pelleted and stored at -80ºC. Genomic DNA were extracted  the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany), according to manufacturer's instructions. DNA were quantified with Nanodrop ND-2100 and Qubit® DNA assay kit (invitrogen).

tag: gender

value: F

tag: classification


title: DZA,204,3356

tag: genotype


title: genomic DNA from CD4+ T-cell_VAS94

source_name: SAMPLE_95 genomic DNA from CD4+ T-cell_VAS94


title: genomic DNA from CD4+ T-cell_VAS99

source_name: SAMPLE_98 genomic DNA from CD4+ T-cell_VAS99

value: M


title: A17,206,3357


title: DZA,746B,3344


title: DZA,724B,3353


title: genomic DNA from CD4+ T-cell_VAS97

source_name: SAMPLE_96 genomic DNA from CD4+ T-cell_VAS97


title: A17,176A,3355


title: genomic DNA from CD4+ T-cell_VAS93

source_name: SAMPLE_94 genomic DNA from CD4+ T-cell_VAS93


title: A17,216,3343


title: A17,724B,3352


title: genomic DNA from CD4+ T-cell_VAS92

source_name: SAMPLE_93 genomic DNA from CD4+ T-cell_VAS92


title: DZA,176A,3342


title: genomic DNA from CD4+ T-cell_VAS90

source_name: SAMPLE_91 genomic DNA from CD4+ T-cell_VAS90


title: A17,199,3341


title: genomic DNA from CD4+ T-cell_VAS9

source_name: SAMPLE_90 genomic DNA from CD4+ T-cell_VAS9


title: DZA,204,3339


title: DZA,25B,3340


title: genomic DNA from CD4+ T-cell_VAS89

source_name: SAMPLE_89 genomic DNA from CD4+ T-cell_VAS89


title: genomic DNA from CD4+ T-cell_VAS91

source_name: SAMPLE_92 genomic DNA from CD4+ T-cell_VAS91


title: genomic DNA from CD4+ T-cell_VAS88

source_name: SAMPLE_88 genomic DNA from CD4+ T-cell_VAS88


title: genomic DNA from CD4+ T-cell_VAS87

source_name: SAMPLE_87 genomic DNA from CD4+ T-cell_VAS87


title: DZA,176A,3338


title: DZA,748B,3327


title: A17,335,3322


title: genomic DNA from CD4+ T-cell_VAS86

source_name: SAMPLE_86 genomic DNA from CD4+ T-cell_VAS86


title: DZA,182,3330


title: genomic DNA from CD4+ T-cell_VAS84

source_name: SAMPLE_85 genomic DNA from CD4+ T-cell_VAS84


title: genomic DNA from CD4+ T-cell_VAS83

source_name: SAMPLE_84 genomic DNA from CD4+ T-cell_VAS83


title: genomic DNA from CD4+ T-cell_VAS82

source_name: SAMPLE_83 genomic DNA from CD4+ T-cell_VAS82


title: A17,283,3320

source_name: Nodule


title: DZA,746B,3318


title: genomic DNA from CD4+ T-cell_VAS81

source_name: SAMPLE_82 genomic DNA from CD4+ T-cell_VAS81


title: DZA,748B,3314


title: A17,31,3319


title: DZA,216,3316


title: genomic DNA from CD4+ T-cell_VAS8

source_name: SAMPLE_80 genomic DNA from CD4+ T-cell_VAS8


title: genomic DNA from CD4+ T-cell_VAS80

source_name: SAMPLE_81 genomic DNA from CD4+ T-cell_VAS80


title: genomic DNA from CD4+ T-cell_VAS79

source_name: SAMPLE_79 genomic DNA from CD4+ T-cell_VAS79


title: A17,144B,3309


title: genomic DNA from CD4+ T-cell_VAS78

source_name: SAMPLE_78 genomic DNA from CD4+ T-cell_VAS78


title: genomic DNA from CD4+ T-cell_VAS77

source_name: SAMPLE_77 genomic DNA from CD4+ T-cell_VAS77


title: DZA,282,3307


title: A17,199,3313


title: genomic DNA from CD4+ T-cell_VAS76

source_name: SAMPLE_76 genomic DNA from CD4+ T-cell_VAS76


title: DZA,182,3305


title: genomic DNA from CD4+ T-cell_VAS75

source_name: SAMPLE_75 genomic DNA from CD4+ T-cell_VAS75


title: A17,25B,3300


title: A17,182,3304


title: genomic DNA from CD4+ T-cell_VAS73

source_name: SAMPLE_74 genomic DNA from CD4+ T-cell_VAS73


title: genomic DNA from CD4+ T-cell_VAS71

source_name: SAMPLE_72 genomic DNA from CD4+ T-cell_VAS71


title: genomic DNA from CD4+ T-cell_VAS72

source_name: SAMPLE_73 genomic DNA from CD4+ T-cell_VAS72


title: A17,182,3298


title: A17,121,3297


title: genomic DNA from CD4+ T-cell_VAS70

source_name: SAMPLE_71 genomic DNA from CD4+ T-cell_VAS70


title: A17,335,3295


title: genomic DNA from CD4+ T-cell_VAS7

source_name: SAMPLE_70 genomic DNA from CD4+ T-cell_VAS7


title: genomic DNA from CD4+ T-cell_VAS69

source_name: SAMPLE_69 genomic DNA from CD4+ T-cell_VAS69


title: DZA,746B,3293


title: A17,176A,3294


title: DZA,176A,3292


title: genomic DNA from CD4+ T-cell_VAS68

source_name: SAMPLE_68 genomic DNA from CD4+ T-cell_VAS68


title: genomic DNA from CD4+ T-cell_VAS66

source_name: SAMPLE_66 genomic DNA from CD4+ T-cell_VAS66


title: genomic DNA from CD4+ T-cell_VAS67

source_name: SAMPLE_67 genomic DNA from CD4+ T-cell_VAS67


title: DZA,283,3287

source_name: Nodule


title: A17,335,3282


title: genomic DNA from CD4+ T-cell_VAS65

source_name: SAMPLE_65 genomic DNA from CD4+ T-cell_VAS65


title: A17,31,3277


title: genomic DNA from CD4+ T-cell_VAS64

source_name: SAMPLE_64 genomic DNA from CD4+ T-cell_VAS64


title: genomic DNA from CD4+ T-cell_VAS62

source_name: SAMPLE_62 genomic DNA from CD4+ T-cell_VAS62


title: DZA,199,3285


title: A17,746B,3281


title: genomic DNA from CD4+ T-cell_VAS63

source_name: SAMPLE_63 genomic DNA from CD4+ T-cell_VAS63


title: genomic DNA from CD4+ T-cell_VAS6

source_name: SAMPLE_61 genomic DNA from CD4+ T-cell_VAS6


title: DZA,89,3275


title: genomic DNA from CD4+ T-cell_VAS59

source_name: SAMPLE_60 genomic DNA from CD4+ T-cell_VAS59


title: DZA,121,3262


title: A17,283,3276


title: genomic DNA from CD4+ T-cell_VAS58

source_name: SAMPLE_59 genomic DNA from CD4+ T-cell_VAS58


title: DZA,283,3258


title: genomic DNA from CD4+ T-cell_VAS56

source_name: SAMPLE_57 genomic DNA from CD4+ T-cell_VAS56


title: A17,278,3273


title: A17,278,3257


title: DZA,724B,3255


title: genomic DNA from CD4+ T-cell_VAS54

source_name: SAMPLE_55 genomic DNA from CD4+ T-cell_VAS54


title: genomic DNA from CD4+ T-cell_VAS55

source_name: SAMPLE_56 genomic DNA from CD4+ T-cell_VAS55


title: DZA,121,3253


title: A17,282,3248


title: genomic DNA from CD4+ T-cell_VAS5

source_name: SAMPLE_53 genomic DNA from CD4+ T-cell_VAS5


title: genomic DNA from CD4+ T-cell_VAS53

source_name: SAMPLE_54 genomic DNA from CD4+ T-cell_VAS53


title: A17,724B,3246


title: DZA,144B,3243


title: genomic DNA from CD4+ T-cell_VAS49

source_name: SAMPLE_52 genomic DNA from CD4+ T-cell_VAS49


title: genomic DNA from CD4+ T-cell_VAS48

source_name: SAMPLE_51 genomic DNA from CD4+ T-cell_VAS48


title: A17,204,3244


title: DZA,144B,3239


title: genomic DNA from CD4+ T-cell_VAS45

source_name: SAMPLE_48 genomic DNA from CD4+ T-cell_VAS45


title: genomic DNA from CD4+ T-cell_VAS46

source_name: SAMPLE_49 genomic DNA from CD4+ T-cell_VAS46


title: genomic DNA from CD4+ T-cell_VAS47

source_name: SAMPLE_50 genomic DNA from CD4+ T-cell_VAS47


title: A17,746B,3238

source_name: Nodule


title: A17,25B,3234


title: genomic DNA from CD4+ T-cell_VAS43

source_name: SAMPLE_47 genomic DNA from CD4+ T-cell_VAS43


title: A17,230,3233


title: genomic DNA from CD4+ T-cell_VAS42

source_name: SAMPLE_46 genomic DNA from CD4+ T-cell_VAS42


title: A17,278,3232


title: genomic DNA from CD4+ T-cell_VAS57

source_name: SAMPLE_58 genomic DNA from CD4+ T-cell_VAS57


title: genomic DNA from CD4+ T-cell_VAS40

source_name: SAMPLE_44 genomic DNA from CD4+ T-cell_VAS40


title: DZA,206,3229


title: genomic DNA from CD4+ T-cell_VAS4

source_name: SAMPLE_43 genomic DNA from CD4+ T-cell_VAS4


title: DZA,25B,3236


title: DZA,144B,3223


title: DZA,216,3216


title: genomic DNA from CD4+ T-cell_VAS41

source_name: SAMPLE_45 genomic DNA from CD4+ T-cell_VAS41


title: genomic DNA from CD4+ T-cell_VAS39

source_name: SAMPLE_42 genomic DNA from CD4+ T-cell_VAS39


title: genomic DNA from CD4+ T-cell_VAS37

source_name: SAMPLE_40 genomic DNA from CD4+ T-cell_VAS37


title: genomic DNA from CD4+ T-cell_VAS38

source_name: SAMPLE_41 genomic DNA from CD4+ T-cell_VAS38


title: DZA,144B,3215


title: DZA,199,3210


title: genomic DNA from CD4+ T-cell_VAS35

source_name: SAMPLE_39 genomic DNA from CD4+ T-cell_VAS35


title: DZA,204,3205


title: DZA,282,3203


title: genomic DNA from CD4+ T-cell_VAS34

source_name: SAMPLE_38 genomic DNA from CD4+ T-cell_VAS34


title: genomic DNA from CD4+ T-cell_VAS33

source_name: SAMPLE_37 genomic DNA from CD4+ T-cell_VAS33


title: A17,282,3202


title: DZA,141,3199


title: genomic DNA from CD4+ T-cell_VAS32

source_name: SAMPLE_36 genomic DNA from CD4+ T-cell_VAS32


title: DZA,748B,3197


title: genomic DNA from CD4+ T-cell_VAS3

source_name: SAMPLE_33 genomic DNA from CD4+ T-cell_VAS3


title: genomic DNA from CD4+ T-cell_VAS31

source_name: SAMPLE_35 genomic DNA from CD4+ T-cell_VAS31


title: genomic DNA from CD4+ T-cell_VAS30

source_name: SAMPLE_34 genomic DNA from CD4+ T-cell_VAS30


title: A17,746B,3187

source_name: Nodule


title: A17,141,3194


title: A17,206,3174


title: genomic DNA from CD4+ T-cell_VAS27

source_name: SAMPLE_30 genomic DNA from CD4+ T-cell_VAS27


title: genomic DNA from CD4+ T-cell_VAS24

source_name: SAMPLE_29 genomic DNA from CD4+ T-cell_VAS24


title: genomic DNA from CD4+ T-cell_VAS28

source_name: SAMPLE_31 genomic DNA from CD4+ T-cell_VAS28


title: DZA,206,3170


title: A17,204,3168


title: genomic DNA from CD4+ T-cell_VAS29

source_name: SAMPLE_32 genomic DNA from CD4+ T-cell_VAS29


title: DZA,141,3153


title: A17,176A,3161


title: A17,748B,3159


title: genomic DNA from CD4+ T-cell_VAS23

source_name: SAMPLE_28 genomic DNA from CD4+ T-cell_VAS23


title: A17,25B,3137


title: A17,282,3135


title: genomic DNA from CD4+ T-cell_VAS22

source_name: SAMPLE_27 genomic DNA from CD4+ T-cell_VAS22


title: genomic DNA from CD4+ T-cell_VAS2

source_name: SAMPLE_24 genomic DNA from CD4+ T-cell_VAS2


title: genomic DNA from CD4+ T-cell_VAS21

source_name: SAMPLE_26 genomic DNA from CD4+ T-cell_VAS21


title: genomic DNA from CD4+ T-cell_VAS20

source_name: SAMPLE_25 genomic DNA from CD4+ T-cell_VAS20


title: DZA,748B,3124


title: genomic DNA from CD4+ T-cell_VAS19

source_name: SAMPLE_23 genomic DNA from CD4+ T-cell_VAS19


title: DZA,278,3119


title: genomic DNA from CD4+ T-cell_VAS18

source_name: SAMPLE_22 genomic DNA from CD4+ T-cell_VAS18


title: genomic DNA from CD4+ T-cell_VAS17

source_name: SAMPLE_21 genomic DNA from CD4+ T-cell_VAS17


title: A17,216,3118


title: A17,199,3116


title: genomic DNA from CD4+ T-cell_VAS16

source_name: SAMPLE_20 genomic DNA from CD4+ T-cell_VAS16


title: genomic DNA from CD4+ T-cell_VAS14

source_name: SAMPLE_18 genomic DNA from CD4+ T-cell_VAS14


title: A17,206,3108


title: genomic DNA from CD4+ T-cell_VAS12

source_name: SAMPLE_16 genomic DNA from CD4+ T-cell_VAS12


title: genomic DNA from CD4+ T-cell_VAS13

source_name: SAMPLE_17 genomic DNA from CD4+ T-cell_VAS13


title: A17,283,3101

source_name: Nodule


title: A17,216,3110


title: A17,141,3100


title: genomic DNA from CD4+ T-cell_VAS113

source_name: SAMPLE_14 genomic DNA from CD4+ T-cell_VAS113


title: genomic DNA from CD4+ T-cell_VAS115

source_name: SAMPLE_15 genomic DNA from CD4+ T-cell_VAS115


title: genomic DNA from CD4+ T-cell_VAS112

source_name: SAMPLE_13 genomic DNA from CD4+ T-cell_VAS112


title: A17,204,3120