title: Onset_10_RNAseq


title: LTED.Pool1_21day_Rep2

status: Public on Jun 27 2024

type: SRA

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

library_source: genomic

data_processing:
Hard trimming was performed using Trim-Galore v0.4.0 (--hardtrim5 20)
Reads were mapped to the sgRNA library using Bowtie v2.2.9 (PMID: 22388286). Reads with MAPQ lower than 30 were excluded from further analyses.
sgRNA counts were derived from the aligned reads using functions in the GenomicAlignments R package.
Genome_build: Custom (design.fa.gz)
Supplementary_files_format_and_content: txt (tab-delimited, raw count for each sgRNA)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: RM condition (full growth media +oestrogen): MCF7-dcas9-KRAB were maintained in DMEM (Gibco #11885-084) supplemented with 10% FBS (Seradigm #1500-500, Lot:077B15), 10mM HEPES, 1mM Sodium-Pyruvate, 1% P/S. For WM (oestrogen-deprived media): MCF7-dCas9-KRAB and LTED-dCas9-KRAB were maintained in Phenol-free DMEM (Gibco #11880-028) supplemented with 10% Fetal Bovine Serum, charcoal-stripped, USDA-approved regions (Gibco #12676029), 2mM L-Glutamine, 10mM HEPES, 1mM Sodium-Pyruvate, 1% P/S.

extract_protocol:
Cells were harvested and sgDNA isolated using the QIAamp DNA maxi kit (QIAGEN).
Amplicons containing the sgRNA sequences were amplified using NEBNext High-Fidelity (NEB).

treatment_protocol: MCF7-dCas9-KRAB and LTED-dCas9-KRAB cells were infected with lentiviral particles at low MOI (≈0.3) in two independent replicates. We transduced ≈1'000 cells per plasmid present in the library to guarantee a good representation of all sgRNAs in the population of cells under screening. The cells were selected using 2μg/ml puromycin (Invitrogen) starting at 24 hours post-transduction and maintained in culture in CellStacks (Corning) in the described conditions and for the indicated time points.

tag: sgrnas pool

tag: medium

value: White Media

tag: days post transfection

tag: replicate


title: Onset_07_RNAseq

city: Rome

first: Stefano

last: Di Giovenale

address: Via Elio Chianesi,  53

country: Italy

institute: IRCCS National Cancer Institute Regina Elena

library_source: transcriptomic

data_processing:
RNAseq samples were aligned to hg19 through STAR and quantified with RSEM. Both the alignment and quantification were performed through the nf-core/rnaseq v3.0 from NEXTFLOW v21.05.0-edg with parameters: --aligner star_rsem.
Assembly: hg19

molecule: total RNA

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted from patient samples using Qiazol (Qiagen, IT), purified from DNA contamination through a DNase I (Qiagen, IT) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen, IT)
RNA libraries were generated using the same amount of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA). The libraries were quantified by qPCR and sequenced in paired-end mode (2×75 bp) with NextSeq 500 (Illumina, CA).

tag: tissue

value: Bone Marrow

tag: disease state

value: Pediatric B-cell acute lymphoblastic leukemia

tag: cell type

value: B-cell CD138+

tag: tumor stage

value: Primary


title: LTED.Pool1_21day_Rep1


title: MCF7.Pool1_Depleted_21day_Rep1


title: P3, ST-seq

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: 38 Xueyuan Road

department: Institute of Systems Biomedicine

country: China

institute: Peking University

description: 10x Visium

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.3.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
R package Seurat (4.0.3) was used for downstream analysis such as normalization, integration, dimensionality reduction and clustering (https://satijalab.org/seurat/).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files and HE figure

source_name: thyroid

growth_protocol: Our study was approved by the Ethics Committee of Peking University Third Hospital (LM2023126). Six patients, including 4 diagnosed with PTC in combination with Hashimoto thyroiditis and 2 diagnosed with Hashimoto thyroiditis were recruited in our study. All the patients signed the informed written consent for each subject and agreed to donate the specimens. For samples of adequate size, small fragments of each sample were snap frozen in optical cutting tissue (OCT) compound (Fisher Healthcare) and/or fixed in 10% formalin (Sigma-Aldrich).

extract_protocol:
The ST protocol was optimized for PTC and HT tissues according to manufacturer’s instructions (10x Genomics, CG000239 Rev E). The optimal incubation time for permeabilization was determined to be 22 min. Once optimal conditions were established, the cryosections (10 μm thick) per patient were cut onto the ST slides and processed immediately. Fixation, H&E staining, and imaging protocols were as describe by the manufacturer (10x Genomics, CG000239 Rev E). Sectioned slides were incubated at 37 ℃ for 1 min, fixed in 3.7% - 3.8% formaldehyde (Sigma-Aldrich) in PBS for 10 min, and then washed in 1x PBS (Medicago). For staining, sections were incubated in Mayer’s hematoxylin (Dako, Agilent) for 4 min, bluing buffer (Dako) for 30 sec, followed by eosin (Sigma-Aldrich) diluted 1:5 in Tris-base (0.45 M Tris, 0.5 M acetic acid, pH 6.0) for 30 sec. The slides were washed in water free of RNase and DNase after each of the staining steps. After air-drying, the slides were mounted with 85% glycerol (Merck Millipore) and coverslips. Bright-field images were taken at 20 × magnification using a Metafer Slide Scanning platform (MetaSystems). Raw images were stitched with VSlide software (MetaSystems). The coverslips and glycerol were removed after imaging by immersing slides in water free of RNase and DNase.
Library was performed according to the manufacter’s instructions (10x Genomics, CG000239 Rev E). After Reverse transcription, wells were washed with 0.1×SSC and incubated at 56 ℃ with interval shaking for 1.5 h with a tissue removal mix of Proteinase K (QIAGEN) and PKD buffer (QIAGEN, pH7.5) at a 1:1 ratio. The spatially barcoded cDNA was enzymatically released as previously described. Supernatants containing released cDNA were collected and transferred to 96-well plates for ST library preparation with an automated MBS 8000 system. Second-strand cDNA synthesis was followed by in vitro transcription, adaptor ligation, and a second RT. Sequencing handles and indexes were added in an indexing PCR, and the finished libraries were purified and quantified according to the manufacturer’s instructions (Visium spatial gene expression reagent kits, No. CG000239 Rev E). The libraries were sequenced on an Illumina NextSeq platform.

value: thyroid


title: LTED.Pool1_14day_Rep2


title: LTED.Pool1_14day_Rep1


title: Healthy_3_RNAseq

value: Healthy


title: Healthy_2_RNAseq


title: Healthy_12_RNAseq


title: LAL-B_Rep1_ATACseq

data_processing:
The ATAC-sequencing reads quality was assessed with FastQC v0.11.9. Reads were aligned to the reference genome hg19 using bowtie v2.3.5.1 with default parameters. The conversion from sam to bam file was performed through view function of SAMtools v1.7. BAM files were deduplicated with GATK v4.1.9.0 markDuplicates with default parameters. ATAC-seq peaks were called by MACS2 v2.2.6 with parameters --format AUTO --nomodel --shift -100 --extsize 200 -B --SPMR --call-summit -q 0.01 -g hs. BigWig (bw) files were obtained from the BedGraph (bdg) files with bedGraphToBigWig v4 with default parameters. Finally, all peaks matching blacklisted regions were removed with the function intersect of bedtools suite v2.29.2.
Assembly: hg19

extract_protocol:
ATACseq : The nuclei were centrifuged at 500g for 5 minutes at 4°C and subsequently resuspended on ice in 50μl transposase reaction buffer containing 2.5μl of Tn5 transposase and 25μl of 2xTD buffer (Nextera DNA Sample preparation kit from Illumina). After incubation at 37°C for 30 minutes, the samples were purified with MiniElute PCR Purification Kit (Qiagen), eluting in 10µl elution buffer (10mM Tris-HCl pH 8).
ATACseq's  libraries were purified by adding Agencourt Ampure XP (Beckman) magnetic beads (1:1 ratio) to remove remaining adapters (left side selection) and double purified (1:0.5 and 1:1.15 ratio) for right side selection. Libraries were controlled using a High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies). Each library was then paired end sequenced (2×75bp) on a NextSeq 500 instrument (Illumina).

value: Primary B-cell CD138+

tag: cell line

value: LAL-B


title: RNA3, WT, rep2

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

country: Japan

institute: Graduate School of Science, The University of Tokyo

data_processing:
ChIP-seq reads were mapped on the TAIR10 genome using Bowtie ver 1.2.1.1. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.26. The bigwig files were created using deeptools software.
RNA-seq reads were mapped on the TAIR10 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- clip3pNbases, 50; -- quantMode GeneCounts parameters.
EM-seq reads were mapped on the TAIR10 genome using Bismark ver. 0.10.1 with -n 1 -l 20 -e 90 parameters. Deduplication and methylation extraction were also performed using Bismark. Counting methylated C was conducted using map function of BEDTools. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: TAIR10
Supplementary files format and content: bigwig file for ChIP-seq and EM-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

organism: Arabidopsis thaliana

source_name: 2-week-old seedling

extract_protocol:
ChIP was performed as described in Zhao et al (2020) Nat. Commun. 11: 2658. Total RNA was extracted from whole plants using Rneasy Plant Mini Kit (Qiagen). Genome DNA was extracted using Nucleon PhytoPure (Cytiva).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). RNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). EM-seq libraries were constructed using the NEBNext Enzymatic Methyl-seq (EM-seq) Kit (NEB).

value: 2-week-old seedling

tag: genotype

value: wild type


title: patient_26_Remission_ATACseq

value: Remission


title: patient_25_Remission_ATACseq


title: LAL-B_Rep2_ATACseq


title: LAL-B_Rep3_ATACseq


title: RNA3, WT, rep1


title: RNA3, cxs, rep2

value: ASHH3 cmt23 x ASHH3 suvh456


title: RNA3, cxs ashh3, rep3

value: ashh3 cmt23 x ashh3 suvh456


title: RNA3, WT, rep3


title: patient_23_Remission_ATACseq


title: RNA3, cxs ashh3, rep1


title: ChIP6, cxs ldl2, H3K4me1, rep2

tag: chip antibody

value: H3K4me1 ChIP


title: RNA3, cxs, rep1


title: patient_24_Remission_ATACseq


title: patient_22_Remission_ATACseq


title: patient_21_Remission_ATACseq


title: ChIP6, cxs, H3K4me1, rep2


title: patient_20_Remission_ATACseq


title: Healthy_1_RNAseq


title: ChIP6, sxc ldl2, H3K4me1, rep2

value: ashh3 suvh456 x ashh3 cmt23


title: RNA3, cxs, rep3


title: patient_18_Remission_ATACseq


title: ChIP6, sxc, H3K4me1, rep2

value: ASHH3 suvh456 x ASHH3 cmt23


title: RNA3, cxs ashh3, rep2


title: ChIP6, WT, H3K4me1, rep2


title: patient_32_Relapse_ATACseq

value: Relapse


title: ChIP6, cxs ldl2, H3K9me2, rep2

value: H3K9me2 ChIP


title: patient_31_Relapse_ATACseq

value: Bone Marrow

value: Pediatric B-cell acute lymphoblastic leukemia


title: ChIP6, cxs, H3K9me2, rep2


title: ChIP6, sxc, H3K9me2, rep2


title: patient_29_Relapse_ATACseq

value: B-cell CD138+


title: ChIP6, sxc ldl2, H3K9me2, rep2


title: patient_30_Relapse_ATACseq


title: patient_28_Relapse_ATACseq


title: patient_14_Relapse_ATACseq


title: patient_27_Relapse_ATACseq


title: ChIP6, cxs ldl2, H3K36me3, rep2

value: H3K36me3 ChIP


title: ChIP6, sxc, H3K36me3, rep2


title: patient_27_Primary_ATACseq

value: Primary


title: patient_26_Primary_ATACseq


title: ChIP6, cxs, H3K36me3, rep2


title: patient_19_Primary_ATACseq


title: ChIP6, sxc ldl2, H3K36me3, rep2


title: ChIP6, WT, H3K36me3, rep2


title: ChIP6, cxs ldl2, H3, rep2

value: H3 ChIP


title: patient_33_Relapse_ATACseq


title: patient_17_Primary_ATACseq


title: ChIP6, sxc ldl2, H3, rep2


title: patient_16_Primary_ATACseq


title: ChIP6, cxs, H3, rep2


title: ChIP6, sxc, H3, rep2


title: patient_14_Primary_ATACseq


title: patient_11_Primary_ATACseq


title: ChIP6, WT, H3K9me2, rep2


title: patient_13_Primary_ATACseq


title: ChIP6, cxs ldl2, H3K4me1, rep1


title: ChIP6, WT, H3, rep2


title: patient_7_Primary_ATACseq


title: patient_5_Healthy_ATACseq

value: Healthy


title: ChIP6, sxc ldl2, H3K4me1, rep1

value: 2-week-old seedling


title: patient_12_Primary_ATACseq


title: ChIP6, cxs, H3K4me1, rep1


title: ChIP6, WT, H3K4me1, rep1

value: wild type


title: patient_4_Healthy_ATACseq


title: ChIP6, sxc, H3K4me1, rep1


title: VL RNA Control at baseline before Bedrest rep2

type: RNA

city: Irvine

first: Fadia

last: Haddad

state: CA

address: 101 Academy Way, Suite 150

department: Pediatrics/Exercise Medicine Division

country: USA

institute: University of California Irvine

description: Gene Expression at Baseline before Bed Rest

hyb_protocol: 1.2 ug of Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization bufferHI-RPM was added to the fragmentation mixture and hybridized to and hybridized to Agilent Human Gene Expression (8x60 k) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C with GE Wash buffer 2 (Agilent). Triton X-102 was added at 0.005% to all wash buffers before use.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters. Text files were imported in GeneSpring software version 14.9.1, data was processed and quantile normalized. Additional data filtration was perfomed to exclude non detected and nonuniform /outlier features before further analysis

source_name: Vastus Lateralis muscle RNA Control baseline before Bedrest

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Adult male subjects (25-45y/o) were randomized to one of three groups: 1) control; no exercise, bed rest only (CON; n = 7), 2) bed rest + exercise using traditional exercise equipment (EX;  n = 7), and 3) bed rest + exercise using a flywheel device (FLY; n = 8).

extract_protocol: Total RNA was extracted from muscle using the Trizol reagent following the manufacturer's recommendations (Life technologies). Total RNA was cleaned using Qiagen RNeasy then quantified using a Nanovue GE-spectrophotometer and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Muslce biopsies were collected from vastus lateralis muscle from participants at Baseline before bedrest, then ~70 days after bedrest with or without exercise intervention.

value: Vastus Lateralis Skeletal Muscle

tag: gender

value: male

tag: age (y)


title: patient_6_Healthy_ATACseq


title: patient_9_Healthy_ATACseq


title: patient_7_Healthy_ATACseq


title: ChIP6, cxs ldl2, H3K9me2, rep1

value: ashh3 cmt23 x ashh3 suvh456


title: patient_8_Healthy_ATACseq


title: ChIP6, sxc, H3K9me2, rep1


title: ChIP6, WT, H3K9me2, rep1


title: ChIP6, cxs, H3K9me2, rep1

value: ASHH3 cmt23 x ASHH3 suvh456


title: ChIP6, sxc ldl2, H3K9me2, rep1

value: ashh3 suvh456 x ashh3 cmt23


title: ChIP6, cxs ldl2, H3K36me3, rep1


title: ChIP6, sxc ldl2, H3K36me3, rep1


title: patient_10_Primary_ATACseq


title: VL RNA after 70d Bedrest+Flywheel Exercise rep7

description: Gene Expression after 70d Bed Rest with Flywheel Exercise protocol

hyb_protocol: Cy3-labeled RNA from each sample was hybridized to Agilent Human microRNA microarrays Agilent Chip 8x60K cat# G4872A (Agilent technologies) for 20 hours at 55°C in a rotating oven. After hybridization, microarrays were washed 5 minute at room temperature with GE wash buffer 1 (Agilent technologies) then immediately dried and scanned

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent technologies, Santa Clara, CA, US) using default parameters. Raw data text files were imported in GeneSpring software version 14.9.1,(Agilent technologie, Santa Clara, CA US),  data was processed and quantile normalized.  Additional data filtration was perfomed to exclude non detected and nonuniform /outlier features before further analysis.

source_name: Vastus Lateralis muscle RNA Control post 70d Bedrest+flywheel exercise

label_protocol: One hundred ng of total RNA from each sample was labeled with the fluorescent dye Cyanine 3-pCp (Cy3) using the microRNA Labeling Reagent and Hybridization Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

growth_protocol: Adult male subjects (25-45 y/o) were randomized to one of three groups: 1) control; no exercise, bed rest only (CON; n = 7), 2) bed rest + exercise using traditional exercise equipment (EX;  n = 7), and 3) bed rest + exercise using a flywheel device (FLY; n = 8).

extract_protocol: Total RNA was extracted from muscle using the Trizol reagent following the manufacturer's recommendations (Life technologies). Total RNA was quantified using a Nanovue GE-spectrophotometer and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Muslce biopsies were collected from vastus lateralis muscle from participants at baseline before bedrest, then ~70 days after bedrest with or without exercise intervention.


title: ChIP6, cxs, H3K36me3, rep1


title: VL RNA after 70d Bedrest+Flywheel Exercise rep8


title: ChIP6, sxc, H3K36me3, rep1

value: ASHH3 suvh456 x ASHH3 cmt23


title: VL RNA FLY at baseline before Bedrest rep7

source_name: Vastus Lateralis muscle RNA Control at baseline before Bedrest+flywheel exercise


title: Cultured_VSMCs_AR016

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Raw reads were trimmed using Trim Galore and Cutadapt. Alignment of the reads to the GRCm38 genome was performed using TopHat. Reads per gene were counted using Seqmonk. Reads were Log2 transformed.
Genome_build: GRCm38
RNA-seq report: A text delimited file with Log2 RPM values per gene.

organism: Mus musculus

source_name: Medial layer of mouse aorta

growth_protocol: Aortas from healthy male mice (8-14 weeks) were dissected free of fat and connective tissue, the medial layer was isolated after predigest in  Collagenase (1mg/ml) & Elastase (1U/ml) in DMEM, and medial cells digested to a single cell suspension in fresh digestion mix. Cells were washed 2x in growth medium (DMEM supplemented with 10% FCS and Pen/strep/glutamine) and plated in growth medium. Cells were passaged 3-5 times.

extract_protocol:
Cells were washed in PBS, lysed in Trizol (Thermo-Fisher) and total RNA isolated. The extracted RNA was cleaned on a RNeasy column (Qiagen) and quality-assessed on a Bioanalyzer (Agilent, RNA integrity number [RIN] 7.8-9)
Sequencing libraries were made from 4 ug total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: vascular smooth muscle cells

tag: background


title: Cultured_VSMCs_AR007


title: VL RNA FLY at baseline before Bedrest rep8


title: Cultured_VSMCs_AR004


title: hpGUS243_10

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

description: hpGUS[Δ24nt-3] rep 3

data_processing:
Reads were trimmed using cut adapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --minimum-length=15
Trimmed reads were mapped to the tobacco genome, GUS gene and sense strand of the stem of asymmetric bulge hairpins
Reads were mapped using Bowtie 1.3.1 with options -v 0 -a --best --strata -l 18
awk commands were used to filter out reads mapping to GUS with only unique reads retained for downstream analysis
Assembly: GCA_002210045.1_Nitab4.5_genomic.fna
Supplementary files format and content: raw files are in fastq format
Supplementary files format and content: processed files are unique reads mapped to the GUS gene in a  .bed format.  Rows are 1 = mapping to GUS or asymmetric bulge sense strands; 2 = Start; 3= End; 4 = read name; 5 = quality; 6 = strand; 7 = sRNA size

organism: Nicotiana tabacum

source_name: leaf

growth_protocol: tobacco plants were grown under long day condiitions and leaf material collected for sequencing

extract_protocol:
RNA was extracted using trizol
sRNA library Prep

value: leaf


title: ChIP6, WT, H3K36me3, rep1


title: hpGUS243_3

description: hpGUS[Δ24nt-3] rep 1


title: ChIP6, cxs ldl2, H3, rep1


title: Cultured_VSMCs_AR002


title: hpGUS242_11

description: hpGUS[Δ24nt-2] rep 3


title: hpGUS243_7

description: hpGUS[Δ24nt-3] rep 2


title: VL RNA FLY at baseline before Bedrest rep5


title: VL RNA after 70d Bedrest+Flywheel Exercise rep6


title: VL RNA FLY at baseline before Bedrest rep6


title: ChIP6, sxc ldl2, H3, rep1


title: hpGUS241_10

description: hpGUS[Δ24nt-1] rep 3


title: hpGUS242_5

description: hpGUS[Δ24nt-2] rep 1


title: hpGUS241_8

description: hpGUS[Δ24nt-1] rep 2


title: ChIP6, cxs, H3, rep1


title: ChIP6, sxc, H3, rep1


title: hpGUS241_2

description: hpGUS[Δ24nt-1] rep 1


title: VL RNA after 70d Bedrest+Flywheel Exercise rep4


title: ChIP6, WT, H3, rep1


title: hpGUS23_9

description: hpGUS[Δ23nt] rep 3


title: VL RNA FLY at baseline before Bedrest rep4


title: hpGUS23_4

description: hpGUS[Δ23nt] rep 1


title: hpGUS22_14

description: hpGUS[Δ22nt] rep 3


title: EM2, sxc ashh3, rep2

data_processing:
ChIP-seq reads were mapped on the TAIR10 genome using Bowtie ver 1.2.1.1. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.26. The bigwig files were created using deeptools software.
RNA-seq reads were mapped on the TAIR10 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- clip3pNbases, 50; -- quantMode GeneCounts parameters.
EM-seq reads were mapped on the TAIR10 genome using Bismark ver. 0.10.1 with -n 1 -l 20 -e 90 parameters. Deduplication and methylation extraction were also performed using Bismark. Counting methylated C was conducted using map function of BEDTools. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: TAIR10
Supplementary files format and content: bigwig file for ChIP-seq and EM-seq
Supplementary files format and content: tab-delimited text file for RNA-seq
Library strategy: EM-seq

tag: treatment

value: Enzymatic DNA methylation


title: hpGUS22_9

description: hpGUS[Δ22nt] rep 2


title: hpGUS242_10

description: hpGUS[Δ24nt-2] rep 2


title: VL RNA after 70d Bedrest+Flywheel Exercise rep5


title: hpGUSWT_15

description: hpGUS[WT] rep3


title: hpGUSWT_4

description: hpGUS[WT] rep2


title: EM2, cxs, rep2


title: hpGFP_4

description: CONTROL


title: EM2, sxc, rep2


title: hpGUSWT_3

description: hpGUS[WT] rep1


title: VL RNA FLY at baseline before Bedrest rep3


title: EM2, cmt23 ashh3, rep2

value: ashh3 cmt23


title: WT_Input

city: Shanghai

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

description: WT,Input

data_processing:
The obtained DNA library  was  sequenced on Illumina sequencing platform.
Low quality bases were trimmed by using Trimmomatic(version: 0.36). Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. It works with FASTQ or gzipp'ed FASTQ. With 'simple' trimming, each adapter sequence is tested against the reads, and if a sufficiently accurate match is detected, the read is clipped appropriately.
Clean reads were mapped to Arabidopsis thaliana(ENSEMBLE) using Bowtie2 (version:2.3.4.3) with default parameters. The alignment file(SAM) was transformed to BAM file and was filtered by the following criteria: (1) only keep unique aligned reads; (2) remove reads with low MAPQ(<30).
The MACS2 (version: 2.1.2) was used to identify transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity.
The peaks were annotated by ChIPseeker (version: 2.16.0), an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes. Comparison of ChIP peak profiles and annotation are also supported.
Assembly: Saccharopolyspora erythraea NRRL 2338(NCBI,ASM6288v1)
Supplementary files format and content: bigWig, Peak

organism: Saccharopolyspora erythraea

source_name: Saccharopolyspora erythraea

growth_protocol: TSB medium

extract_protocol:
Collected the cultured cells in centrifuge tube and then washed with 1X PBS buffer. After centrifugation and removing the supernatant, 1% formaldehyde in PBS buffer was used to cross-link DNA and proteins for about 10min at 37 ℃.
After that, 0.125 M of glycine was used to stop the crosslinking reaction. the cells were washed with precooled PBS with 0.5% bovine serum and by PBS supplemented with protease inhibitor compound (PIC). The cells were collected by centrifugation at 850 rpm for 3 min after each wash. The cells were resuspended in 200 μl ice-cold lyses buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 7.5 plus PIC) and then thawed on ice for 10 min to allow cell lyses. The cell lysate was sonicated using Bioruptor Pico to generate chromatin fragments of size range from 100 to 800 bp. One-tenth of the sonicated chromatin sample was separated for input control. The remaining chromatin was immunoprecipitated in ChIP dilution buffer (1% Triton, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 7.5) with 4 μg of antibody that has been pre-incubated with protein A/G magnetic beads (Invitrogen; 10003D). The immunoprecipitation reaction was incubated overnight at 4 °C and the beads were washed twice with each of the following buffers at 4 °C: RIPA buffer (10 mM Tris, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.1% Triton X-100); RIPA buffer plus 0.3 M NaCl; LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and TE buffer. The captured DNA and input control sample were reverse cross-linked by eluting the beads with elution buffer (1% SDS, 0.1 M NaHCO3) at 65 °C for 2 h, respectively. The eluted DNA was purified by phenol-chloroform extraction and precipitated with ethanol and glycogen. The obtained DNA was subjected to library preparation and sequenced on Illumina sequencing platform.

value: Saccharopolyspora erythraea

tag: fraction

value: input

value: wild type DasR


title: VL RNA after 70d Bedrest+Flywheel Exercise rep1


title: VL RNA FLY at baseline before Bedrest rep1


title: VL RNA after 70d Bedrest+Flywheel Exercise rep2


title: hpGUS23_8

description: hpGUS[Δ23nt] rep 2


title: K78Q_IP

value: IP

tag: antibody

value: anti-DasR

value: K78Q mutation of DasR


title: VL RNA FLY at baseline before Bedrest rep2


title: EM2, cmt23, rep2

value: 2-week-old seedling

value: ASHH3 cmt23


title: EM2, cxs ashh3, rep2


title: K78Q_Input


title: VL RNA after 70d Bedrest+Flywheel Exercise rep3

value: Vastus Lateralis Skeletal Muscle

value: male


title: hpGUS22_6

description: hpGUS[Δ22nt] rep 1


title: EM2, suvh456 ashh3, rep2

value: ashh3 suvh456


title: lib.Pool2

organism: mixed DNA library

source_name: Library

tag: sgrnas pool


title: lib.Pool1


title: VL RNA after 70d Bedrest+traditional exercise rep7

description: Gene Expression after 70d Bed Rest with standard Exercise protocol

source_name: Vastus Lateralis muscle RNA Control post 70d Bedrest+traditional exercise


title: VL RNA EX at baseline before Bedrest rep7

source_name: Vastus Lateralis muscle RNA Control at baseline before Bedrest+traditional exercise


title: EM2, suvh456, rep2

value: ASHH3 suvh456


title: EM2, WT, rep2

value: wild type


title: WT_IP

description: WT,IP


title: KO_4, miRNA passage 7

city: Poznań

first: Emilia

last: Kozłowska

address: Noskowskiego 12/14

country: Poland

institute: IBCH PAS

description: iPSC line KO was generated via CRISPR-Cas9 of the ND42222 cell line obtained from NINDS Repository. Generation of the KO line was described by Dabrowska et al.. 2020

data_processing:
The samples were sequenced with a paired-end 2x100 cycle procedure, 10MR/sample.
Differential expression analysis was performed using DESeq2.
Assembly: MiRBase v. 22
Supplementary files format and content: excel format; RPM values

source_name: HTT-KO

growth_protocol: iPSC lines were grown in StemFlex (Gibco) medium on a Geltrex (Gibco)-coated 6-well plates. After differentiation NSCs were grown in Neural Progenitor Medium (STEMCELL Technologies). All cells were cultured in humified atmosphere with 5% CO2 at 37 0C

extract_protocol:
Total RNA was isolated with Direct-zol RNA Microprep (ZYMO RESEARCH).
TruSeq Small RNA Library Prep (Illumina)

treatment_protocol: iPSC lines were differentiated into NSCs using STEMdiff SMADi Neural Induction Kit (STEMCELL Technologies).

value: HTT-KO

value: NSC

value: Differentiation from iPSC to NSC


title: KO_3, miRNA passage 6


title: HD_4, miRNA passage 7

description: The human HD iPSC line ND42222 was obtained from the NINDS Repository.

value: HTT mutation, 109CAG


title: EM2, cxs ashh3, rep1

value: ashh3 cmt23 x ashh3 suvh456

value: Enzymatic DNA methylation


title: KO_1, miRNA passage 4


title: VL RNA EX at baseline before Bedrest rep6


title: VL RNA after 70d Bedrest+traditional exercise rep6


title: HD_3, miRNA passage 6


title: HD_2, miRNA passage 5


title: EM2, sxc ashh3, rep1

value: ashh3 suvh456 x ashh3 cmt23


title: VL RNA EX at baseline before Bedrest rep5


title: IC1_3, miRNA passage 6

description: iPSC line IC1 was generated via CRISPR-Cas9 of the ND42222 cell line obtained from NINDS Repository. Generation of the IC1 line was described by Dabrowska et al.. 2020

value: control


title: VL RNA after 70d Bedrest+traditional exercise rep5


title: EM2, cxs, rep1

value: ASHH3 cmt23 x ASHH3 suvh456


title: IC1_1, miRNA passage 4


title: KO_4, RNA passage 7

data_processing:
The samples were sequenced with a paired-end 2x100 cycle procedure, 50MR/sample.
Quality reports were generated with FastQC v0.11.9.
The reads were mapped against the rRNAs with Bowtie 2 v.2.3.5.1, with the -X 1000 parameter (for mapped read distance) and  the -un-conc parameter, to obtain unmapped reads as the output (genome assembly)
The expression values were obtained with RSEM v. v1.3.1
Differential expression analysis was performed using DESeq2.
Assembly: ENSEMBL v.102 Homo_sapiens.GRCh38.102
Supplementary files format and content: excel format; TPM values

extract_protocol:
Total RNA was isolated with Direct-zol RNA Microprep (ZYMO RESEARCH).
Sequencing libraries were generated using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosciences) and IDT adapters from Illumina TruSeq DNA UD Indexes (96 Indexes, 96 Samples).


title: KO_3, RNA passage 6


title: EM2, cmt23 ashh3, rep1

value: ashh3 cmt23


title: EM2, sxc, rep1

value: 2-week-old seedling

value: ASHH3 suvh456 x ASHH3 cmt23


title: VL RNA after 70d Bedrest+traditional exercise rep4

value: Vastus Lateralis Skeletal Muscle


title: KO_2, RNA passage 5


title: VL RNA EX at baseline before Bedrest rep4

value: male


title: KO_2, miRNA passage 5


title: HD_4, RNA passage 7


title: KO_1, RNA passage 4


title: HD_2, RNA passage 5


title: HD_3, RNA passage 6


title: EM2, cmt23, rep1

value: ASHH3 cmt23


title: HD_1, RNA passage 4


title: IC1_3, RNA passage 6


title: HD_1, miRNA passage 4


title: VL RNA after 70d Bedrest+traditional exercise rep2


title: VL RNA EX at baseline before Bedrest rep3


title: VL RNA EX at baseline before Bedrest rep2


title: IC1_2, miRNA passage 5


title: RNA2, cxs ldl2, rep3

value: cmt23 ldl2 x suvh456 ldl2 F1


title: IC1_1, RNA passage 4


title: EM2, WT, rep1

value: wild type


title: RNA2, cxs, rep3

value: cmt23 LDL2 x suvh456 LDL2 F1


title: VL RNA EX at baseline before Bedrest rep1


title: RNA2, sxc ldl2, rep3

value: suvh456 ldl2 x cmt23 ldl2 F1


title: VL RNA after 70d Bedrest+traditional exercise rep1


title: HCT116 cells, shKAT7-2

city: Guangzhou

first: Zhongjie

last: Huang

state: Guangdong

address: No. 253, Middle Industrial Avenue

institute: Zhuujiang hospital

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online platform.
Assembly: hg38
Supplementary files format and content: txt file includes raw counts and FPKM values for each Sample

extract_protocol:
RNA was havested using the RNAprep Pure Plant Kit (Tiangen, Beijing, China). 1 ug of total RNA was used for the construction of sequencing librares.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: colorectal cancer cell

value: KAT7 knockdown


title: HCT-116 cells, shControl-3


title: EM2, suvh456 ashh3, rep1

value: ashh3 suvh456


title: VL RNA Control at baseline before Bedrest rep7


title: EM2, suvh456, rep1

value: ASHH3 suvh456

value: Enzymatic DNA methylation


title: VL RNA after 70d Bedrest+traditional exercise rep3


title: KL2A drug released, rechallenged with RM-042, Rep 7

city: Redwood City

first: Ximo

last: Pechuan-Jorge

address: 700 Saginaw Drive

institute: Revolution Medicines

data_processing:
Count matrices were obtained aligning sequencing reads by running count from Cell Ranger with default settings (version 7.1.0) against the GRCm38 (mm10-3.0.0) mouse reference. Potential ambient RNA was removed using CellBender. The resulting ambient corrected count matrices were analyzed with Seurat (version 5.0.0). Normalization, dimensionality reduction, and clustering were done following Seurat procedure.
Assembly: GRCm38 (mm10-3.0.0)
Supplementary files format and content: R data serialization (.rds) file holding seurat object of clustered single cells.

source_name: Lung

extract_protocol:
Harvested tumors were immersed in cold RPMI-1640 and processed into 2-4 mm3 pieces. Tumor pieces were placed in a solution (25 μg/ml Liberase, 30 U/ml Dnase 1, and 0.01% Hyaluronidase in serum-free RPMI-1640 medium), incubated for 45 minutes at 37°C and dissociated in a gentleMACS Octo Dissociator. Suspensions were strained twice using a 70-μm cell strainer. Cold 10% FBS RPMI-1640 was added to solution to halt enzymatic reaction before the suspension was strained through a 70-μm cell strainer twice. Dead cells and debris were removed using a dead cell removal kit (Miltenyi Biotec Inc, #130090101). Cells were resuspended in PBS with 0.04% BSA and underwent viability assessment using Trypan Blue Stain (0.4%) and the Countess™ II FL cell counter.
Library preparation was done following the 10 Genomics Single Cell Chromium 5’V2 protocols. Libraries were pooled to achieve a final concentration of 10 nM, verified by qPCR prior to sequencing. Sequencing was done with a NovaSeq6000 sequencer, utilizing the S4 200 cycles flow cell and sequencing with 26 cycles for read1, 10 cycles for i7 index, 10 cycles for i5, and 90 cycles for read 2 through the ATGC core at MD Anderson Cancer Center.

value: Lung

value: Drug released, retreated with RM-042


title: HCT-116 cells, shControl-2

value: control


title: RNA2, sxc, rep3

value: 2-week-old seedling

value: suvh456 LDL2 x cmt23 LDL2 F1


title: HCT116 cells, shKAT7-1


title: KL2A drug released, rechallenged with RM-042, Rep 8


title: KL2A drug released, rechallenged with RM-042, Rep 6


title: RNA2, cmt23 ldl2, rep3

value: cmt23 ldl2


title: HCT-116 cells, shControl-1


title: VL RNA Control after 70d Bedrest rep7

description: Gene Expression after 70d Bed Rest with no exercise intervention

source_name: Vastus Lateralis muscle RNA Control post 70d Bedrest

value: Vastus Lateralis Skeletal Muscle

value: male


title: KL2A drug released, rechallenged with RM-042, Rep 5


title: IC1_2, RNA passage 5

value: NSC

value: Differentiation from iPSC to NSC


title: HCT116 cells, shKAT7-3


title: VL RNA Control at baseline before Bedrest rep6


title: RNA2, cmt23, rep3

value: cmt23 LDL2


title: KL2A drug released, rechallenged with RM-042, Rep 4


title: VL RNA Control at baseline before Bedrest rep5


title: RNA2, suvh456 ldl2, rep3

value: suvh456 ldl2


title: VL RNA Control after 70d Bedrest rep5


title: EP300_2

city: Hangzhou

first: Qianyu

last: Liu

address: YuhangTang Road

institute: Zhejiang University

data_processing:
Raw data of fastq format were firstly processed using fastp software (version 0.19.11). In this step, clean data were obtained by removing reads containing adapter, ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Assembly: NCBI_GRCh38
Supplementary files format and content: Tab-delimited txt file include binding peak

source_name: H9 hESC

growth_protocol: PXGL naïve hESC was cultured in N2B27 medium supplemented with 1 mM PD0325901, 2 mM XAV939 , 2 mM Go¨ 6983  and 10 ng/mL human LIF on the MEF layer.

extract_protocol:
Cells were washed with PBS and cross-linked with 1% formaldehyde for 10 min. After quenching with 0.125 M glycine for 5 min, cells were scraped, lysed, and sheared by sonication
The samples were sent to Novogene Corporation (Beijing, China) for library construction.

value: H9 hESC

value: Human embryonic stem cell

value: WT


title: RNA2, suvh456, rep3

value: suvh456 LDL2


title: EP300_1


title: KL2A drug released, rechallenged with RM-042, Rep 2


title: RNA2, WT, rep3

value: wild type


title: KL2A drug released, rechallenged with RM-042, Rep 1

value: Lung


title: VL RNA Control after 70d Bedrest rep6


title: RNA2, sxc ldl2, rep2

value: suvh456 ldl2 x cmt23 ldl2 F1


title: KL2A drug released, rechallenged with Vehicle, Rep 2

value: Drug released, retreated with Vehicle


title: sample_Relapse_2_scMultiomics_ATAC

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, gene counts, peaks calling and aggregations were made using the Cell Ranger Arc v. 2.0.2
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix file

extract_protocol:
Sorted B-cells were subjected to nuclei isolation protocol (10X).The nuclei were immediately processed with 10x Genomics Chromium controller using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit.
The libraries were generated according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol and the quality was checked using Agilent High Sensitivity DNA 1000 Kit on Agilent Tape Station. Libraries were quantified using dsDNA High-Sensitivity (HS) Assay Kit (Invitrogen) on Qubit fluorometer and the qPCR-based KAPA quantification kit. RNA libraries were sequenced on an Illumina Nova-Seq 6000 with 18.10.10.90 paired-end format and ATAC libraries with 50.8.24.49 paired-end format.

value: Bone Marrow

value: Pediatric B-cell acute lymphoblastic leukemia


title: input


title: VL RNA Control at baseline before Bedrest rep4


title: RNA2, cxs ldl2, rep2

value: 2-week-old seedling

value: cmt23 ldl2 x suvh456 ldl2 F1


title: sample_Onset_2_scMultiomics_ATAC


title: sample_Relapse_1_scMultiomics_ATAC


title: RNA2, cxs, rep2

value: cmt23 LDL2 x suvh456 LDL2 F1


title: KL2A drug released, rechallenged with Vehicle, Rep 1


title: KL2A drug released, rechallenged with Vehicle, Rep 3


title: sample_Relapse_2_scMultiomics_GEX

molecule: polyA RNA


title: sample_Onset_1_scMultiomics_ATAC


title: VL RNA Control after 70d Bedrest rep4

value: Vastus Lateralis Skeletal Muscle

value: male


title: RNA2, sxc, rep2

value: suvh456 LDL2 x cmt23 LDL2 F1


title: VL RNA Control at baseline before Bedrest rep3


title: KL2A drug released, rechallenged with RM-042, Rep 3

value: Drug released, retreated with RM-042


title: VL RNA Control after 70d Bedrest rep3


title: KL2 treated with Combo RM-029 + RM-4550 for 7 days, Rep 4


title: sample_Relapse_1_scMultiomics_GEX


title: RNA2, cmt23 ldl2, rep2

value: cmt23 ldl2


title: KL2 treated with Sotorasib for 7 days, Rep 4

value: Sotorasib


title: VL RNA Control after 70d Bedrest rep2


title: RNA2, cmt23, rep2

value: cmt23 LDL2


title: sample_Onset_1_scMultiomics_GEX


title: VL RNA Control at baseline before Bedrest rep1


title: KL2 treated with Combo RM-029 + RM-042 for 7 days, Rep 3

value: RM-029 + RM-042 Combo


title: sample_Onset_2_scMultiomics_GEX


title: KL2 treated with RM-042 for 7 days, Rep 3


title: RNA2, suvh456, rep2

value: suvh456 LDL2


title: VL RNA Control at baseline before Bedrest rep2


title: KL2 treated with Combo RM-029 + RM-4550 for 7 days, Rep 3

value: Lung


title: KL2 treated with RM-029 for 7 days, Rep 3


title: RNA2, WT, rep2

value: wild type


title: Day 9 of reprogrammed chondrocytes

city: Okayama

first: Ziyi

last: Wang

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Molecular Biology and Biochemistry

institute: Okayama University

description:
ChondroD09
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCh38.p13
Supplementary files format and content: A compressed file contains the tab-separated values of feature-barcode matrices and web summary HTML file resulting from the Cell Ranger software.

source_name: Human Knee Articular Chondrocytes

growth_protocol: Human normal articular chondrocytes were commercially available (Lonza, Basel, Switzerland). The chondrocytes in the original stock were collected via centrifugation and resuspended in the basal medium (Lonza) containing human recombinant fibroblast growth factor 2 (rhFGF-B: Lonza), R3-insulin-like growth factor-I (R3-IGF-1: Lonza), fetal bovine serum (FBS), gentamicin/amphotericin-B (GA), and insulin and transferrin (chondrocyte growth medium: CGMTM). Cells were plated, expanded in the monolayer culture at 37 °C in a 5% CO2 and detached for subcultures using 0.05% trypsin/0.02% EDTA (Biowest, Nuaillé, France).

extract_protocol:
Chondrocytes collected at each time course were labeled with a 10X Genomics 3’ CellPlex kit. After the cellular labeling, all cells were mixed, and cell sorting was performed on a FACSAria III Cell Sorter (BD Biosciences, San Diego, CA, USA) to remove dead cells and debris via forward scatter (FSC), side scatter (SSC), and 4',6-diamidino-2-phenylindole (DAPI)/Calcein-AM staining.
Cells were then processed with Chromium Next GEM Single Cell 3ʹ GEM kit v.3.1 (10X Genomics Inc., Pleasanton, CA, USA) according to the manufacturer’s instructions. Briefly, gel bead-in-emulsions (GEMs) were generated by loading gel beads, a master mix containing cell suspension, and partitioning oil onto a chip. Within each GEM, poly-A RNA from cell lysates was retrotranscripted into cDNA, incorporating an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and a 10x Barcode specific to each cell. After GEM generation, the emulsions were broken, and the barcoded cDNA was cleaned using Silane DynaBeads. Subsequently, cDNA is amplified by PCR, incorporating P5 and P7 sequences essential for Illumina sequencing, ensuring that each cDNA molecule contains both the necessary elements for sequencing (Illumina R2 sequence, P5, and P7) and a sample index for multiplexing. The appropriate-sized fragments are selected using SPRIselect reagent for final library construction. This meticulous process ensures each cDNA fragment is equipped for high-throughput sequencing, maintaining the integrity and specificity of the single-cell RNA profiling.

treatment_protocol: The chondrocytes were infected with SRV iPSC-3 recombinant virus, incubated for 2 hours at room temperature and further incubated in a CO2 incubator overnight at 37 °C. The following day, cells were collected and seeded on an iMatrix-511-coated (Takara Bio, Kusatsu, Japan) plate with a Stemfit Basic 02 medium (Ajinomoto, Tokyo, Japan). The medium was removed and replenished every 2 days until day 8. Thereafter, the medium was changed to the basal medium containing rhFGF-2, and cells were cultured until day 10.

value: Human Knee Articular Chondrocytes

value: NHAC-kn

value: Chondrocytes

tag: time point

value: Day 9 of reprogrammed chondrocytes


title: Day 10 of reprogrammed chondrocytes

description:
ChondroD10
10x Genomics

value: Day 10 of reprogrammed chondrocytes


title: Old_Delta_2

city: Paris

first: Vincent

last: Laville

address: 25-28 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Sequencing reads were mapped to the mouse genome version GenCode M23 (GRCm38.p6 release 93) using STAR v2.5.2b
Transcripts were quantified using RSEM software
The counts matrix was normalized using the vst function from DESeq2 v1.36.0
Assembly: GRCm38.p6
Supplementary files format and content: space delimited matrix of raw counts (genesx

extract_protocol:
RNA was isolated using the Single Cell RNA Purification Kit (#51800, NorgenBioTek Corp) per themanufacturer’sinstructions
For library construction,20 ng high-quality (RIN>7) total RNA was processed usingtheOvation Solo RNA-seq kit (#0501-96, NuGEN, Leek, The Netherlands) per themanufacturer’sinstructions.

value: Pancreatic islets

tag: strain

tag: age


title: Old_Alpha_3

source_name: CD24low CD71-

value: CD24low CD71-


title: Old_Beta_3

source_name: CD24low CD71+

value: CD24low CD71+


title: KL2 treated with Sotorasib for 7 days, Rep 3

tag: tissue


title: Old_Beta_2


title: Old_Delta_3


title: Day 7 of reprogrammed chondrocytes

description:
ChondroD07
10x Genomics

value: Day 7 of reprogrammed chondrocytes


title: RNA2, cxs ldl2, rep1

source_name: 2-week-old seedling

value: 2-week-old seedling

value: cmt23 ldl2 x suvh456 ldl2 F1


title: Day 8 of reprogrammed chondrocytes

description:
ChondroD08
10x Genomics

value: Day 8 of reprogrammed chondrocytes


title: RNA2, sxc ldl2, rep1

value: suvh456 ldl2 x cmt23 ldl2 F1


title: Old_Alpha_2


title: KL2 treated with Vehicle for 7 days, Rep 3

value: Vehicle


title: Day 6 of reprogrammed chondrocytes

description:
ChondroD06
10x Genomics

value: Day 6 of reprogrammed chondrocytes


title: RNA2, cxs, rep1

value: cmt23 LDL2 x suvh456 LDL2 F1


title: KL2 treated with Combo RM-029 + RM-042 for 7 days, Rep 4

value: Lung

value: RM-029 + RM-042 Combo


title: RNA2, suvh456 ldl2, rep2

value: suvh456 ldl2


title: RNA2, sxc, rep1

value: suvh456 LDL2 x cmt23 LDL2 F1


title: Day 5 of reprogrammed chondrocytes

description:
ChondroD05
10x Genomics

value: Human Knee Articular Chondrocytes

value: NHAC-kn

value: Chondrocytes

value: Day 5 of reprogrammed chondrocytes


title: Old_Delta_1

value: Pancreatic islets


title: VL RNA Control after 70d Bedrest rep1

value: Vastus Lateralis Skeletal Muscle

value: male


title: KL2 treated with RM-029 for 7 days, Rep 4


title: Old_Beta_1

value: CD24low CD71+


title: RNA2, cmt23 ldl2, rep1

value: 2-week-old seedling

value: cmt23 ldl2


title: KL2 treated with Combo RM-029 + RM-042 for 7 days, Rep 2


title: RNA2, cmt23, rep1

value: cmt23 LDL2


title: Day 2 of reprogrammed chondrocytes

description:
ChondroD02
10x Genomics

value: Day 2 of reprogrammed chondrocytes


title: Young_Delta_3


title: KL2 treated with RM-042 for 7 days, Rep 2


title: Day 1 of reprogrammed chondrocytes

description:
ChondroD01
10x Genomics

value: Day 1 of reprogrammed chondrocytes


title: Young_Alpha_3

value: CD24low CD71-


title: RNA2, suvh456, rep1

value: suvh456 LDL2


title: Day 0 of reprogrammed chondrocytes

description:
ChondroD00
10x Genomics

value: Day 0 of reprogrammed chondrocytes


title: KL2 treated with RM-029 for 7 days, Rep 2

value: Lung


title: KL2 treated with Combo RM-029 + RM-4550 for 7 days, Rep 2


title: Young_Beta_3


title: RNA2, WT, rep1

value: wild type


title: RNA2, suvh456 ldl2, rep1

value: suvh456 ldl2


title: Young_Delta_2


title: KL2 treated with Vehicle for 7 days, Rep 2

value: Vehicle


title: KL2 treated with Sotorasib for 7 days, Rep 2

value: Sotorasib


title: Young_Beta_2

value: Pancreatic islets


title: PXGL_shOGA_2_CUT&Tag

data_processing:
The raw sequencing data were filtered by fatsp (version 0.20.0) to obtain the clean reads and mapped to reference human genome (GRCh38.p13) using bowtie2 (version 2.3.4.3). Reads below 60-70bp were excluded from the quality control analysis, thus minimizing the influence of PCR-artifacts. In addition, we used E. coli carry-over DNA from pAG-Transposome as the spike-in to exclude non-specific amplification, and the proportion of detected ecoli data is used as a reference to normalize the data. Peaks were called using Sparse Enrichment Analysis for CUT&RUN (SEACR, version 1.3) and annotated using ChIPseeker (version 1.12.1).
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: NCBI_GRCh38
Supplementary files format and content: excel file include binding peak
Library strategy: CUT&Tag

extract_protocol:
The CUT &Tag assays were conducted with NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (for Illumina®) (NovoProtein, N259-YH01).
Libraries were generated according to the manufacturer’s instruction.

value: H9 hESC

value: Human embryonic stem cell

value: OGA knockdown


title: ChIP5, WT, H3K4me1, rep2

value: 2-week-old seedling

value: H3K4me1 ChIP


title: Day 3 of reprogrammed chondrocytes

description:
ChondroD03
10x Genomics

value: Human Knee Articular Chondrocytes

value: NHAC-kn

value: Chondrocytes

value: Day 3 of reprogrammed chondrocytes


title: PXGL_shOGA_1_CUT&Tag


title: KL2 treated with RM-042 for 7 days, Rep 4


title: Young_Alpha_2

value: CD24low CD71-


title: PXGL_ctrl_2_CUT&Tag

value: WT


title: KL2 treated with Vehicle for 7 days, Rep 4

value: Lung


title: Old_Alpha_1


title: ChIP5, cxs ldl2, H3K4me1, rep2

value: cmt23 ldl2 x suvh456 ldl2 F1


title: Young_Delta_1


title: PXGL_ctrl_1_CUT&Tag


title: KL2 treated with Combo RM-029 + RM-042 for 7 days, Rep 1

value: RM-029 + RM-042 Combo


title: Young_Beta_1

value: CD24low CD71+


title: ChIP5, sxc ldl2, H3K4me1, rep2

value: suvh456 ldl2 x cmt23 ldl2 F1


title: ChIP5, cxs, H3K4me1, rep2

value: cmt23 LDL2 x suvh456 LDL2 F1


title: ChIP5, sxc, H3K4me1, rep2

value: suvh456 LDL2 x cmt23 LDL2 F1


title: DKD1

city: St. Louis

first: Dian

last: Li

state: MO

address: 660 S. Euclid Ave., CB 8118

department: Nephrology / Medicine

institute: Washington University in St. Louis School of Medicine

description: Fresh frozen Spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed to generate FASTQ files using 10x Genomics Space Ranger pipeline version 2.0.1.
The generated FASTQ files were aligned to Genome Reference Consortium Human Build 38 (GRCh38) using 10x Genomics Space Ranger pipeline version 2.0.1.
Assembly: GRCh38 / hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features .tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count table in Matrix Market Exchange Format
Supplementary files format and content: DKD1_filtered_feature_bc_matrix.h5: gene expression count table with barcode and gene IDs in HDF5 format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: scalefactors_json.json: scale factors for alignment in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of the tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of the tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: Morph-based_v2.csv: Morphology-based annotation for each Visium spot
Supplementary files format and content: spots_selection - dkd_glom_v2_1.csv: Morphology-based subclustering of Glomeruli Visium spots
Supplementary files format and content: Tubules_CD-LH.csv: Morphology-based subclustering of Loop-of-Henle-Collecting-Duct (CD-LH) Visium spots
Library strategy: Spatial Transcriptome

source_name: CKD kidney with diabetic nephropathy

extract_protocol:
Fresh frozen tissues were FFPE embedded, and 10 um sections were cut using Leica microtome
Visium Human Transcriptome Probe Set v2.0 and Visium V4 Slide - FFPE v2 chemistry were used for library preparation
Spatial RNA libraries were generated using standard protocol from 10X Visium

value: CKD kidney with diabetic nephropathy


title: Huh7 cells treated with 5μM 25HC for 16h, rep2

city: Xi'an

first: Yamei

last: Dang

state: Shaanxi

address: No.169 Changle West Road, Xincheng District,

institute: Fourth Military Medical University

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence ,then mapped to mm8 whole genome using v0.12.2
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Data fitering steps prior to assembly,the low quality reads(1,reads containing sequencing adaptors;2, reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed, Cutadapt software(version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination
After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome. The mapped reads of each sample were assembled using StringTie with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: Huh7 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated and purified usingTRIzol reagent (Invitrogen, Carlsbad, CA, USA)following the manufacturer's procedure.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Huh7 cells treated with EtOH vehicle or 5μM 25HC for 4 or 16 hours.

value: Liver

value: Huh7 cells

value: Hepatocellular carcinoma cells

value: 5μM 25HC for 16h


title: Huh7 cells treated with 5μM 25HC for 16h, rep3


title: ChIP5, WT, H3K9me2, rep2

data_processing:
ChIP-seq reads were mapped on the TAIR10 genome using Bowtie ver 1.2.1.1. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.26. The bigwig files were created using deeptools software.
RNA-seq reads were mapped on the TAIR10 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- clip3pNbases, 50; -- quantMode GeneCounts parameters.
EM-seq reads were mapped on the TAIR10 genome using Bismark ver. 0.10.1 with -n 1 -l 20 -e 90 parameters. Deduplication and methylation extraction were also performed using Bismark. Counting methylated C was conducted using map function of BEDTools. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: TAIR10
Supplementary files format and content: bigwig file for ChIP-seq and EM-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

extract_protocol:
ChIP was performed as described in Zhao et al (2020) Nat. Commun. 11: 2658. Total RNA was extracted from whole plants using Rneasy Plant Mini Kit (Qiagen). Genome DNA was extracted using Nucleon PhytoPure (Cytiva).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). RNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). EM-seq libraries were constructed using the NEBNext Enzymatic Methyl-seq (EM-seq) Kit (NEB).

value: 2-week-old seedling

value: wild type

value: H3K9me2 ChIP


title: Adult_Delta_3

value: Pancreatic islets


title: ChIP5, cxs ldl2, H3K9me2, rep2


title: Young_Alpha_1

value: CD24low CD71-


title: Adult_Beta_3


title: Huh7 cells treated with 5μM 25HC for 4h, rep3

value: 5μM 25HC for 4h


title: KL2 treated with Sotorasib for 7 days, Rep 1

value: Lung

value: Sotorasib


title: KL2 treated with RM-042 for 7 days, Rep 1


title: ChIP5, sxc ldl2, H3K9me2, rep2


title: KL2 treated with RM-029 for 7 days, Rep 1


title: Adult_Alpha_3


title: Huh7 cells treated with 5μM 25HC for 4h, rep2


title: KL2 treated with Vehicle for 7 days, Rep 1

value: Vehicle


title: Adult_Delta_2


title: ChIP5, cxs, H3K9me2, rep2


title: ChIP5, sxc, H3K9me2, rep2


title: Huh7 cells treated with 5μM 25HC for 4h, rep1


title: Huh7 cells treated with EtOH vehicle, 4h, rep3

value: EtOH vehicle, 4h


title: ChIP5, WT, H3, rep2

value: H3 ChIP


title: Adult_Beta_2

value: CD24low CD71+


title: Mouse 1262 targeting-virus thalamus

city: Tübingen

first: Philipp

last: Reautschnig

address: Auf der Morgenstelle

country: Germany

institute: University of Tübingen

library_source: other

data_processing:
Raw FASTQ quality was assessed using FastQC (v0.11.8)
Reads were uniquely aligned to the mm10 reference genome using STAR (v2.7.3a)
The RNA Editing Index tool was used to assess the overall editing for all the CDS regions of the mouse genome.
REDItools was used to calculate the editing levels in the known editing sites from the REDIPortal.
Assembly: mm10
Supplementary files format and content: A2GEditingIndex.csv - The A2G editing levels in the CDS regions for every sample calculated with the RNA editing index tool.
Supplementary files format and content: REDITools_S9664Nr1.csv, REDITools_S9664Nr2.csv, REDITools_S9664Nr4.csv - REDITools results for the samples S9664Nr1, S9664Nr2, and S9664Nr4

molecule: other

source_name: thalamus

growth_protocol: All mice were housed under conventional laboratory housing and controlled humidity (target value 44%, minimum 24%, maximum 64%), temperature (target value 21 °C, minimum 18 °C, maximum 24 °C) and lighting (12/12-h light/dark period) and free access to food (regular mouse chow) and water.

extract_protocol:
Four weeks post injection, brains were dissected in 5 mM HEPES in HBSS and total RNA was isolated from individual brain regions using QIAzol reagent (Qiagen, #79306) and the Qiagen miRNeasy Kit reagent (Qiagen, #217004) according to the manufacturer’s instructions.
The library was prepared with the KAPA RNA HyperPrep Library Prep Kit with RiboErase (HMR) and KAPA Globin Depletion Hybridization Oligos (Roche).

treatment_protocol: P30 to P34 male mice were deeply anesthetized with 3% isofluorane (vol/vol) and placed on a prewarmed surface. For each animal, 100 μL volume containing 4E12 viral genomes was injected into the retro-orbital sinus. Following injections, mice were monitored for pain and distress while recovering on a heated pad prior to being returned to their home cage.

value: thalamus

value: Mecp2 G311A/y

value: targeting-virus


title: Mouse 1269 non-targeting-virus thalamus

description: This sample was not used for the final analysis due to the low RIN value

value: non-targeting-virus


title: KL2 treated with Combo RM-029 + RM-4550 for 7 days, Rep 1


title: Adult_Alpha_2


title: Huh7 cells treated with 5μM 25HC for 16h, rep1

value: Liver

value: Huh7 cells

value: Hepatocellular carcinoma cells

value: 5μM 25HC for 16h


title: Huh7 cells treated with EtOH vehicle, 4h, rep2


title: Mouse 1332 targeting-virus thalamus


title: ChIP5, cxs ldl2, H3, rep2

value: 2-week-old seedling

value: cmt23 ldl2 x suvh456 ldl2 F1


title: Adult_Delta_1

value: Pancreatic islets


title: ChIP5, sxc ldl2, H3, rep2

value: suvh456 ldl2 x cmt23 ldl2 F1


title: Mouse 1266 non-targeting-virus thalamus


title: Huh7 cells treated with EtOH vehicle, 4h, rep1


title: Adult_Beta_1


title: ChIPseq_53__Input_Hypo

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
RNA-seq: Preprocessing was performed using CETO Toolbox. Sequence quality was assessed using FastQC v 0.11.2, and quality trimming was done using Trimmomatic with parameters TRAILING:30 MINLEN:20. RNA-seq reads were aligned to the GRCh38 genome using STAR v.2.5.2 and only uniquely mapped reads with a two-mismatch threshold were considered for downstream analysis and quantified to the gene level using HTSeq . Output bam files were converted into bigwig track files to display coverage throughout the genome (in rpm).  Gene count tables were constructed following Ensembl GRCh38, release 78 annotation
ChIP-seq: Reads were trimmed using Cutadapt v4.1 with parameters --nextseq-trim=30 --minimum-length=20. D. melanogaster spiked-in samples were aligned using Bowtie2 v2.2.6 with parameters --sensitive --no-unal, while non-spiked-in data were aligned using Bowtie v1.1.2 with parameters -m 1 -v 2, to human GRCh38 genome assembly with Ensembl gene annotation GRCh38 release 78. Bigwig files were generated using an in-house R script utilizing bam2bw function, with a parameter to extend reads length -extLen=150 and scaled to reads-per-million (rpm).
Assembly: hg38
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: DLD1 cells were purchased from ATCC (cat# CCL-221), pIAA7 tagged BRD4 DLD1 cells expressing different BRD4 mutants were used from Zheng et.al, 2023 [53]. Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Millipore Sigma, cat# D6429) supplemented with 10% Fetal Bovine Serum (FBS) (Millipore Sigma, cat# F2442). Cells were grown in cell culture incubator at 37°C with 5% CO2 (Normoxia). For hypoxic cell culture, cells were grown at 37°C with 1% O2.

extract_protocol:
cell culture medium was aspirated, and cells were washed at least twice with ice cold PBS (ThermoFisher, cat# 14190250). Fixation was performed using 1% paraformaldehyde (PFA) (ThermoFisher, cat# 28908) while shaking for 10 min at room temperature (RT). Successively, PFA was quenched using 0.125M glycine (FisherScientific, Cat# BP381-5) for 5 min at RT. Cells were washed again with ice cold PBS followed by centrifugation at 500g for 5 min at 4°C. For RNAPII, PAF1, CDK9, and BRD4 ChIP-Seq, chromatin sonication was performed using 20% duty cycle, 140 peak intensity power, 200 cycles per burst for 5 min.
ChIP-seq libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes compatible with Illumina systems. DNA libraries were sequenced on an Illumina NovaSeq 6000 instrument as paired end 50b reads.

value: colon

value: colorectal carcinoma

value: WT

tag: agent

value: NT

value: Hypoxia


title: ChIP5, cxs, H3, rep2

value: cmt23 LDL2 x suvh456 LDL2 F1

value: H3 ChIP


title: Adult_Alpha_1

value: CD24low CD71-

tag: cell type


title: 19237x3 21487wt [scRNA-seq]

city: Salt Lake City

first: Allie

last: Grossmann

state: Utah

address: 2000 Circle of Hope

department: Pathology

institute: University of Utah

description: 10X Genomics

data_processing:
The Fastq files were aligned to the refdata-gex-mm10-2020-A mouse reference dataset from 10X genomics using cellranger count version 6.0.1
The filtered gene barcode matrices were loaded into the Seurat 4.1.1 package and normalized using the sctransform method.
Assembly: mm10
Supplementary files format and content: Filtered gene barcode matrices in H5 format

source_name: Melanoma Tumor

extract_protocol: 10X Genomics Next GEM Single Cell 3' Gene Expression Library prep v3.1 with UDI

value: Melanoma Tumor

value: cd45+ Tumor cells


title: ChIPseq_52__Input_Norm

value: Normoxia


title: 19255x1 21483wt [scRNA-seq]

description: 10X Genomics


title: omental_treg_ST2_POS_Conv_3

city: Birmingham

first: Selene

last: Meza-Perez

address: 1825 Unuversity blvd

institute: UAB

data_processing:
FASTQ reads were first processed by Trim Galore! (version 0.44) to trim adapter and low-quality reads.
Trimmed reads were mapped to the mm10 mouse genome using TopHat2 (version 2.1.1) with the default parameters.
Samtools (version 1.9) was used to sort the resulting BAM files and generate SAM files, which were then processed by htseq-count of HTSeq (version 0.6.1) with the parameter “-s no” to create gene counts.
The count matrix was analyzed using the R package DESeq2 (version 1.20.0).
Assembly: mm10
Supplementary files format and content: read counts generated using htseq-count for each Sample

source_name: omental treg ST2 POS

growth_protocol: EG7.1.15 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) (Peak serum), 50 mM 2-Mercaptoethanol (Gibco), 0.024 mM NaHCO3 (Cellgro), 600 mg/mL G418 (Gibco), 10 mg/mL kanamycin (Gibco), 200 μg/mL penicillin (Corning) and streptomycin (Corning).

extract_protocol:
Total RNA was purified using the Quick-RNA MicroPrep kit (Zymo Research) and used as input for the SMART-seq v4 cDNA synthesis kit (Takara).
200 pg of cDNA was used as input for the NexteraXT kit (Illumina) for tagmentation, PCR amplification and indexing. Final libraries were quantitated by Qubit and pooled at equimolar ratio.

treatment_protocol: At 8-12 weeks of age, Conventional non-arginine treated (Conv) or Arginine treated (Arg) mice were intraperitoneally (i.p) injected with 3 × 10^6 EG7.1.15 cells.

tag: group

value: Arg untreated

value: omental treg ST2 POS

value: tumor-bearing

tag: tumor stage

tag: sorting markers

value: Live/Dead- CD45.2+ CD4+ CD25+ FoxP3(GFP)+ST2+

tag: Sex

value: female


title: ChIP5, WT, H3K4me1, rep1

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

institute: Graduate School of Science, The University of Tokyo

value: 2-week-old seedling

tag: genotype

value: wild type

tag: chip antibody

value: H3K4me1 ChIP


title: ChIPseq_51__Pol2_BRD4_C_iPAF1_Norm

value: colon

tag: cell line

value: colorectal carcinoma


title: 19237x2 21485wt [scRNA-seq]

description: 10X Genomics


title: omental_treg_ST2_POS_Conv_2

tag: treatment


title: ChIPseq_50__Pol2_BRD4_IAA7_iPAF1_Norm


title: ChIP5, cxs ldl2, H3K4me1, rep1

value: cmt23 ldl2 x suvh456 ldl2 F1


title: ChIPseq_49__Pol2_HS_Input

value: WT

value: NT


title: omental_treg_ST2_POS_Conv_1


title: ChIP5, sxc ldl2, H3K4me1, rep1

value: suvh456 ldl2 x cmt23 ldl2 F1


title: 19203x3 21469Arf6null [scRNA-seq]

description: 10X Genomics

value: Melanoma Tumor

value: BrafCA;Cdkn2af/f; Arf6f/f


title: ChIPseq_48__Pol2_Norm_Input

value: Normoxia


title: 19237x1 21463Arf6null [scRNA-seq]

description: 10X Genomics

value: cd45+ Tumor cells


title: omental_treg_ST2_POS_Arg_3

value: Arg treated

value: omental treg ST2 POS


title: ChIP5, cxs, H3K4me1, rep1

value: cmt23 LDL2 x suvh456 LDL2 F1


title: omental_treg_ST2_POS_Arg_2

value: tumor-bearing

value: Live/Dead- CD45.2+ CD4+ CD25+ FoxP3(GFP)+ST2+

value: female


title: 17983x24 20570Arf6null

data_processing:
The mouse GRCm38 genome and gene annotation files were downloaded from Ensembl release 100
Trimmed reads were aligned to the reference database using STAR 2.7.3a in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0
Assembly: mm10
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited matrix

extract_protocol:
Direct-zol RNA Miniprep Plus Kit (Zymogenetics)
llumina TruSeq Stranded mRNA Library Prep with UDI


title: ChIPseq_47__Pol2_KL2_HS_2h


title: ChIP5, sxc, H3K4me1, rep1

value: 2-week-old seedling

value: suvh456 LDL2 x cmt23 LDL2 F1

value: H3K4me1 ChIP


title: ChIPseq_46__Pol2_NT_HS_2h

value: colon

value: colorectal carcinoma


title: omental_treg_ST2_POS_Arg_1


title: 17983x23 20001Arf6null


title: ChIP5, sxc, H3, rep2

value: H3 ChIP


title: ChIPseq_45__Pol2_BRD4_C_iPAF1_Hypoxia

value: Hypoxia


title: 17983x22 19959Arf6null

value: Melanoma Tumor


title: ChIPseq_44__Pol2_BRD4_C_DMSO_Norm

value: Dox,Aux


title: omental_treg_ST2_Neg_Conv_2

source_name: omental treg ST2 Neg

value: Arg untreated

value: omental treg ST2 Neg

value: Live/Dead- CD45.2+ CD4+ CD25+ FoxP3(GFP)+ST2-


title: 17983x21 19846Arf6null


title: ChIP5, cxs ldl2, H3K9me2, rep1

value: cmt23 ldl2 x suvh456 ldl2 F1

value: H3K9me2 ChIP


title: omental_treg_ST2_Neg_Conv_1

value: tumor-bearing


title: ChIP5, sxc ldl2, H3K9me2, rep1

value: suvh456 ldl2 x cmt23 ldl2 F1


title: ChIPseq_43__Pol2_BRD4_IAA7_iPAF1_Hypoxia


title: ChIP5, cxs, H3K9me2, rep1

value: cmt23 LDL2 x suvh456 LDL2 F1


title: 17983x20 19837Arf6null


title: ChIPseq_41__PAF1_BRD4_C_DMSO_Hypoxia


title: omental_treg_ST2_Neg_Arg_2

value: Arg treated

value: female


title: 17983x19 19836Arf6null


title: ChIP5, sxc, H3K9me2, rep1

value: 2-week-old seedling

value: suvh456 LDL2 x cmt23 LDL2 F1


title: 19203x1 21467Arf6null [scRNA-seq]

description: 10X Genomics

value: cd45+ Tumor cells

value: BrafCA;Cdkn2af/f; Arf6f/f


title: ChIP5, WT, H3, rep1

value: wild type

value: H3 ChIP


title: ChIPseq_42__PAF1_BRD4_C_iPAF1_Hypoxia

value: colon

value: colorectal carcinoma

value: Hypoxia


title: 17983x6 5588wt

value: Melanoma Tumor


title: ChIPseq_40__PAF1_BRD4_C_DMSO_Norm

value: Dox,Aux

value: Normoxia


title: ChIP5, WT, H3K9me2, rep1

value: H3K9me2 ChIP


title: omental_treg_ST2_Neg_Arg_1

value: omental treg ST2 Neg

value: tumor-bearing

value: Live/Dead- CD45.2+ CD4+ CD25+ FoxP3(GFP)+ST2-


title: omental_treg_ST2_Neg_Arg_3

value: Arg treated

value: female


title: ChIPseq_39__PAF1_BRD4_IAA7_iPAF1_Hypoxia


title: omental_treg_ST2_Neg_Conv_3

value: Arg untreated


title: KO_7.6_PGE2_6h_3

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

data_processing:
Alignment with STAR
Followed by RSEM
Downstream analysis with custom R and Python script
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample in csv file format

source_name: Bone Marrow Derived Denderitic Cell

growth_protocol: BMDCs were differentiated from bone marrow in DMEM (10% heat-inactivated FBS, GlutaMAX, 1% penicillin-streptomycin) containing 20ng/mL rmGM-CSF (Peprotech) for 7 days, supplemented with additional DMEM + rmGM-CSF on Day 3. Cells were then scraped and seeded at 1e5 cells per well in a 96-well microplate and allowed to adhere overnight.

extract_protocol:
Centrifuge plates at 100xg for 3 mins, remove supernatant. Wash 1X with 100uL PBS, aspirate. Add 100uL lysis buffer, pipet up and down and freeze at -80C.
Libraries were constructed using a modified SmartSeq2 protocol.RNA lysate were purified with Dynabeads mRNA Direct Purification kit (Life Technologies),followed by reverse transcription with Maxima Reverse Transcriptase (Life Technologies) and whole transcription amplification (WTA) with KAPA HotStart HiFi 2x ReadyMix (Kapa Biosystems).WTA products were purified with Ampure XP beads (Beckman Coulter). RNA-Seq libraries were constructed using Nextera XT DNA Library Preparation kit (Illumina).
Libraries were sequenced with Nextseq500(75cycles) paired-end and the following parameters : paired End: Index1 8, Index2 8, Read1 38, Read2 38

treatment_protocol: For stimulation, media was removed and replaced with 80uL DMEM (10% heat-inactivated FBS, GlutaMAX, 1% penicillin-streptomycin), no rmGM-CSF, adjusted to pH 6.6, 7.2, or 7.6. Each well then received 10uL of media w/ zymosan and 10uL of  DMSO/PGE2/BRD5075. Final concentrations: 5uM PGE2, 20uM BRD5075, 5ug/mL Zymosan, 0.25% DMSO. Stimulated for either 2 or 6 hours at 37C, 5% CO2.

value: Bone Marrow Derived Denderitic Cell

value: GPR65 KO Homozygous

value: 6.5 weeks

value: KO

value: Stimulated for 6 hours at pH 7.6 using PGE2


title: 17983x4 7657wt


title: ChIP5, sxc ldl2, H3, rep1

value: 2-week-old seedling

value: suvh456 ldl2 x cmt23 ldl2 F1

value: H3 ChIP


title: 17983x3 5548wt

value: Melanoma Tumor


title: KO_7.6_PGE2_6h_2


title: ChIPseq_38__PAF1_BRD4_IAA7_DMSO_Auxin_Hypoxia

value: colon

value: colorectal carcinoma

value: Auxin

value: Hypoxia


title: ChIP5, cxs, H3, rep1

value: cmt23 LDL2 x suvh456 LDL2 F1


title: ChIPseq_37__PAF1_BRD4_IAA7_DMSO_Hypoxia

value: DMSO


title: KO_7.6_PGE2_6h_1


title: ChIP5, cxs ldl2, H3, rep1

value: cmt23 ldl2 x suvh456 ldl2 F1


title: 17983x5 20681wt


title: ChIPseq_36__Input_PAF1_Hypo

value: NT


title: 17983x2 5527wt


title: ChIP5, sxc, H3, rep1

value: suvh456 LDL2 x cmt23 LDL2 F1


title: KO_7.6_DMSO_6h_3

value: Bone Marrow Derived Denderitic Cell

value: GPR65 KO Homozygous

value: Stimulated for 6 hours at pH 7.6 using DMSO


title: KO_7.6_DMSO_6h_2

value: 6.5 weeks

value: KO


title: 17983x1 5526wt


title: ChIPseq_35__Input_PAF1_Nor

value: Normoxia


title: ChIPseq_34_PAF1_BRD4_IAA7_DMSO_Norm


title: EM1, cxs, rep2

data_processing:
ChIP-seq reads were mapped on the TAIR10 genome using Bowtie ver 1.2.1.1. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.26. The bigwig files were created using deeptools software.
RNA-seq reads were mapped on the TAIR10 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- clip3pNbases, 50; -- quantMode GeneCounts parameters.
EM-seq reads were mapped on the TAIR10 genome using Bismark ver. 0.10.1 with -n 1 -l 20 -e 90 parameters. Deduplication and methylation extraction were also performed using Bismark. Counting methylated C was conducted using map function of BEDTools. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: TAIR10
Supplementary files format and content: bigwig file for ChIP-seq and EM-seq
Supplementary files format and content: tab-delimited text file for RNA-seq
Library strategy: EM-seq

value: 2-week-old seedling

value: Enzymatic DNA methylation


title: KO_7.6_DMSO_6h_1


title: KO_7.2_BRD5075_6h_3

value: Stimulated for 6 hours at pH 7.2 using BRD5075


title: EM1, sxc ldl2, rep2

value: suvh456 ldl2 x cmt23 ldl2 F1


title: EM1, sxc, rep2


title: ChIPseq_32__PAF1_BRD4_dCTM_Hypoxia

value: colon

value: colorectal carcinoma

value: Dox,Aux


title: ChIPseq_33__PAF1_BRD4_C_Hypoxia

value: Hypoxia


title: EM1, cmt23 ldl2, rep2

value: cmt23 ldl2


title: KO_7.2_BRD5075_6h_2


title: KO_7.2_BRD5075_6h_1


title: EM1, cmt23, rep2

value: cmt23 LDL2


title: EM1, cxs ldl2, rep2

value: cmt23 ldl2 x suvh456 ldl2 F1


title: 06-mo CD45- thymic stoma cells - Foxn1LacZ mutant - rep2 [singe cell]

city: Duarte

first: Anastasia

middle: I

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.01).
Assembly: GRCm38.p5 (mm10)
Supplementary files format and content: Foxn1LacZ_annotated.h5ad: H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format
Supplementary files format and content: metrics_summary.csv: metrics for quality assessment in CSV format
Supplementary files format and content: molecule_info.h5: contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or Feature Barcode; this file is a required input to run cellranger aggr

source_name: thymus

extract_protocol:
All steps were performed at 4 C unless indicated. 10-15 thymi of 6-month-old female C57BL/6 mice were excised and enzymatically digested. Briefly, thymi were mechanically dissociated into ca. 2 mm pieces. Tissue pieces were incubated with a digestion buffer (RPMI, 10% FCS, 62.5 um/mL liberase TM, 0.4 mg/ml DNase I) twice for 30 min at 37 C. Between incubation steps, supernatant containing dissociated cells was transferred to 50 mL conical tubes equipped with 100 um filter. Cells were pelleted by centrifugation at 400g for 5 min. Cell pellets were incubated with anti-mouse CD45 microbeads and CD45-positive cells were depleted from cell suspension using magnetic-associated cell sorting (MACS) on LS columns according to manufacturer’s protocol. Following red blood cell lysis using ACK buffer, the CD45-depleted cell fraction was incubated with an antibody cocktail for 15 min at 4 C and cells of interest were purified by fluorescent-associated cell sorting (FACS) on a BD Biosciences Aria II using a 100 um nozzle. Cells were sorted into tubes containing RPMI supplemented with 2% BSA. FACS-purified cells were spun down at 400g for 5 min and resuspended in PBS supplemented with 0.04 % BSA for generation of single-cell suspensions.
The single-cell RNA-seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual (CG00052 Rev E) and using Single Cell 3’ Reagent Kit (v2). The viability of cells prior to loading onto the encapsulation chip was 73-98%, as confirmed with 0.2% (w/v) Trypan Blue stain. Each sample, containing approximately 8000 cells, was encapsulated in microfluidic droplets at a final dilution of 66–70 cells/µl (a multiplet rate ~3.9%). Following reverse transcription step the emulsion droplets were broken, barcoded-cDNA purified with DynaBeads and amplified by 12-cycles of PCR: 98 ̊C for 180 s, 12x (98 ̊C for 15 s, 67 ̊ C for 20 s, 72 ̊C for 60 s), and 72 ̊C for 60 s. The 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit, purified with SPRI beads and resulting DNA library was ligated to the sequencing adapter followed by indexing PCR: 98 ̊C for 45 s; 12x 98 ̊C for 20 s, 54 ̊C for 30 s, 72 ̊C for 20 s), and 72 ̊C for 60 s. The final DNA library was double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina Nova-Seq platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) at depth of 200-270 million reads per sample.

value: thymus

value: CD45- thymic stroma cells

value: homozygous LacZ

value: 06-month old

value: untreated

value: male


title: ChIPseq_30__PAF1_BRD4_FL_Hypoxia


title: ChIPseq_31__PAF1_BRD4_dBD_Hypoxia


title: KO_7.2_DMSO_6h_2

city: Cambridge

value: Bone Marrow Derived Denderitic Cell

value: GPR65 KO Homozygous

value: 6.5 weeks

value: KO

value: Stimulated for 6 hours at pH 7.2 using DMSO


title: 06-mo CD45- thymic stoma cells - Foxn1LacZ mutant - rep1 [singe cell]


title: EM1, suvh456 ldl2, rep2

value: 2-week-old seedling

value: suvh456 ldl2

value: Enzymatic DNA methylation


title: KO_7.2_DMSO_6h_1


title: EM1, suvh456, rep2

value: suvh456 LDL2


title: ChIPseq_29__PAF1_BRD4_IAA7_auxin_Hypoxia

value: colon

value: colorectal carcinoma

value: Auxin

value: Hypoxia


title: EM1, WT, rep2

value: wild type


title: ChIPseq_28__PAF1_BRD4_IAA7_NT_Hypoxia

value: NT


title: 06-mo CD45- thymic stoma cells - Foxn1LacZ mock - rep1 [singe cell]

value: thymus

value: CD45- thymic stroma cells

value: 06-month old

value: untreated


title: KO_6.6_DMSO_6h_3

value: Bone Marrow Derived Denderitic Cell

value: GPR65 KO Homozygous

value: 6.5 weeks

value: Stimulated for 6 hours at pH 6.6 using DMSO


title: EM1, cxs ldl2, rep1

value: 2-week-old seedling

value: cmt23 ldl2 x suvh456 ldl2 F1


title: ChIPseq_27__PAF1_BRD4_IAA7_NT_Norm

value: Normoxia


title: KO_6.6_DMSO_6h_2

value: KO


title: ChIPseq_26__Input_CDK9

value: colon

value: colorectal carcinoma


title: EM1, sxc ldl2, rep1

value: suvh456 ldl2 x cmt23 ldl2 F1

value: Enzymatic DNA methylation


title: ChIPseq_25__Input_BRD4

value: NT


title: Transitional AT2 -1

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

institute: University of Pennsylvania

description: Transition Cell Day 4_2

data_processing:
Fastq files from paired end reads were trimmed, processed and evaluated for quality control using fastp. Resulting files were aligned against the mouse genome (mm10) using bowtie2 and quantified via featureCounts. Duplicate reads and chimeric fragments were flagged and excluded from the analysis.
Assembly: mm10
Supplementary files format and content: tab seperated file

extract_protocol:
Lungs were harvested from control and 4 day infected mice, single cells suspension was prepared by mehcanical and enzymatic digetsion.  CD45+ and CD31+ cells were depleted using biotinylated antibodies followed by surface staining with antibody mix to identify At2 and transitional At2 cells. At2 cells were identified as CD45-CD31-Epcam+CD104-MHCII hiCD51- and transitional At2 cells  CD45-CD31-Epcam+CD104-MHCII hiCD51+. Dead cells were excluded by Dapi staining.
Libraries were prepared using Illumina stranded total RNA with Ribo-zero Plus kit accordine to manufacture instructions

value: Lung

value: A/J

value: Transitional AT2 Cell

value: Infected


title: KO_6.6_DMSO_6h_1

value: Bone Marrow Derived Denderitic Cell


title: KO_7.2_DMSO_6h_3

value: GPR65 KO Homozygous

value: Stimulated for 6 hours at pH 7.2 using DMSO


title: Infected AT2 -4

description: AT2_Day 4_4

value: alveolar type 2 (AT2) cells


title: 06-mo CD45- thymic stoma cells - Foxn1LacZ mock - rep2 [singe cell]

value: thymus

value: CD45- thymic stroma cells

value: wild type

value: 06-month old

value: untreated

value: male


title: I231L_7.6_PGE2_6h_3

value: GPR65 I231L Homozygous

value: 6.5 weeks

value: Stimulated for 6 hours at pH 7.6 using PGE2


title: ChIPseq_23__CDK9_BRD4_IAA7_auxin_Hypoxia

value: colon

value: colorectal carcinoma

value: Auxin

value: Hypoxia


title: I231L_7.6_PGE2_6h_2

value: Bone Marrow Derived Denderitic Cell


title: Infected AT2 -3

description: AT2_Day 4_3

value: Lung

value: A/J

value: Infected


title: I231L_7.6_PGE2_6h_1


title: ChIPseq_22__CDK9_BRD4_IAA7_NT_Hypoxia

value: NT


title: EM1, sxc, rep1

value: 2-week-old seedling

value: suvh456 LDL2 x cmt23 LDL2 F1

value: Enzymatic DNA methylation


title: Transitional AT2 -3

description: Transition Cell Day 4_4

value: Transitional AT2 Cell


title: EM1, cmt23, rep1

value: cmt23 LDL2


title: Infected AT2 -2

description: AT2_Day 4_2

value: alveolar type 2 (AT2) cells


title: Infected AT2 -1

description: AT2_Day 4_1


title: I231L_7.6_DMSO_6h_3

value: GPR65 I231L Homozygous

value: 6.5 weeks

value: Stimulated for 6 hours at pH 7.6 using DMSO


title: Transitional AT2 -2

description: Transition Cell Day 4_3


title: I231L_7.6_DMSO_6h_2


title: WT AT2 - 3

value: Vehicle


title: EM1, suvh456 ldl2, rep1

value: suvh456 ldl2


title: ChIPseq_20__CyclinT_BRD4_IAA7_auxin_Hypoxia

value: colon

value: colorectal carcinoma

value: Auxin

value: Hypoxia

value: CyclinT


title: ChIPseq_21__CDK9_BRD4_IAA7_NT_Norm

value: NT

value: Normoxia


title: WT AT2 - 2

value: Lung

value: A/J


title: EM1, suvh456, rep1

value: 2-week-old seedling

value: suvh456 LDL2

value: Enzymatic DNA methylation


title: EM1, cxs, rep1

value: cmt23 LDL2 x suvh456 LDL2 F1


title: WT AT2 - 1

value: alveolar type 2 (AT2) cells


title: ChIPseq_19__CyclinT_BRD4_IAA7_Hypoxia


title: EM1, WT, rep1

value: wild type


title: I231L_7.2_BRD5075_6h_3

value: Bone Marrow Derived Denderitic Cell

value: GPR65 I231L Homozygous

value: 6.5 weeks

value: Stimulated for 6 hours at pH 7.2 using BRD5075


title: ChIPseq_24__BRD4_BRD4_C_Hypoxia

value: colon

value: colorectal carcinoma

value: Dox,Aux


title: ChIPseq_18__CyclinT_BRD4_IAA7_Norm

value: NT

value: CyclinT


title: ChIP4, FLAG-ASHH3 in ibm1, FLAG, rep2

value: FLAG-ASHH3 in ibm1

value: FLAG ChIP


title: ChIP4, FLAG-ASHH3 in WT, FLAG, rep2

value: 2-week-old seedling

value: FLAG-ASHH3 in WT


title: EM1, cmt23 ldl2, rep1

value: cmt23 ldl2

value: Enzymatic DNA methylation


title: I231L_7.2_BRD5075_6h_2


title: ChIPseq_17__Pol2_BRD4_C_DMSO_Hypoxia

value: Dox,Aux,DMSO

value: Hypoxia


title: 02-mo CD45- thymic stoma cells - day 7 after SL-TBI rep2 [bulk]

description: Sanger / Illumina 1.9

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (version 0.38, default parameters).
Trimmed reads were then mapped to GRCm38.p5 whole genome using STAR (version 2.7.0e) with default parameters for paired end reads.
featureCounts (version 1.6.3) was used to quantify the gene counts with default options for paired-end reads.
Assembly: GRCm38.p5 (mm10)
Supplementary files format and content: bulk_CD45neg_samples.txt: tab-delimited text file includes raw counts for each sample

extract_protocol: Bulk RNA-seq profiles of CD45- thymic cells from 2-month-old at steady state (PBS) and at days 1, 4 and 7 after sublethal total body irradiation (SL-TBI).

value: thymus

value: CD45- thymic stroma cells

value: wild type

value: 02-month old

value: day 7 after SL-TBI


title: ChIP4, WT, FLAG, rep2


title: I231L_7.2_BRD5075_6h_1

value: Bone Marrow Derived Denderitic Cell

value: GPR65 I231L Homozygous

value: 6.5 weeks

value: Stimulated for 6 hours at pH 7.2 using BRD5075


title: ChIPseq_16__Pol2_BRD4_IAA7_DMSO_Auxin_Hypoxia

value: colon

value: colorectal carcinoma

value: DMSO


title: 02-mo CD45- thymic stoma cells - day 7 after SL-TBI rep1 [bulk]

description: Sanger / Illumina 1.9


title: ChIPseq_15__Pol2_BRD4_IAA7_DMSO_Hypoxia


title: I231L_7.2_DMSO_6h_3

value: Stimulated for 6 hours at pH 7.2 using DMSO


title: I231L_7.6_DMSO_6h_1

value: Stimulated for 6 hours at pH 7.6 using DMSO


title: I231L_7.2_DMSO_6h_2


title: 02-mo CD45- thymic stoma cells - day 4 after SL-TBI rep3 [bulk]

description: Sanger / Illumina 1.9

value: day 4 after SL-TBI


title: ChIP4, FLAG-ASHH3 in WT, FLAG, rep1

value: 2-week-old seedling

value: FLAG-ASHH3 in WT

value: FLAG ChIP


title: ChIPseq_13__Input_ser2Pol2

value: NT

value: Hypoxia


title: ChIP4, WT, FLAG, rep1

value: wild type


title: 02-mo CD45- thymic stoma cells - day 4 after SL-TBI rep1 [bulk]

description: Sanger / Illumina 1.9

value: thymus

value: CD45- thymic stroma cells

value: 02-month old


title: 02-mo CD45- thymic stoma cells - day 7 after SL-TBI rep3 [bulk]

description: Sanger / Illumina 1.9

value: day 7 after SL-TBI


title: I231L_6.6_DMSO_6h_3

value: Bone Marrow Derived Denderitic Cell

value: GPR65 I231L Homozygous

value: 6.5 weeks

value: Stimulated for 6 hours at pH 6.6 using DMSO


title: RNA1, ibm1 ashh3, rep3

value: ibm1 ashh3


title: 02-mo CD45- thymic stoma cells - day 1 after SL-TBI rep3 [bulk]

description: Sanger / Illumina 1.9

value: day 1 after SL-TBI


title: ChIPseq_12__ser2Pol2_BRD4_IAA7_auxin_Hypoxia

value: colon

value: colorectal carcinoma

value: Auxin


title: ChIPseq_11__ser2Pol2_BRD4_IAA7_NT_Hypoxia


title: I231L_6.6_DMSO_6h_2


title: RNA1, ibm1, rep3

value: 2-week-old seedling


title: I231L_6.6_DMSO_6h_1


title: ChIP4, FLAG-ASHH3 in ibm1, FLAG, rep1

value: FLAG-ASHH3 in ibm1

value: FLAG ChIP


title: 02-mo CD45- thymic stoma cells - day 1 after SL-TBI rep2 [bulk]

description: Sanger / Illumina 1.9

value: wild type


title: WT_7.6_PGE2_6h_3

value: GPR65 WT Homozygous

value: WT

value: Stimulated for 6 hours at pH 7.6 using PGE2


title: ChIPseq_10__ser2Pol2_BRD3_AID_auxin_Hypoxia

value: Hypoxia


title: 02-mo CD45- thymic stoma cells - steady state rep4 [bulk]

description: Sanger / Illumina 1.9

value: thymus

value: CD45- thymic stroma cells

value: 02-month old

value: untreated


title: RNA1, ashh3, rep3


title: RNA1, WT, rep3


title: ChIPseq_09__ser2Pol2_BRD3_AID_NT_Hypoxia

value: NT


title: I231L_7.2_DMSO_6h_1

value: Bone Marrow Derived Denderitic Cell

value: GPR65 I231L Homozygous

value: 6.5 weeks

value: Stimulated for 6 hours at pH 7.2 using DMSO


title: ChIPseq_08__ser2Pol2_BRD2_AID_auxin_Hypoxia

value: colon

value: colorectal carcinoma

value: Auxin


title: 02-mo CD45- thymic stoma cells - day 4 after SL-TBI rep2 [bulk]

description: Sanger / Illumina 1.9

value: wild type

value: day 4 after SL-TBI


title: WT_7.6_PGE2_6h_1

value: GPR65 WT Homozygous

value: WT


title: ChIPseq_07__ser2Pol2_BRD2_AID_NT_Hypoxia

value: Hypoxia


title: RNA1, ibm1, rep2

value: 2-week-old seedling


title: 02-mo CD45- thymic stoma cells - day 1 after SL-TBI rep1 [bulk]

description: Sanger / Illumina 1.9

value: thymus

value: CD45- thymic stroma cells

value: day 1 after SL-TBI


title: 02-mo CD45- thymic stoma cells - steady state rep2 [bulk]

description: Sanger / Illumina 1.9

value: 02-month old

value: untreated


title: RNA1, ibm1 ashh3, rep2

value: ibm1 ashh3


title: WT_7.6_DMSO_6h_3

value: Bone Marrow Derived Denderitic Cell

value: 6.5 weeks

value: Stimulated for 6 hours at pH 7.6 using DMSO


title: 02-mo CD45- thymic stoma cells - steady state rep3 [bulk]

description: Sanger / Illumina 1.9


title: ChIPseq_14__Pol2_BRD4_IAA7_DMSO_Norm

value: colon

value: colorectal carcinoma

value: DMSO

value: Normoxia


title: 02-mo CD45- thymic stoma cells - steady state rep1 [bulk]

description: Sanger / Illumina 1.9

value: wild type


title: RNA1, ashh3, rep2


title: RNA1, WT, rep2


title: ChIPseq_06__Pol2_KL2_Hypoxia_6h

value: WT


title: WT_7.6_DMSO_6h_2

value: GPR65 WT Homozygous


title: WT_7.6_DMSO_6h_1


title: 18-mo CD45- thymic fibroblasts - day 7 after SL-TBI [singe cell]

description: Chromium - Single Cell 3’ Reagent Kit (v2)

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.01).
Assembly: GRCm38.p5 (mm10)
Supplementary files format and content: CD45neg_thymic_stroma_all+annotation.h5ad: H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format
Supplementary files format and content: metrics_summary.csv: metrics for quality assessment in CSV format
Supplementary files format and content: molecule_info.h5: contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or Feature Barcode; this file is a required input to run cellranger aggr

extract_protocol:
All steps were performed at 4 C unless indicated. 10-15 thymi of 2-month-old or 18-month-old female C57BL/6 mice were excised and enzymatically digested. Briefly, thymi were mechanically dissociated into ca. 2 mm pieces. Tissue pieces were incubated with a digestion buffer (RPMI, 10% FCS, 62.5 um/mL liberase TM, 0.4 mg/ml DNase I) twice for 30 min at 37 C. Between incubation steps, supernatant containing dissociated cells was transferred to 50 mL conical tubes equipped with 100 um filter. Cells were pelleted by centrifugation at 400g for 5 min. Cell pellets were incubated with anti-mouse CD45 microbeads and CD45-positive cells were depleted from cell suspension using magnetic-associated cell sorting (MACS) on LS columns according to manufacturer’s protocol. Following red blood cell lysis using ACK buffer, the CD45-depleted cell fraction was incubated with an antibody cocktail for 15 min at 4 C and cells of interest were purified by fluorescent-associated cell sorting (FACS) on a BD Biosciences Aria II using a 100 um nozzle. Cells were sorted into tubes containing RPMI supplemented with 2% BSA. FACS-purified cells were spun down at 400g for 5 min and resuspended in PBS supplemented with 0.04 % BSA for generation of single-cell suspensions.
The single-cell RNA-seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual (CG00052 Rev E) and using Single Cell 3’ Reagent Kit (v2). The viability of cells prior to loading onto the encapsulation chip was 73-98%, as confirmed with 0.2% (w/v) Trypan Blue stain. Each sample, containing approximately 8000 cells, was encapsulated in microfluidic droplets at a final dilution of 66–70 cells/µl (a multiplet rate ~3.9%). Following reverse transcription step the emulsion droplets were broken, barcoded-cDNA purified with DynaBeads and amplified by 12-cycles of PCR: 98 ̊C for 180 s, 12x (98 ̊C for 15 s, 67 ̊ C for 20 s, 72 ̊C for 60 s), and 72 ̊C for 60 s. The 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit, purified with SPRI beads and resulting DNA library was ligated to the sequencing adapter followed by indexing PCR: 98 ̊C for 45 s; 12x 98 ̊C for 20 s, 54 ̊C for 30 s, 72 ̊C for 20 s), and 72 ̊C for 60 s. The final DNA library was double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina Nova-Seq platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) at depth of 200-270 million reads per sample.

value: CD45-PDGFRA+ thymic stroma cells

value: 18-month old

value: day 7 after SL-TBI


title: ChIPseq_04__Pol2_dBET_Hypoxia_6h

value: Hypoxia


title: RNA1, ibm1 ashh3, rep1

value: 2-week-old seedling


title: WT_7.6_PGE2_6h_2

value: Stimulated for 6 hours at pH 7.6 using PGE2


title: ChIPseq_03__Pol2_dBET_Norm


title: WT_7.2_BRD5075_6h_2

value: Stimulated for 6 hours at pH 7.2 using BRD5075


title: WT_7.2_BRD5075_6h_3

value: Bone Marrow Derived Denderitic Cell


title: 18-mo CD45- thymic endothelial cells - day 7 after SL-TBI [singe cell]

value: thymus

value: CD45-PECAM1+ thymic stroma cells


title: ChIPseq_02__Pol2_NT_Hypoxia_6h

value: colon

value: NT


title: ChIPseq_01__Pol2_NT_Norm

value: colorectal carcinoma


title: RNA1, WT, rep1


title: RNA1, ashh3, rep1


title: WT_7.2_BRD5075_6h_1

value: 6.5 weeks


title: 18-mo CD45- thymic fibroblasts - day 4 after SL-TBI [singe cell]

value: wild type

value: day 4 after SL-TBI


title: 18-mo CD45- thymic endothelial cells - day 4 after SL-TBI [singe cell]


title: RNAseq_84__BRD4_C_Norm_rep3

extract_protocol:
Extraction of total RNA was performed using RNeasy Mini kit (Qiagen, Cat# 74106). Briefly, at least 1 million cells were plated in 6-well plate one day before treatments. Next day, drug was added directly into the medium for 2h (Auxin, dBET6), 6h (JQ1, KL2, iPAF1C). For performing RNA-seq, polyadenylated RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L)
isolated poly(A)+ RNA was used to prepare libraries using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Cat# E7760L). RNA-seq libraries were sequenced on Illumina NovaSeq 6000 instrument as paired end 50b reads.

value: Dox,Aux

value: Normoxia


title: WT_7.2_DMSO_6h_3

value: GPR65 WT Homozygous

value: WT

value: Stimulated for 6 hours at pH 7.2 using DMSO


title: ChIPseq_05__Pol2_KL2_Norm


title: RNAseq_83__BRD4_C_Norm_rep2


title: ChIP3, ibm1, H3, rep2

value: 2-week-old seedling

value: H3 ChIP


title: ChIP3, ibm1 ashh3, H3, rep2

value: ibm1 ashh3


title: WT_7.2_DMSO_6h_2

value: Bone Marrow Derived Denderitic Cell


title: WT_7.2_DMSO_6h_1


title: 18-mo CD45- thymic stoma cells - day 4 after SL-TBI [singe cell]

value: thymus

value: CD45- thymic stroma cells

value: 18-month old


title: RNAseq_82__BRD4_C_Norm_rep1

value: colon


title: ChIP3, ashh3, H3, rep2


title: WT_6.6_DMSO_6h_3

value: Stimulated for 6 hours at pH 6.6 using DMSO


title: RNA1, ibm1, rep1


title: RNAseq_81__BRD4_dCTM_Norm_rep3

value: colorectal carcinoma


title: ChIP3, WT, H3, rep2

value: wild type


title: WT_6.6_DMSO_6h_2

value: 6.5 weeks


title: 18-mo CD45- thymic stoma cells - day 7 after SL-TBI [singe cell]

value: day 7 after SL-TBI


title: RNAseq_80__BRD4_dCTM_Norm_rep2

value: Dox,Aux

value: Normoxia