title: 18-mo CD45- thymic endothelial cells - day 1 after SL-TBI [singe cell]

value: CD45-PECAM1+ thymic stroma cells

value: day 1 after SL-TBI


title: ChIP3, ibm1 ashh3, H3K9me2, rep2

status: Public on Jun 27 2024

type: SRA

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

country: Japan

institute: Graduate School of Science, The University of Tokyo

library_source: genomic

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

molecule: genomic DNA

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).

tag: tissue

value: 2-week-old seedling

tag: genotype

value: ibm1 ashh3

tag: chip antibody

value: H3K9me2 ChIP


title: 18-mo CD45- thymic stoma cells - day 1 after SL-TBI [singe cell]

city: Duarte

first: Anastasia

middle: I

last: Kousa

state: CA

address: 1500 E Duarte Rd

department: Hematology / HCT

country: USA

institute: City of Hope

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

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism: Mus musculus

source_name: thymus

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: thymus

tag: strain

tag: cell type

value: CD45- thymic stroma cells

value: wild type

tag: age

value: 18-month old

tag: treatment


title: RNAseq_79__BRD4_dCTM_Norm_rep1

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

library_source: transcriptomic

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

organism: Homo sapiens

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:
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: colon

tag: cell line

value: colorectal carcinoma

tag: agent

value: Dox,Aux

value: Normoxia


title: 18-mo CD45- thymic fibroblasts - steady state [singe cell]

value: CD45-PDGFRA+ thymic stroma cells

value: untreated


title: ChIP3, ibm1, H3K9me2, rep2


title: ChIP3, ashh3, H3K9me2, rep2


title: RNAseq_77__BRD4_dBD_Norm_rep2


title: 18-mo CD45- thymic endothelial cells - steady state [singe cell]


title: KO_7.6_PGE2_2h_2

city: Cambridge

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

molecule: total RNA

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 2 hours at pH 7.6 using PGE2


title: KO_7.6_PGE2_2h_3


title: 18-mo CD45- thymic fibroblasts - day 1 after SL-TBI [singe cell]

value: day 1 after SL-TBI


title: ChIP3, ibm1 ashh3, H3K4me1, rep2

value: 2-week-old seedling

value: ibm1 ashh3

value: H3K4me1 ChIP


title: ChIP3, WT, H3K9me2, rep2

value: wild type

value: H3K9me2 ChIP


title: 02-mo CD45- thymic fibroblasts - day 7 after SL-TBI [singe cell]

value: thymus

value: 02-month old

value: day 7 after SL-TBI


title: RNAseq_75__BRD4_FL_Norm_rep3

value: colon

value: colorectal carcinoma

value: Dox,Aux

value: Normoxia


title: KO_7.6_PGE2_2h_1

value: Bone Marrow Derived Denderitic Cell

value: GPR65 KO Homozygous


title: 18-mo CD45- thymic stoma cells - steady state rep1 [singe cell]

value: CD45- thymic stroma cells

value: 18-month old

value: untreated


title: 18-mo CD45- thymic stoma cells - steady state rep2 [singe cell]


title: RNAseq_76__BRD4_dBD_Norm_rep1


title: KO_7.6_DMSO_2h_3

value: 6.5 weeks

value: KO

value: Stimulated for 2 hours at pH 7.6 using DMSO


title: ChIP3, ibm1, H3K4me1, rep2

value: 2-week-old seedling

value: H3K4me1 ChIP


title: ChIP3, ashh3, H3K4me1, rep2


title: KO_7.6_DMSO_2h_1


title: RNAseq_73__BRD4_FL_Norm_rep2


title: WT_6.6_DMSO_6h_1

value: GPR65 WT Homozygous

value: WT

value: Stimulated for 6 hours at pH 6.6 using DMSO


title: KO_7.6_DMSO_2h_2


title: 02-mo CD45- thymic endothelial cells - day 7 after SL-TBI [singe cell]

value: thymus

value: CD45-PECAM1+ thymic stroma cells

value: wild type

value: 02-month old

value: day 7 after SL-TBI


title: ChIP3, WT, H3K4me1, rep2


title: RNAseq_73__BRD4_FL_Norm_rep1

value: colon

value: colorectal carcinoma

value: Dox,Aux

value: Normoxia


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

value: CD45- thymic stroma cells


title: RNAseq_78__BRD4_dBD_Norm_rep3


title: KO_7.2_BRD5075_2h_3

value: Bone Marrow Derived Denderitic Cell

value: GPR65 KO Homozygous

value: 6.5 weeks

value: KO

value: Stimulated for 2 hours at pH 7.2 using BRD5075


title: RNAseq_72__BRD4_IAA7_10uMJQ1_6h_Hypoxia_rep3

value: Hypoxia


title: KO_7.2_BRD5075_2h_2


title: RNAseq_71__BRD4_IAA7_10uMJQ1_6h_Hypoxia_rep2


title: 02-mo CD45- thymic fibroblasts - day 4 after SL-TBI [singe cell]

value: CD45-PDGFRA+ thymic stroma cells

value: day 4 after SL-TBI


title: KO_7.2_BRD5075_2h_1


title: 02-mo CD45- thymic endothelial cells - day 4 after SL-TBI [singe cell]

value: thymus

value: CD45-PECAM1+ thymic stroma cells


title: KO_7.2_DMSO_2h_3

value: Stimulated for 2 hours at pH 7.2 using DMSO


title: ChIP3, ashh3, H3K36me3, rep2

value: 2-week-old seedling

value: H3K36me3 ChIP


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

value: wild type

value: 02-month old


title: ChIP3, WT, H3K36me3, rep2


title: RNAseq_69__BRD4_IAA7_10uMJQ1_Norm_rep3

value: colon

value: colorectal carcinoma

value: Normoxia


title: ChIP3, ibm1 ashh3, H3, rep1

value: ibm1 ashh3

value: H3 ChIP


title: RNAseq_67_BRD4_IAA7_10uMJQ1_Norm_rep1


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

value: CD45- thymic stroma cells


title: KO_7.2_DMSO_2h_1

value: Bone Marrow Derived Denderitic Cell

value: GPR65 KO Homozygous

value: 6.5 weeks

value: KO


title: KO_7.2_DMSO_2h_2


title: ChIP3, ibm1, H3, rep1


title: 02-mo CD45- thymic fibroblasts - day 1 after SL-TBI [singe cell]

value: thymus

value: CD45-PDGFRA+ thymic stroma cells

value: day 1 after SL-TBI


title: RNAseq_68__BRD4_IAA7_10uMJQ1_Norm_rep2


title: ChIP3, ibm1 ashh3, H3K36me3, rep2

value: 2-week-old seedling


title: RNAseq_66__BRD4_IAA7_5uMJQ1_6h_Hypoxia_rep3

value: Hypoxia


title: KO_6.6_DMSO_2h_3

value: Stimulated for 2 hours at pH 6.6 using DMSO


title: ChIP3, ashh3, H3, rep1


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

value: wild type

value: 02-month old


title: RNAseq_65__BRD4_IAA7_5uMJQ1_6h_Hypoxia_rep2

value: colon

value: colorectal carcinoma


title: ChIP3, WT, H3, rep1


title: 02-mo CD45- thymic endothelial cells - day 1 after SL-TBI [singe cell]

value: CD45-PECAM1+ thymic stroma cells


title: KO_6.6_DMSO_2h_2


title: ChIP3, ibm1, H3K36me3, rep2

value: H3K36me3 ChIP


title: KO_6.6_DMSO_2h_1


title: RNAseq_70_BRD4_IAA7_10uMJQ1_6h_Hypoxia_rep1


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

value: CD45- thymic stroma cells


title: ChIP3, ibm1 ashh3, H3K9me2, rep1

value: ibm1 ashh3

value: H3K9me2 ChIP


title: I231L_7.6_PGE2_2h_3

value: Bone Marrow Derived Denderitic Cell

value: GPR65 I231L Homozygous

value: 6.5 weeks

value: Stimulated for 2 hours at pH 7.6 using PGE2


title: I231L_7.6_PGE2_2h_2


title: RNAseq_63__BRD4_IAA7_5uMJQ1_Norm_rep3

value: Normoxia


title: RNAseq_62__BRD4_IAA7_5uMJQ1_Norm_rep2


title: ChIP3, ibm1, H3K9me2, rep1

value: 2-week-old seedling


title: 02-mo CD45- thymic fibroblasts - steady state [singe cell]

value: thymus

value: CD45-PDGFRA+ thymic stroma cells

value: untreated


title: 02-mo CD45- thymic endothelial cells - steady state [singe cell]

value: wild type

value: 02-month old


title: I231L_7.6_DMSO_2h_3

value: Stimulated for 2 hours at pH 7.6 using DMSO


title: ChIP3, ashh3, H3K9me2, rep1


title: I231L_7.6_PGE2_2h_1


title: ChIP3, WT, H3K9me2, rep1


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


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


title: ChIP3, ibm1 ashh3, H3K4me1, rep1

value: H3K4me1 ChIP


title: RNAseq_60__HIFB_KO_6h_Hypoxia_rep3

value: colon

value: colorectal carcinoma

value: NT

value: Hypoxia


title: I231L_7.6_DMSO_2h_2

value: Bone Marrow Derived Denderitic Cell


title: RNAseq_59__HIFB_KO_6h_Hypoxia_rep2


title: I231L_7.6_DMSO_2h_1

value: GPR65 I231L Homozygous


title: ChIP3, ibm1, H3K4me1, rep1


title: P10 BL/6J Wild type 2

city: New York

first: Saptarshi Biswas

last: Biswas

state: NY

address: 650 West 168 Street

department: Neurology

institute: Columbia University Irving Medical Center

description: single cell RNA seq

data_processing:
The barcoded processing, gene counting and aggregation were done using the Cell Ranger software 5.0.1 and 6.1.2
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
The neural dissociation kit (P) was used to dissociate the retinas into a single cell suspension. Following that, the samples were stained with CD31-APC and PI, and live endothelial cells were FACS sorted for single cell RNA sequencing
Library construction was performed according to the manufacturer's instruction (single cell 3' v2 protocol, 10x Genomics)

value: Retina

value: Endothelial cell

value: Wild type


title: 18-mo thymus - steady state [visium]

data_processing:
FASTQ files were processed using the 10x Space Ranger package (v1.3.1).
Assembly: GRCm38 (mm10)
Supplementary files format and content: .tif: visium slide image
Supplementary files format and content: filtered_feature_bc_matrix.h5: HD5F file with feature barcode matrices that contains only tissue-associated barcodes
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz: gzipped folder file with feature barcode matrices that contains only tissue-associated barcodes
Supplementary files format and content: raw_feature_bc_matrix.h5: HD5F file with feature barcode matrices that contains both tissue-associated as well as background barcodes
Supplementary files format and content: raw_feature_bc_matrix.tar.gz: gzipped folder with feature barcode matrices that contains both tissue-associated as well as background barcodes
Supplementary files format and content: spatial.tar.gz: gzipped folder containing visium-specific outs (QC images to check image processing pipeline, downsampled input images, and files that describe spot barcode locations in the images)
Supplementary files format and content: metrics_summary.csv: metrics for quality assessment in CSV format
Supplementary files format and content: molecule_info.h5: molecule level information used in additional pipelines (spaceranger aggr, spaceranger targeted-compare)
Library strategy: Spatial Transcriptomics

extract_protocol:
Visium spatial gene expression slides were permeabilized at 37 °C for 12–18 min and polyadenylated. mRNA was captured by primers bound to the slides. RT, second-strand synthesis, cDNA amplification and library preparation proceeded using the Visium Spatial Gene Expression Slide & Reagent Kit (10X Genomics PN 1000184) according to the manufacturer’s protocol. After evaluation by real-time PCR, cDNA amplification included 11–12 cycles.
Sequencing libraries were prepared with 8 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/120 run using the NovaSeq 6000 S1 Reagent Kit (200 cycles; Illumina).

value: 18-month old


title: RNAseq_64__BRD4_IAA7_5uMJQ1_6h_Hypoxia_rep1


title: I231L_7.2_BRD5075_2h_3

value: 6.5 weeks

value: Stimulated for 2 hours at pH 7.2 using BRD5075


title: RNAseq_58__HIFB_KO_6h_Hypoxia_rep1


title: 02-mo thymus - steady state [visium]

value: thymus

value: untreated


title: RNAseq_57__HIFB_KO_Norm_rep3

value: Normoxia


title: ChIP3, ashh3, H3K4me1, rep1

value: 2-week-old seedling


title: ChIP3, WT, H3K4me1, rep1

value: wild type

value: H3K4me1 ChIP


title: P10 BL/6J Wild type 1

description: single cell RNA seq


title: I231L_7.2_BRD5075_2h_2


title: RNAseq_61__BRD4_IAA7_5uMJQ1_Norm_rep1

value: colon

value: colorectal carcinoma


title: RNAseq_56__HIFB_KO_Norm_rep2

value: NT


title: ChIP3, ibm1 ashh3, H3K36me3, rep1

value: ibm1 ashh3

value: H3K36me3 ChIP


title: P10 Vglut1 KO

description: single cell RNA seq

value: Retina


title: I231L_7.2_BRD5075_2h_1

value: Bone Marrow Derived Denderitic Cell

value: GPR65 I231L Homozygous


title: I231L_7.2_DMSO_2h_3

value: Stimulated for 2 hours at pH 7.2 using DMSO


title: RNAseq_55__HIFB_KO_Norm_rep1


title: RNAseq_54__gRNA_ctrl_6h_Hypoxia_rep3

value: WT

value: gRNA

value: Hypoxia


title: MULTI-seq barcode library [Pool_2_MS]

city: Adelaide

first: Peter

middle: James

last: Psaltis

state: South Australia

address: North Terrace

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

data_processing:
Cell Ranger v7.0.0 (10x Genomics) was used to process raw sequencing data from the two runs to quantify gene expression and barcode enrichments per cell.  (Two sequencing runs were performed to achieve ~50,000 mean reads per cell). This pipeline aligned sequencing reads from FASTQ files to the mm10 transcriptome using the STAR aligner and quantified the expression of genes in each cell. FASTQ files from two sequencing runs were then combined and performed cell ranger analysis on combined FASTQ files to quantify gene expression and barcode enrichments per cell.
The Seurat demultiplexing pipeline (Hao et al. 2021) was applied to demultiplex cells to their original sample-of-origin.
Cells detected with zero barcodes (Negatives) or more than one barcode (Doublets) were discarded. From the remaining singlets, cells containing expression values for <200 genes or >9000 genes were filtered out as initial quality control measures. Moreover, cells with more than 20% of mitochondrial genes were filtered out to exclude low-quality and dying cells
These resulted in 16,088 singlets corresponding to three barcodes, BC1:CFU-M population (7977 cells), BC2:Mat population (4795 cells), and BC3:Fm population (3316 cells). For the CFU-M population, a further quality control measure of 10% mitochondrial gene cut-off was applied. The remaining cells were then used to characterise the cellular heterogeneity of CFU-M progenitors.
Processed scRNA-seq data was analysed in R v4.1.3 using the Seurat R package v4.1.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Aortas from two 12-week-old C57BL/6J male mice were dissected out intact and flushed extensively with PBS, before microscopic dissection of surrounding perivascular fat. The dissected aortas were digested with LiberaseTM (50 μg/mL; Roche) for 1 h at 37°C, digests neutralized with Iscove’s Modified Dulbecco’s Medium supplemented with 10% fetal bovine serum and passed through a 40-µm nylon mesh to remove undigested material, before cell collection by centrifugation. The freshly isolated cells were plated in methylcellulose (MethoCult) in replicate wells of 24-well plate for colony formation. After 14 days, colony forming unit - macrophage (CFU-M) were isolated and disaggregated into single-cell suspensions. The resulting progenitor cells were stained with DAPI, and fluorescence assisted cell sorting (FACS)-purified viable cells used for scRNA-seq.
Purified progenitor cells were subjected to MULTI-seq labeling as previously described by McGinnis et al. (2019). Briefly, cells were resuspended in 18 µL of 1x PBS, labeled with a unique 2 µM anchor lipid-modified oligonucleotide (LMO)-Barcoded Oligo complex for 5’ on ice. After that, 2 µM co-anchor was added and cells incubated on ice for another 5 min. Labeling was quenched with 1 mL of PBS + 2% BSA and cells from each sample in the run mixed for washing the pool with PBS + 1% BSA (twice); final resuspension was in PBS + 1% BSA. From pooled cells, single cell sequencing libraries were prepared using the Chromium Next GEM single-cell 3’ kit (v3.1, 10x Genomics) and Chromium system according to manufacturer’s specifications. Paired-end sequencing was performed first, on an Illumina Nextseq High using v2 chemistry and subsequently, to increase read depth, on an Illumina Novaseq 6000 using one lane of an S4 flowcell (Illumina).


title: ChIP3, ibm1, H3K36me3, rep1


title: ChIP3, ashh3, H3K36me3, rep1


title: RNAseq_53__gRNA_ctrl_6h_Hypoxia_rep2


title: I231L_7.2_DMSO_2h_2

value: 6.5 weeks


title: hpGUS[Δ22nt]_19

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

institute: csiro

description: hpGUS[Δ22nt] 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
NEBNext® Small RNA Library Prep
libraries sequenced on a Novaseq

value: leaf


title: ChIP3, WT, H3K36me3, rep1

value: 2-week-old seedling


title: ChIP2, ibm1 suvh4, H3K36me3, rep2

value: ibm1 suvh4


title: RNAseq_52__gRNA_ctrl_6h_Hypoxia_rep1


title: I231L_7.2_DMSO_2h_1


title: I231L_6.6_DMSO_2h_3

value: Stimulated for 2 hours at pH 6.6 using DMSO


title: ChIP2, ibm1, H3K36me3, rep2


title: RNAseq_51__gRNA_ctrl_Norm_rep3

value: colon

value: Normoxia


title: I231L_6.6_DMSO_2h_2


title: hpGUS[Δ22nt]_12

description: hpGUS[Δ22nt] rep 2


title: hpGUS[Δ22nt]_11

description: hpGUS[Δ22nt] rep 1


title: RNAseq_50__gRNA_ctrl_Norm_rep2

value: colorectal carcinoma


title: ChIP2, suvh4, H3K36me3, rep2


title: hpGUS[G:U]_11

description: hpGUS[G:U] rep 3


title: I231L_6.6_DMSO_2h_1


title: RNAseq_49__gRNA_ctrl_Norm_rep1


title: ChIP2, WT, H3K36me3, rep2

value: wild type


title: hpGUS[G:U]_10

description: hpGUS[G:U] rep 2


title: WT_7.6_PGE2_2h_3

value: GPR65 WT Homozygous

value: Stimulated for 2 hours at pH 7.6 using PGE2


title: aorta, cultured CFU-M progenitors [Pool_1_GEX]

source_name: dorsal aorta

value: dorsal aorta

value: CFU-M progenitors


title: ChIP2, ibm1 suvh4, H3, rep2

value: H3 ChIP


title: RNAseq_48__BRD4_C_Hypoxia_rep3

value: Dox,Aux


title: WT_7.6_PGE2_2h_2

value: Bone Marrow Derived Denderitic Cell

value: WT


title: RNAseq_47__BRD4_C_Hypoxia_rep2

value: Hypoxia


title: ChIP2, ibm1, H3, rep2


title: WT_7.6_PGE2_2h_1

value: 6.5 weeks


title: RNAseq_46__BRD4_C_Hypoxia_rep1


title: hpGUSWT_13

description: hpGUS[WT] rep2

value: leaf


title: ChIP2, suvh4, H3, rep2

value: 2-week-old seedling


title: WT_7.6_DMSO_2h_3

value: Stimulated for 2 hours at pH 7.6 using DMSO


title: hpGUSWT_12

description: hpGUS[WT] rep1


title: WT_7.6_DMSO_2h_2


title: ChIP2, WT, H3, rep2


title: RNAseq_44__BRD4_dCTM_Hypoxia_rep2

value: colon


title: ChIP2, ibm1 suvh4, H3K36me3, rep1

value: ibm1 suvh4

value: H3K36me3 ChIP


title: RNAseq_45__BRD4_dCTM_Hypoxia_rep3

value: colorectal carcinoma


title: G2M m6A, R3

city: Cerdanyola del Vallés

first: Alicia

last: Roque

state: Barcelona

address: Carrer de la Vall Moronta, C2

department: Bioquímica i biologia molecular

country: Spain

institute: Universitat Autónoma de Barcelona

description:
DESeq2-DEG-res-2022-04-05-G2M-m6A.txt
m6A-rawdata.txt

data_processing:
Alignment to GRCh38.87 with Kallisto STAR in biojupies.cloud
Genes with at least 1 CpM in at least 2 replicates were used for DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include rawcounts and DESeq2 parameters for each gene

source_name: HeLa

growth_protocol: HeLa cells were grown in DMEM media supplemented with 10% FBS and antibiotics in humified atmosphere at 37ºC, 5% CO2

extract_protocol:
Total RNA was extracted using Invitrogen purelink kit and inmunoprecipitated with m6A antibody (abcam 151230) for 2h. RNA was precipitated and sequenced.
Sequencing with DNBSEQ was performed with 100bp reads and 20M clean reads per sample using lpWGS

treatment_protocol: Cell cycle was arrested with a double timidine block for 18h at 2mM with a pause of 9h in DMEM media. Cells were then incubated with DMEM media for  3h (S phase), 9h (G2/M) phase) and 15h (G1 phase). Cell cycle was checked by flow cytometry with propidium iodide staining

value: HeLa

value: Epithelial cervix

tag: cell cycle

tag: rip antibody

value: m6A antibody (abcam 151230)


title: RNAseq_43__BRD4_dCTM_Hypoxia_rep1


title: ChIP2, ibm1, H3K36me3, rep1


title: WT_7.2_BRD5075_2h_3

value: GPR65 WT Homozygous

value: Stimulated for 2 hours at pH 7.2 using BRD5075


title: RNAseq_42__BRD4_dBD_Hypoxia_rep3

value: Dox,Aux


title: G2M m6A, R2


title: ChIP2, suvh4, H3K36me3, rep1


title: hpGUSWT_18

description: hpGUS[WT] rep3


title: G2M m6A, R1


title: RNAseq_41__BRD4_dBD_Hypoxia_rep2


title: S m6A, R3

description:
DESeq2-DEG-res-2022-04-05-S-m6A.txt
m6A-rawdata.txt

value: S


title: hpGUS[G:U]_2

description: hpGUS[G:U] rep 1


title: ChIP2, ibm1 suvh4, H3, rep1

value: H3 ChIP


title: RNAseq_40__BRD4_dBD_Hypoxia_rep1

value: Hypoxia


title: S m6A, R2


title: WT_7.2_DMSO_2h_3

value: Bone Marrow Derived Denderitic Cell

value: 6.5 weeks

value: WT

value: Stimulated for 2 hours at pH 7.2 using DMSO


title: WT_7.2_BRD5075_2h_2


title: RNAseq_39__BRD4_FL_Hypoxia_rep3

value: colon


title: S m6A, R1


title: WT_7.6_DMSO_2h_1

value: Stimulated for 2 hours at pH 7.6 using DMSO


title: ChIP2, ibm1, H3, rep1

value: 2-week-old seedling


title: WT_7.2_BRD5075_2h_1


title: WT_7.2_DMSO_2h_2


title: RNAseq_38__BRD4_FL_Hypoxia_rep2

value: colorectal carcinoma


title: ChIP2, suvh4, H3, rep1


title: G1 m6A, R2

description:
DESeq2-DEG-res-2022-04-05-G1-m6A.txt
m6A-rawdata.txt

value: HeLa


title: ChIP2, WT, H3, rep1

value: wild type


title: ChIP1, ldl2, H3, rep2


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

value: thymus

value: CD45- thymic stroma cells

value: 02-month old

value: day 7 after SL-TBI


title: RNAseq_35__HIFB_KO_Hypoxia_rep2

value: NT


title: ChIP2, WT, H3K36me3, rep1

value: H3K36me3 ChIP


title: WT_6.6_DMSO_2h_1

value: GPR65 WT Homozygous

value: Stimulated for 2 hours at pH 6.6 using DMSO


title: RNAseq_34__HIFB_KO_Hypoxia_rep1

value: Hypoxia


title: ChIP1, ibm1, H3, rep2

value: H3 ChIP


title: WT_7.2_DMSO_2h_1

value: Bone Marrow Derived Denderitic Cell

value: 6.5 weeks

value: WT

value: Stimulated for 2 hours at pH 7.2 using DMSO


title: G2M Input, R3

description:
DESeq2-DEG-res-2022-04-05-S-G2M
Input cell cycle-rawdata.txt

extract_protocol:
Total RNA was extracted using Invitrogen purelink kit
Sequencing with DNBSEQ was performed with 100bp reads and 20M clean reads per sample

value: Epithelial cervix


title: RNAseq_37__BRD4_FL_Hypoxia_rep1

value: colon

value: colorectal carcinoma

value: Dox,Aux


title: G1 m6A, R3

value: HeLa

value: m6A antibody (abcam 151230)


title: ChIP1, WT, H3, rep2

value: 2-week-old seedling

value: wild type


title: RNAseq_36__HIFB_KO_Hypoxia_rep3

value: NT


title: ChIP1, ldl2, H2Bub, rep2

value: H2Bub ChIP


title: G2M Input, R2


title: Tibia, z2

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description:
RawCounts.txt
TMM_Normalized_counts.txt

data_processing:
FASTQ files were processed and demultiplexed with CASAVA 1.8.1 (Illumina) and uploaded to Partek Flow for analysis
Contaminants were removed with Bowtie 2 v2.2.5
Reads were aligned mm10 using STAR v2.7.8a
Reads were quantified with Ensembl Transcripts release 102
Normalization was done with TMM followed by log2 transformation
Assembly: mm10
Supplementary files format and content: txt files containing Raw counts
Supplementary files format and content: txt files containing TMM normalizaed counts

source_name: Bone tissue (tibia)

extract_protocol:
Total RNA was extracted from tibia bones, isolated using trizol and purified using RNeasy plus Mini Kit.
Llibraries were constructed using the Illumina Stranded mRNA Prep Ligation kit and following manufacturer’s protocol, then sequenced on an Illumina NextSeq 500
RNA-seq Illumina Stranded mRNA library Prep

treatment_protocol: C57Bl/6 underwent either sham or ovariectomy surgery and treated with PBS(control), HA, 3-3-PPA, or ZA fro 8 weeks.

value: Bone tissue (tibia)

value: Female

value: Wild-type

value: Ovariectomy + Zoledronic Acid


title: Tibia, z3

description:
RawCounts.txt
TMM_Normalized_counts.txt


title: S Input, R3

description:
DESeq2-DEG-res-2022-04-05-G1-S-OK
Input cell cycle-rawdata.txt

value: S


title: RNAseq_32__HIFB_KO_Norm_rep2

value: Normoxia


title: WT_6.6_DMSO_2h_3

value: Bone Marrow Derived Denderitic Cell

value: GPR65 WT Homozygous

value: 6.5 weeks

value: WT

value: Stimulated for 2 hours at pH 6.6 using DMSO


title: G1 m6A, R1

value: HeLa

value: Epithelial cervix


title: RNAseq_31__HIFB_KO_Norm_rep1

value: colon

value: colorectal carcinoma


title: ChIP1, ibm1 ldl2, H2Bub, rep2

value: 2-week-old seedling

value: ibm1 ldl2


title: RNAseq_30__BRD4_IAA7_auxin_Hypoxia_rep3

value: Auxin

value: Hypoxia


title: RNAseq_33__HIFB_KO_Norm_rep3

value: NT


title: Tibia, s3

description:
RawCounts.txt
TMM_Normalized_counts.txt

value: Bone tissue (tibia)

value: Female

value: Wild-type

value: Sham Control


title: S Input, R1

value: S


title: S Input, R2


title: Tibia, s2

description:
RawCounts.txt
TMM_Normalized_counts.txt


title: ChIP1, ibm1, H2Bub, rep2

value: H2Bub ChIP


title: ChIP1, WT, H2Bub, rep2

value: wild type


title: G1 Input, R3

description:
DESeq2-DEG-res-2022-04-05-G2M-G1
Input cell cycle-rawdata.txt


title: RNAseq_29__BRD4_IAA7_auxin_Hypoxia_rep2


title: G1 Input, R2


title: Tibia, s1

description:
RawCounts.txt
TMM_Normalized_counts.txt


title: G2M Input, R1


title: G1 Input, R1


title: ChIP1, ibm1 ldl2, H3K9me2, rep2

value: H3K9me2 ChIP


title: RNAseq_28__BRD4_IAA7_auxin_Hypoxia_rep1


title: ChIP1, ibm1, H3K9me2, rep2


title: RNAseq_27__BRD4_IAA7_NT_Hypoxia_rep3


title: RNAseq_26__BRD4_IAA7_NT_Hypoxia_rep2


title: Tibia, p1

description:
RawCounts.txt
TMM_Normalized_counts.txt

value: Ovariectomy + 3'(3'hydroxyphenyl) propionic acid


title: Tibia, ov3

description:
RawCounts.txt
TMM_Normalized_counts.txt

value: Ovariectomy + PBS


title: ChIP1, WT, H3K9me2, rep2


title: RNAseq_25__BRD4_IAA7_NT_Hypoxia_rep1

value: colon


title: ChIP1, ldl2, H3K9me2, rep2


title: Tibia, ov2

description:
RawCounts.txt
TMM_Normalized_counts.txt


title: ChIP1, ldl2, H3K4me1, rep2

value: H3K4me1 ChIP


title: Tibia, ov1

description:
RawCounts.txt
TMM_Normalized_counts.txt


title: Tibia, p2

description:
RawCounts.txt
TMM_Normalized_counts.txt


title: RNAseq_24__BRD4_IAA7_auxin_Norm_rep3

value: colorectal carcinoma

value: Normoxia


title: ChIP1, ibm1 ldl2, H3K4me1, rep2

value: 2-week-old seedling

value: ibm1 ldl2


title: 3D7-BDP5-FKBP, noBiotin, no RAPA, 32to40hpi, DiBioCUT&Tag

city: Nijmegen

first: Jonas

last: Gockel

email: jonas-gockel@web.de, jonas.gockel@ru.nl

address: Geert Grooteplein-Zuid 8

country: Netherlands

institute: Radboud University

data_processing:
Sequencing reads were mapped against the reference genome PlasmoDB v26 3D7 with bowtie2 (v2.5.2)
Reads were filtered for mapping quality higher or equal than 30 and mitrochondrial and apicoplast reads were removed with samtools (v1.18)
BigWig files normalised to RPMK were generated with deeptools (v3.5.4)
Bedgraphs were generated for visualisation on UCSC genome browser with bedtools (v2.31.0) normalised to reads per million
Assembly: PlasmoDB v26 3D7
Supplementary files format and content: bedGraph

organism: Plasmodium falciparum

source_name: 3D7 BDP5-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo

growth_protocol: RPMI 1640 medium supplemented with 0.2% NaHCO3 and 10% human serum at 37 °C under low oxygen conditions (3% O2, 4% CO2 and 93% N2) in human red blood cells at 5% hematocrit

extract_protocol:
For nuclei isolation, parasite cultures were lightly crosslinked with 0.1% formaldehyde (Sigma, F8775), incubating for 2 min at 37 °C while shaking. Crosslinking was stopped by addition of glycine to 0.125 M final concentration. Samples were handled on ice from here onwards. Cells were harvested by 440 g centrifugation for 8 min at 4 °C, and washed with ice-cold PBS. Centrifugation was repeated and the pellet was washed with PBS supplemented with 1x EDTA-free Protease Inhibitor (Roche, 04693132001). Parasites were extracted by adding saponin (0.05% total concentration) and incubating at room temperature (RT) for 10 min. Nuclei were isolated by carefully transferring the extracted parasite mixture on top of a 0.25 M to 0.1 M sucrose gradient in cell lysis buffer (10 mM Tris pH 8, 3 mM MgCl2, 0.2% NP-40, 1x EDTA free Protease inhibitor (Roche, 04693132001); 15 mL 0.25 M Sucrose and 17.5 mL 0.1M Sucrose for 50 mL tubes, 4 mL 0.25 M Sucrose and 6 mL 0.1 M Sucrose for 15 mL tubes) and centrifuging for 12 min, 3100 g, 4 °C with acceleration and deceleration set to 1 (Eppendorf 5910 Ri, Rotor S-4x400). Supernatant was removed and nuclei washed in cell lysis buffer (10 min, 3500 g, 4 °C; Heraeus Fresco 21). Nuclei were counted in an automatic hemocytometer (BioRad, TC10 Automated Cell Counter) and were directly used for CUT&Tag. Optionally, nuclei were washed with cell lysis buffer containing 20% Glycerol and nuclei pellet was snap frozen in liquid nitrogen prior to storage at -80°C. For parasite isolations, parasite cultures were harvested by 440 g centrifugation for 8 min at RT and pellet was resuspended in 1 mL of 0.15% Saponin/PBS per 10 mL culture and incubated for 5 min on ice. Samples were vortexed shortly every minute. Samples were washed three times with ice-cold PBS (3500 g centrifugation for 3 min at 4 °C; Heraeus Fresco 21). Intact parasites were counted in an automatic hemocytometer and were directly used for CUT&Tag. Optionally, parasites were washed with PBS containing 20% Glycerol and parasite pellets snap frozen in liquid nitrogen prior to storage at -80 °C. Nuclei or whole parasite were resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor) containing 0.1% Triton X-100 and permeabilized for 10 min on ice. Nuclei / parasites were pelleted by centrifugation (3500 g, 10 min, 4 °C) and resuspended in CUT&Tag wash buffer. Concanavalin A beads (Bangs Laboratories, BP531) were activated by resuspending into 10 volumes of Bead Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), washed once on a magnetic rack and resuspended in the starting volume of bead slurry. Purified nuclei or parasites were bound to 10 µL beads per reaction by incubating for 10 min rotating at RT. The supernatant was removed and 50 µL antibody buffer (CUT&Tag wash buffer; 2 mM EDTA, 0.1% BSA) with primary Antibody (0.25 µL polyclonal rabbit αHP1; 0.5 µg αH3K9me3, Abcam 8988; 0.5 µL αBiotin (Cell Signaling Technology #D5A7; for DiBioCUT&Tag) or 0.5 µg normal rabbit IgG (MERCK, #12-370) was added and incubated nutating over night at 4 °C. Unbound primary antibody was removed by washing once with 100 µL CUT&Tag wash buffer and samples were then incubated with secondary antibody (1.2 µg guinea pig anti-rabbit antibody, Antibodies-Online ABIN101961, in 100 µL CUT&Tag wash buffer, 1:100 dilution) for 1h on RT, nutating. The nuclei or parasites were washed on a magnetic stand twice with 100 µL CUT&Tag wash buffer and once with 100 µL CUT&Tag 300 Wash Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor). For all following wash steps CUT&Tag 300 wash buffer was used in order to quench potential affinity of protA-Tn5 to accessible chromatin regions. 2.5 µL commercial proteinA/G-Tn5 fusion protein (CUTANA™ pAG-Tn5 for CUT&Tag, Epicypher, 15-1017) was added in 50 µL CUT&Tag 300 wash buffer and incubated nutating for 1 h. Unbound proteinA/G-Tn5 fusion protein was removed by thrice washing with 100 µL CUT&Tag 300 wash buffer. The supernatant was removed and the nuclei or parasites were resuspended in 200 µL freshly prepared tagmentation buffer (CUT&Tag 300 wash buffer, 10 mM MgCl2). To perform tagmentation, samples were incubated in a PCR thermocycler (BioRad, T100) at 37 °C for 1h. Tagmentation was stopped and nuclei or parasite lysis was facilitated by addition of 10 µL of 0.5M EDTA pH8, 3 µL of 10% SDS and 1 µL of 50 mg/mL proteinase K. Samples were briefly vortexed and then incubated at 55 °C for 1 h. DNA fragments were extracted utilizing the DNA Clean & Concentrator - 5 kit (Zymogen, D4014) following manufactures instructions. DNA was eluted from the column with 26 µL of prewarmed elution buffer and DNA concentrations were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231).
Libraries were generated using maximal 50 ng of extracted DNA from CUT&Tag experiments and tagged fragments were amplified with unique combinations of i5 and i7 barcoded primers, enabling tracing the DNA fragments originating from separate experiments in the sequencing data. PCRs were performed in a total reaction volume of 50 µL using Kapa HiFi polymerase (use non-hotstart version for gap filling; Roche, KK2102) in a thermocycler with the following program: 58 °C for 5 min, 62 °C for 5 min (gap filling), 98 °C for 2 min, 12-16 cycles of 98 °C for 20 second and 62 °C for 10 seconds, 62 °C for 1 min and hold at 4 °C. Post-PCR DNA cleanup was performed by adding 50 µL (1x volume) of AMPure XP bead slurry (Beckman Coulter, A63882) and incubating for 10 min at RT, washing twice with 80% EtOH on a magnetic rack, and eluting in 16.5 µL of 10 mM Tris-HCl pH 8 for 5 min at RT. DNA concentrations of libraries were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231) and library fragment size distribution was accessed by microfluidic gel electrophoresis (Agilent 2100 Bioanalyser) with the corresponding High Sensitivity DNA Kit (Agilent, 5067-4626). Sequencing was performed using an Illumina NextSeq 2000 instrument for 3-10 M reads per CUT&Tag sample; 59bp paired-end reads were generated.
(DiBio)CUT&Tag

tag: cut&tag antibody

value: Biotin (CST, #D5A7)

tag: starting material

value: isolated nuclei


title: 3D7-BDP5-FKBP, Biotin, 32to40hpi, DiBioCUT&Tag

value: 3D7 BDP5-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo


title: RNAseq_23__BRD4_IAA7_auxin_Norm_rep2

value: Auxin


title: Tibia, h2

description:
RawCounts.txt
TMM_Normalized_counts.txt

value: Bone tissue (tibia)

value: Female

value: Wild-type

value: Ovariectomy + Hippuric Acid


title: 3D7-BDP5-FKBP, Biotin, 24to32hpi, DiBioCUT&Tag


title: 3D7-HP1-FKBP, Biotin, DiBioCUT&Tag

source_name: 3D7 HP1-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo


title: ChIP1, WT, H3K4me1, rep2

value: wild type


title: ChIP1, ibm1, H3K4me1, rep2


title: 3D7-HP1-FKBP, HP1, CUT&Tag

value: 3D7 HP1-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo

value: HP1 (Brancucci et. al, 2014)


title: Tibia, h1

description:
RawCounts.txt
TMM_Normalized_counts.txt


title: ChIP1, ldl2, H3K36me3, rep2

value: H3K36me3 ChIP


title: WT_6.6_DMSO_2h_2

value: Bone Marrow Derived Denderitic Cell

value: GPR65 WT Homozygous

value: 6.5 weeks

value: WT

value: Stimulated for 2 hours at pH 6.6 using DMSO


title: RNAseq_22__BRD4_IAA7_auxin_Norm_rep1

value: colon

value: colorectal carcinoma

value: Normoxia


title: ChIP1, ibm1 ldl2, H3, rep2

value: 2-week-old seedling

value: ibm1 ldl2

value: H3 ChIP


title: BMN.4

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the human genome (version: hg19)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes

source_name: lymphoblastoid cell lines

extract_protocol: RNA from tissue samples was extracted with RNeasy Mini Kit (Qiagen), accordingly to the manufacturer’s instructions

value: lymphoblastoid cell lines

value: BMN


title: ChIP1, ibm1 ldl2, H3K36me3, rep2


title: 3D7-BDP5-FKBP, noBiotin, no RAPA, 24to32hpi, DiBioCUT&Tag

value: 3D7 BDP5-2xFKBP-GFP-2A-NeoR / mCherry-FRB-miniTurbo

value: Biotin (CST, #D5A7)

value: isolated nuclei


title: RNAseq_19__BRD4_IAA7_NT_Norm_rep1

value: NT


title: F12, HP1, CUT&Tag, fresh parasites

value: HP1 (Brancucci et. al, 2014)

value: isolated parasites


title: Tibia, h3

description:
RawCounts.txt
TMM_Normalized_counts.txt

value: Bone tissue (tibia)

value: Female

value: Wild-type

value: Ovariectomy + Hippuric Acid


title: RNAseq_17__AFF1_AFF4_AID_auxin_6h_Hypoxia_rep2

value: colon

value: colorectal carcinoma

value: Auxin

value: Hypoxia


title: ChIP1, ibm1, H3K36me3, rep2

value: 2-week-old seedling

value: H3K36me3 ChIP


title: ChIP1, WT, H3K36me3, rep2

value: wild type


title: BMN.2

value: lymphoblastoid cell lines

value: BMN


title: RNAseq_18__AFF1_AFF4_AID_auxin_6h_Hypoxia_rep3


title: RNAseq_21__BRD4_IAA7_NT_Norm_rep3

value: Normoxia


title: F12-E1, HP1, CUT&Tag, parasites


title: BMN.3


title: F12, HP1, CUT&Tag, frozen parasites


title: F12-E1, HP1, CUT&Tag, nuclei

value: isolated nuclei


title: RNAseq_16__AFF1_AFF4_AID_auxin_6h_Hypoxia_rep1


title: veh.2

value: vehicle


title: ChIP1, ibm1 ldl2, H3, rep1

value: ibm1 ldl2

value: H3 ChIP


title: BMN.1


title: F12-C12, HP1, CUT&Tag, 50k

value: HP1 (Brancucci et. al, 2014)


title: F12-C12, HP1, CUT&Tag, 10k


title: RNAseq_20__BRD4_IAA7_NT_Norm_rep2

value: NT


title: RNAseq_14__AFF1_AFF4_AID_NT_6h_Hypoxia_rep2


title: ChIP1, ldl2, H3, rep1


title: RNAseq_15__AFF1_AFF4_AID_NT_6h_Hypoxia_rep3


title: veh.1


title: F12-B2, HP1, CUT&Tag, 100k


title: RNAseq_13__AFF1_AFF4_AID_NT_6h_Hypoxia_rep1


title: GFTU3

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 Tregs, GF, tumor-bearing

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, SPF or GF mice were intraperitoneally (i.p) injected with 3 × 10^6 EG7.1.15 cells.

value: Omental Tregs

tag: group

value: GF

value: tumor-bearing

tag: tumor stage

tag: sorting markers

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

tag: Sex

value: female


title: RNAseq_12__AFF1_AFF4_AID_auxin_6h_Norm_rep3

tag: tissue

value: colon

value: colorectal carcinoma

value: Auxin


title: NF54, IgG, CUT&Tag

value: normal IgG (MERCK #12-370)


title: GFTU2


title: ChIP1, WT, H3, rep1

value: 2-week-old seedling

tag: genotype

value: wild type


title: NF54, H3K9me3, CUT&Tag

value: H3K9me3 (Abcam 8988)

value: isolated nuclei


title: veh.3

value: lymphoblastoid cell lines

value: vehicle


title: GFNaive3

source_name: Omental Tregs, GF, tumor-free

value: tumor-free


title: RNAseq_10__AFF1_AFF4_AID_auxin_6h_Norm_rep1

value: Normoxia


title: ChIP1, ldl2, H2Bub, rep1

tag: chip antibody

value: H2Bub ChIP


title: ChIP1, ibm1, H3, rep1

value: H3 ChIP


title: GFNaive2

value: Omental Tregs

value: GF


title: RNAseq_09__AFF1_AFF4_AID_NT_6h_Norm_rep3

value: NT


title: ChIP1, ibm1, H2Bub, rep1


title: ChIP1, ldl2, H3K9me2, rep1

value: H3K9me2 ChIP


title: GFTU1

value: tumor-bearing

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

value: female


title: F12, HP1, CUT&Tag

value: HP1 (Brancucci et. al, 2014)


title: F12-B2, HP1, CUT&Tag, 10k


title: GFNaive1


title: RNAseq_11__AFF1_AFF4_AID_auxin_6h_Norm_rep2

value: colon

value: colorectal carcinoma

value: Auxin


title: ChIP1, WT, H2Bub, rep1

value: 2-week-old seedling

value: wild type


title: ChIP1, ibm1 ldl2, H3K9me2, rep1

value: ibm1 ldl2


title: RNAseq_07__AFF1_AFF4_AID_NT_6h_Norm_rep1

value: Normoxia


title: ChIP1, ibm1 ldl2, H2Bub, rep1

value: H2Bub ChIP


title: NF54, HP1, CUT&Tag

value: isolated nuclei


title: CONVTU4

source_name: Omental Tregs, SPF, tumor-bearing

value: Omental Tregs

value: SPF


title: RNAseq_06__gRNActrl_Hypoxia_rep3

value: WT

value: gRNA

value: Hypoxia


title: ChIP1, ibm1, H3K9me2, rep1

value: H3K9me2 ChIP


title: neutrophils, infected with L. infantum, subject 08

type: RNA

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

hyb_protocol: Hybridization to the Affymetrix® miRNA 4.1 Array strips was carried out at 48ºC for 20 hours

scan_protocol: GeneAtlas® System (Affymetrix)

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Transcriptome Analysis Console (TAC) 4.0.1 (Thermo Fisher Scientific Co.) using the Robust Multi-array Average (RMA) algorithm

label: biotin

source_name: neutrophils of healthy male donors

label_protocol: Total RNA (500 ng/sample) was labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific Co.), according to the manufacturer’s instructions

growth_protocol: Peripheral blood was collected from healthy male donors was immediately separated using a discontinuous density gradient to obtain neutrophils

extract_protocol: Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.

treatment_protocol: Neutrophils of infected group were exposed to promastigotes at a ratio of five L. infantum for each neutrophil (Multiplicity of Infection - MOI = 5:1). After 3 hours neutrophils were washed (to remove non-internalized promastigotes) and then resuspended in RPMI supplemented medium until 20 hours of total incubation.

value: infected with L. infantum


title: RNAseq_08__AFF1_AFF4_AID_NT_6h_Norm_rep2

value: NT


title: CONVTU3

value: tumor-bearing

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

value: female


title: ChIP1, WT, H3K9me2, rep1

value: 2-week-old seedling


title: neutrophils, infected with L. infantum, subject 07


title: RNAseq_05__gRNActrl_Hypoxia_rep2

value: colon

value: colorectal carcinoma


title: ChIP1, ldl2, H3K4me1, rep1

value: H3K4me1 ChIP


title: CONVTU2


title: RNAseq_03__gRNActrl_Norm_rep3

value: Normoxia


title: neutrophils, infected with L. infantum, subject 06


title: RNAseq_02__gRNActrl_Norm_rep2


title: ChIP1, ibm1, H3K4me1, rep1


title: neutrophils, infected with L. infantum, subject 02


title: ChIP1, ibm1 ldl2, H3K4me1, rep1

value: ibm1 ldl2


title: CONVNaive1

source_name: Omental Tregs, SPF, tumor-free

value: Omental Tregs

value: tumor-free


title: neutrophils, infected with L. infantum, subject 05


title: CONVNaive2

value: SPF


title: RNAseq_01__gRNActrl_Norm_rep1

value: WT

value: gRNA


title: hMSCs 1:6 MoS2 2

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy, Medical Research and Education Building II Suite 4344

department: Department of Molecular and Cellular Medicine

institute: Texas A&M University

description: 1:6 MoS2 treatment

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for all samples

source_name: Mesenchymal stem cells

growth_protocol: hMSCs were cultured under media conditions consisting of α-minimal essential media (alpha-MEM, Hyclone, GE Sciences) with 16.5% fetal bovine serum (Atlanta Biologicals, USA) and 1% penicillin/streptomycin (100 U/100 µg/mL, Gibco). After every 2-3 days, half of culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching confluency of ~70% and seeded at ~2500 cells/cm2. All experiments were completed with cell populations under P5.

extract_protocol:
At the end of 7 days of culture, total RNA was extracted (Zymogen, High Purity RNA Isolation kit), and then converted into cDNA (>1 μg).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hMSCs were cultured and treated with/without and MoS2 nanoparticles with varying degree of atomic vacancies (25 ug/mL)

value: Bone marrow derived mesenchymal stem cells


title: ChIP1, ldl2, H3K36me3, rep1

source_name: 2-week-old seedling

value: H3K36me3 ChIP


title: neutrophils, uninfected, subject 07

value: uninfected


title: neutrophils, uninfected, subject 08


title: neutrophils, uninfected, subject 06


title: corneaGRKO-rep4

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
RNA-SEQ reads (~40M per sample) were aligned to the UCSC mm9 reference genome using bowtie2
The quantification results from htseq-count were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Assembly: mm9
Supplementary files format and content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: whole cornea

extract_protocol:
Total RNA was isolated from the corneas of mice using Trizol-chloroform based extraction and then RNA purification using RNeasy column (Qiagen) according to the manufacturer’ protocols.  Each experimental group had 4 replicates, where each replicate had 4-6 corneas pooled into one sample.
Indexed samples were sequenced using the 75bp pair-end protocol using the Illumina NextSeq500 sequencer as per the manufacturer’s protocol. Reads greater than 40 million reads per sample were aligned to the reference genome UCSC mm10.

treatment_protocol: Male corneaGRKO mice that were 3 months of age and their age-matched control (GRflox) littermates were euthanized, eyes removed, and total RNA was isolated from the whole cornea.

tag: background

tag: gender

value: Male

value: 4-6 corneas (pooled)

value: 3 months

value: GRloxP/loxP-PAX6Cre/+ (corneaGRKO)


title: ChIP1, ibm1 ldl2, H3K36me3, rep1

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


title: CONVNaive3

tag: cell type

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

value: female


title: RNAseq_04__gRNActrl_Hypoxia_rep1

source_name: colon

value: colon

value: colorectal carcinoma

tag: treatment

value: Hypoxia


title: neutrophils, uninfected, subject 05


title: ChIP1, ibm1, H3K36me3, rep1


title: corneaGRKO-rep3

tag: age


title: corneaGRKO-rep1


title: ChIP1, WT, H3K4me1, rep1

value: wild type

value: H3K4me1 ChIP


title: corneaGRKO-rep5


title: neutrophils, uninfected, subject 02


title: GRfloxcontrol-rep5

value: GRloxP/loxP-PAX6+/+ (GRflox)


title: hMSCs 1 control

description: Control


title: ChIP1, WT, H3K36me3, rep1


title: Tibia, z1

description:
RawCounts.txt
TMM_Normalized_counts.txt

value: Bone tissue (tibia)

tag: cell line

value: Female

tag: strain

value: Wild-type

value: Ovariectomy + Zoledronic Acid


title: hMSCs 2 control

description: Control

value: Bone marrow derived mesenchymal stem cells


title: Physioxia Hepatocyte 2

city: Boston

first: Zachary

last: Rogers

address: 360 Huntington Avenue

department: Chemical Engineering

institute: Northeastern University

data_processing:
Trimmomatic
FastQC
STAR alignment
FeatureCounts Counts
Assembly: GRCh38.p14
Supplementary files format and content: tab delimited text file for each sample, with raw counts

source_name: hepatocytes

extract_protocol:
Nucleospin RNA, Macherey Nagel
NEBNext Ultra II RNA Library Prep for Illumina, New England Biolabs

value: hepatocytes

value: Primary

value: Lonza (HUCPG)

value: 36h 7% O2 culture


title: GRfloxcontrol-rep4

value: Male

value: 4-6 corneas (pooled)

value: 3 months


title: 12 HUVEC TGF DAY7

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software (version 5.0.1).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human umbilical vein

growth_protocol: HUVECs were maintaned until passage 4 in M199 medium supplemented with 20% FBS, 2 mM L-glutamine, penicillin and endothelial cell growth factor supplements.

extract_protocol:
Freshly collected umbilical cords were digested by infusing in the vein a collagenase solution (0.2% collagenase in 0.9% NaCl and 2 mM CaCl2) for 13 min. Subsequently, ECs were collected by flushing the vein with medium. The cell supsension was then filtered through a 40 μm cell strainer and pelleted by a 5 min centrifugation at 1000 RPM before being resuspended into a pre-coated flask with 0.1% gelatin. The day after ECs were washed with PBS and maintained in culture until passage 4.
Library was performed according to te manufacterer's instructions (single cell v3.1, 10x Genomics).

treatment_protocol: HUVECs were treated with 10 ng/ml TGF-b1 or vehicle for 7 days. ERG silencing and SNAI overexpression were obtained by lentiviral transduction (10 MOI). HUVECs were transduced overnight and re-fed with fresh medium the next day. Transduced cells were sequenced and used in functional assays 4 days after transduction.

value: human umbilical vein

value: HUVEC donor 936

value: endothelial cells

tag: disease state

value: healthy donor

value: mesenchymal transdifferentation by TGF-b treatment


title: Physioxia Hepatocyte 3


title: Physioxia Hepatocyte 1


title: 11 HUVEC CTL DAY7

description: 10x Genomics

value: control untreated


title: GRfloxcontrol-rep3

value: GRloxP/loxP-PAX6+/+ (GRflox)


title: Normoxia Hepatocyte 3

value: 36h normoxic culture


title: 10 HUVEC TGF DAY7

description: 10x Genomics

value: HUVEC donor 941


title: Normoxia Hepatocyte 2


data_processing:
Quality control of raw reads (fastq files) was carried out using FastQC (Galaxy Version 0.73+galaxy0)
Sequence reads were trimmed for adaptor sequence using Cutadapt (Galaxy Version 4.0+galaxy0) tool
Trimmed reads were aligned to human reference genome with HISAT2 (Galaxy Version 2.2.1+galaxy0)
Read count extraction and normalization were performed using CLC genomic benchwork
Reads overlapping with exons were assigned to genes using FeatureCounts (Galaxy Version 2.0.1+galaxy2)
Differential gene expression analysis was completed using DESeq2 (Galaxy Version 2.11.40.7+galaxy1)
Assembly: assembly GRCh38.p13-v.34
Supplementary files format and content: tabular file include normalized counts for each Sample

source_name: neutrophils

extract_protocol:
Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.
Total RNA-Seq libraries were constructed from 150 ng of total RNA, using Zymo-Seq RiboFree Total RNA Library Kit according to manufacturer’s instructions.

value: neutrophils

value: infected


title: hMSCs 1:1 MoS2 2

description: 1:1 MoS2 treatment

value: Bone marrow derived mesenchymal stem cells


title: hMSCs 1:6 MoS2 1

description: 1:6 MoS2 treatment


title: 9 HUVEC CTL DAY7

description: 10x Genomics


title: hMSCs 1:1 MoS2 1

description: 1:1 MoS2 treatment


title: GRfloxcontrol-rep1


title: 8 HUVEC SNAIOE

description: 10x Genomics

value: mesenchymal transdifferentation by SNAI1 overexpression (transduced with SNAIOE)


title: Male_WT-vehicle-rep4

extract_protocol:
Total RNA was isolated from the corneas of mice using Trizol-chloroform based extraction and then RNA purification using RNeasy column (Qiagen) according to the manufacturer’ protocols.  Each experimental group had 4 replicates, where each replicate had 4-6 corneas pooled into one sample.
Indexed samples were sequenced using the 75bp pair-end protocol using the Illumina NextSeq500 sequencer as per the manufacturer’s protocol. Reads greater than 40 million reads per sample were aligned to the reference genome UCSC mm9.

treatment_protocol: Male wild-type C57BL/6J mice that were 8 weeks old were adrenalectomized (ADX) to remove endogenous glucocorticoids.  Approximately 4 weeks after the surgery, mice were treated with dexamethasone eye drops or vehicle eye drops for 6 hours.  Mice were euthanized, eyes removed, and total RNA was isolated from the whole cornea.

tag: timepoint

value: 6 hour

value: vehicle eye drops

value: wild-type mice (adrenalectomized)


title: Normoxia Hepatocyte 1

value: hepatocytes

value: Primary

value: Lonza (HUCPG)


title: Male_WT-vehicle-rep3

value: Male

value: 4-6 corneas (pooled)


title: Uncultured Hepatocyte 3


title: Male_WT-vehicle-rep2


title: 7 HUVEC pRRL-empty

description: 10x Genomics

value: human umbilical vein

value: HUVEC donor 936

value: endothelial cells

value: healthy donor

value: control transduced with empty vector


value: neutrophils


title: Uncultured Hepatocyte 2


title: 6 HUVEC shERG

description: 10x Genomics

value: mesenchymal transdifferentation by ERG silencing (transduced with shERG)


title: Male_WT-vehicle-rep1


title: neutrophils, uninfected, subject 08

value: uninfected


title: Uncultured Hepatocyte 1


title: 5 HUVEC PLKO-empty

description: 10x Genomics


title: HTN-input H3K9bu

city: Beijing

first: Hui

last: Wang

address: No.2 Yabao Road, Chaoyang District

department: Department of Cardiology

country: China

institute: Children’s Hospital, Capital Institute of Pediatrics

data_processing:
SOAPnuke filter-l 15-q 0.1-n 0.1 -Q 2-c 21 is used to filter raw data
Aligner /SOAP2 Aligner Clean data with the genome sequence of the target species
Peaks were called using MACS2 with p-value < le-05
ChIP-seq data was visualized using the UCSC Genome Browser
The MAnorm method was used to quantitatively compare the ChIP-Seq datasets between samples
Assembly: bw files were generated using the genomic Rangers R package. NarrowPeak files were generated using MACS with default settings
Supplementary files format and content: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: bw, bed (except for input samples)

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
25 mg of mixed kidney tissues were fixed with 1.5% formaldehyde for 20 minutes. After quenching and cell lysis, the chromatin was digested with micrococcal nuclease and sonicated with ultrasonicator
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10ng of DNA was used as starting material for input and ip samples. Post amplification libraries were sized selected at 100-300bp in length using Agencourt AMPure XP beads.

treatment_protocol: Rats in the NC group received ordinary rat maintenance chow, and rats in the HTN group were fed a high-fat diet

value: kidney

value: input

tag: diet

value: High fat diet


title: Male_WT-dex-rep4

value: 6 hour

value: dexamethasone eye drops

value: wild-type mice (adrenalectomized)


title: 4 HUVEC SNAIOE

description: 10x Genomics

value: HUVEC donor 941

value: mesenchymal transdifferentation by SNAI1 overexpression (transduced with SNAIOE)


title: HTN H3K9bu

value: H3K9bu (ab241248, Abcam)


title: Male_WT-dex-rep3

value: Male

value: 4-6 corneas (pooled)


title: neutrophils, uninfected, subject 07


title: 3 HUVEC pRRL-empty

description: 10x Genomics

value: human umbilical vein

value: endothelial cells


title: NC-input H3K9bu

value: rat maintenance chow


title: Male_WT-dex-rep2


title: 2 HUVEC shERG

description: 10x Genomics

value: healthy donor


title: NC H3K9bu


title: Male_WT-dex-rep1


title: 1 HUVEC PLKO-empty

description: 10x Genomics

value: control transduced with empty vector


title: neutrophils, uninfected, subject 02

value: neutrophils

value: uninfected


title: neutrophils, uninfected, subject 05


value: infected


title: NEJF10-3D-Nor-02

status: Public on Jun 26 2024

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
The ATAC-seq raw reads were aligned to the mouse reference genome (mm10) using BWA (version 0.7.12-r1039) to and then removed duplicated reads with Picard (version 1.65), with only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) .  Reads mapping to mitochondrial DNA were excluded from the analysis. All mapped reads were offset by +4 bp for the + strand and -5 bp for the  – strand.
Nucleosome free reads was used  to generate bigwig files and call eanriched regions. MACS2 (version 2.2.7.1) parameters are  “-q 0.01 –nomodel –extsize 200 –shift 100 -f BEDPE --keep-dup all”.
Assembly: GRCm38(mm10)
Supplementary files format and content: narrowPeak

growth_protocol: NEJF10 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum, 1% L-Glutamine, and 1% Penicillin/Streptomycin at 37 °C in an atmosphere of 5% CO2 with 21% oxygen or 1% oxygen.

extract_protocol:
Fresh cultured NEJF10 cells (100,000 per sample) under different culture conditions were harvested and washed with 150µl cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing protease inhibitor (PI). Nuclei were collected by centrifuging at 500 g for 10 minutes at 4°C after cell pellets were resuspended in lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 containing 0.1% NP-40 and PI. Nuclei were incubated with Tn5 transposon enzyme in transposase reaction mix buffer (Illumina) for 30 min at 37°C. DNAs were purified from transposition sample by using Min-Elute PCR purification kit (Qiagen, Valencia, CA) and measured by Qubit.
Polymerase chain reaction (PCR) was performed to amplify with High-Fidelity 2X PCR Master Mix [72°C/5mins+ 98 °C /30 s +12 × (98 °C /10 s + 63 °C /30 s + 72 °C /60 s) + 72 °C /5 min]. The libraries were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA). ATAC-seq libraries followed by pair-end sequencing on HiSeq4000 (Illumina) in the Hartwell Center at St Jude Children's Research Hospital.

treatment_protocol: NEJF10 cells were cultured in 21% and 1% oxygen in monolayer, or 21% oxygen in 3D spheroid.

value: HB

value: 3D Culture with 21% O2


title: NEJF10-3D-Nor-01


title: NEJF10-2D-Nor-02

value: Culture with 21% O2


title: NEJF10-2D-Nor-01


title: NEJF10-2D-Hyp-01

value: Culture with 1% O2


title: NEJF10-2D-Hyp-02


title: 293T Cell, DMSO, Repeat 3

city: Shenzhen

first: Canrong

last: Li

state: Guangdong

address: No.66,Gongchang Road,Guangming District,Shenzhen,Guangdong 518107,P.R.Chinan

institute: Sun yet-sen University

data_processing:
Data filtering  The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification  Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: hg38
Supplementary files format and content: tab-delimited text file  includes raw counts for each Sample

source_name: kidney; Embryo

growth_protocol: 293T cells were mantained in DMEM suppllemented with 10% fetal bovine serum (FBS) and antbiotics in humidfied atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with standard TRIZOL protocol.
2.1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2.2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
2.3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
2.4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
2.5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
2.6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
2.7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
2.8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
2.9 Sequencing

treatment_protocol: Cells were treated with DMSO or Panobinostat (10μM) for 12h.

value: kidney; Embryo

value: epithelial-like cell from kidney

value: WT

value: DMSO


title: 293T Cell, DMSO, Repeat 1


title: 293T Cell, Panobinostat, Repeat 1

value: Panobinostat


title: 293T Cell, Panobinostat, Repeat 3


title: neutrophils, uninfected, subject 06


title: 293T Cell, DMSO, Repeat 2


title: 293T Cell, Panobinostat, Repeat 2


title: GMP cells, Control mouse,rep4

city: Tianjin

first: Yu

last: Liu

state: -- None selected --

address: 288 Nanjing Road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Hisat2 (v 2.0.5) was utilized for sequencing reads mapping to mm10.
Read count extraction was performed using featureCounts (v1.5.0-p3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: bone marrow

growth_protocol: Mice LT-HSC cells and GMP cells were maintained in DMEM with 2% FBS before and after cell sorting.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (QIAGEN).
The sequencing libraries were prepared with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa) and the SMARTer® Stranded RNA-Seq Kit (TaKaRa).

treatment_protocol: Poly[I:C] was administered by intraperitoneal injection at a dose of 5 mg/kg every other day for 4 doses to activate Mx1-Cre recombinase to induce Runx1-Runx1t1 expression. LT-HSCs and GMPs were sorted from mouse bone marrow.

value: bone marrow

value: GMP cells

tag: library type

value: mRNA


title: GMP cells, Control mouse,rep1


title: GMP cells, Control mouse,rep3


title: GMP cells, Control mouse,rep2


title: GMP cells, AML1/ETO mouse, rep3


title: GMP cells, AML1/ETO mouse, rep1


title: LT-HSC cells, Control mouse,rep4

value: LT-HSC cells


title: LT-HSC cells, Control mouse,rep3


title: LT-HSC cells, Control mouse,rep2


title: LT-HSC cells, Control mouse,rep1


title: LT-HSC cells, AML1/ETO mouse, rep3


title: LT-HSC cells, AML1/ETO mouse, rep2


title: LT-HSC cells, AML1/ETO mouse, rep1


title: human acral lentiginous melanoma tumor tissue [244-C]

city: Nanjing

first: Cuicui

last: Tian

address: Jiangwangmiao Road 12#

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 1 7 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.  Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 6 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: tumor tissue

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA from ALM, paired para-cancer tissues and melanoma cell lines was extracted using TRIzol® (Invitrogen; Thermo Fisher Scientific, Inc.). NanoDrop ND-1000 was then used to measure the quality and concentration of RNA. RNA integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: The tumor tissues and paired para-cancer tissues were cut into tissue blocks with a diameter of ＜ 0.5cm, reaching the depth of the adipose layer. Tissues were quickly placed into frozen tubes (Corning, Inc.) containing 1mL RNAlater TM solution (Thermo Fisher Scientific, Inc. ). These samples were stored in a liquid nitrogen tank at -183˚C.

value: tumor tissue

value: female


title: human acral lentiginous melanoma para-cancer tissue [255-S]

source_name: para-cancer tissue

value: male


title: human acral lentiginous melanoma para-cancer tissue [298-S]


title: human acral lentiginous melanoma para-cancer tissue [317-S]


title: human acral lentiginous melanoma para-cancer tissue [244-S]


title: human acral lentiginous melanoma tumor tissue [275-C]


title: human acral lentiginous melanoma tumor tissue [255-C]


title: human acral lentiginous melanoma tumor tissue [271-C]


title: human acral lentiginous melanoma tumor tissue [317-C]


title: human acral lentiginous melanoma para-cancer tissue [271-S]


title: human acral lentiginous melanoma para-cancer tissue [275-S]


title: human acral lentiginous melanoma tumor tissue [298-C]


title: GFP20 CM 1

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-20

data_processing:
Reads were trimmed using Cutadapt v2.3.
Quality control was performed using FastQC version 0.11.8.
Reads were mapped to the reference genome GRCm38 (ENSEMBL) using STAR version 2.7.8a and assigned count estimated to genes with RSEM version 1.3.3.
Alignment options followed ENCODE standards for RNAseq.
Assembly: GRCm38
Supplementary files format and content: raw counts for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (#74134, QIAGEN) following the manufacturer’s protocol.
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files.

value: cell line

value: GFP 20

value: Pancreatic fibroblast

tag: experimental batch

value: Batch 1


title: GFP20 CM 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-21

value: Batch 2


title: GFP20 NT 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-19

value: DMEM

value: Batch 3


title: GMP cells, AML1/ETO mouse, rep2


title: KO16 CM 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-16

value: IL33 KO 16

value: Batch 4


title: KO16 NT 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-13


title: KO16 NT 1

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-12


title: KO16 CM 1

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-15


title: GFP20 NT 1

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-17


title: KO14 CM 1

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-9

value: IL33 KO 14


title: GFP1 NT 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-3

value: GFP 1


title: GFP1 CM 1

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-4


title: KO14 NT 1

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-6


title: GFP1 NT 1

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-2


title: KO14 NT 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with DMEM + 1%FBS + 1% penstrep + doxycycline (1 µg/mL). Cells were harvested for RNA 24h after treatment.
7187-KD-7


title: GFP1 CM 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-5


title: KO14 CM 2

description:
Cells were plated in DMEM + 10%FBS + 1% penstrep and left to adhere overnight. The following day, cells were washed and treated with 50% DMEM + 1%FBS + 1% penstrep & 50% low-serum(1%) 9805 CM. Cells were harvested for RNA 24h after treatment.
7187-KD-10


title: iKrasG12D;Trp53R172H/+ 15 weeks ON + 1 week OFF 2

description: iKrasG12D;Trp53R172H/+ (Ptf1a-Cre;TetO-KrasG12D;Rosa26rtTa/+;Trp53R172H/+) mice were provided doxycycline chow (1.0 gm/kg, #F3949, Bio-Serv) to induce KrasG12D. Mice were aged to 14 weeks and then harvested (“14-week KrasG12D ON”) or remained on doxycycline chow to 15 weeks before being switched back to regular diet for an additional week before harvesting pancreata (“15-week KrasG12D ON + 1-week KrasG12D OFF”). 1 female mouse was sequenced in this submission.

data_processing:
The University of Michigan Advanced Genomics Core performed processing and alignment of the raw data using Cell Ranger (versions 2.2.0-6.1.2 depending on date of sequencing) with default settings and an initial expected cell count of 10,000.
Assembly: mm10, mm10-2020-A, mm10-2020-A_EGFP, mm10-3.0.0, mm10-GFP-3.0.0
Supplementary files format and content: Raw and filtered Cell Ranger outputs

source_name: PanIN pancreas

extract_protocol:
To prepare tissues for sequencing, samples were disrupted to single cell suspension by mechanically mincing the tissue, followed by enzymatic digestion with Collagenase V (1 mg/mL in RPMI, #C9263, Sigma-Aldrich) at 37°C for 30 min under constant shaking. After digestion, suspensions underwent serial filtration through 500 µm, 100 µm, and 40 µm mesh cell strainers. We then enriched for live cells using the MACS Dead Cell Removal Kit (#130-090-101, Miltenyi Biotec). The resulting single cell suspensions were brought to the University of Michigan Advanced Genomics Core for cDNA library preparation and sequencing.
Samples were run using 50-cycle paired-end reads on the HiSeq 4000 (Illumina) or NovaSeq 6000 (Illumina) to a depth of 100,000 reads.

value: PanIN pancreas

tag: number of_mice_pooled

tag: cell ranger_version

tag: genome

tag: run date


title: iKrasG12D 5 weeks ON + 3 days OFF

description: KrasG12D expression in the pancreatic epithelium was induced in adult iKrasG12D (Ptf1a(aka p48)-Cre;TetO-KrasG12D;Rosa26rtTa/+) mice (8-14 weeks of age) by supplementing 5% sucrose water with doxycycline (0.2 g/L, #D9891, Sigma-Aldrich). After maintaining mice on doxycycline water for 3-4 days, acute pancreatitis was induced via intraperitoneal injection of caerulein (75 μg/kg, #C9026, Sigma-Aldrich) 8 times a day for 2 days. Mice were then aged for 5 weeks after the last day of caerulein, at which point a cohort of mice was randomly selected to switch from doxycycline water to regular water, thus terminating the expression of KrasG12D. After 3 additional days of doxycycline (“5-week KrasG12D ON”) or regular water (“5-week KrasG12D ON + 3-day KrasG12D OFF”), animals were sacrificed and pancreata were collected. 1 male and 1 female mouse were pooled for this submission.

tag: tissue

tag: genotype


title: iKrasG12D;Trp53R172H/+ 14 weeks ON 2

description: iKrasG12D;Trp53R172H/+ (Ptf1a-Cre;TetO-KrasG12D;Rosa26rtTa/+;Trp53R172H/+) mice were provided doxycycline chow (1.0 gm/kg, #F3949, Bio-Serv) to induce KrasG12D. Mice were aged to 14 weeks and then harvested (“14-week KrasG12D ON”) or remained on doxycycline chow to 15 weeks before being switched back to regular diet for an additional week before harvesting pancreata (“15-week KrasG12D ON + 1-week KrasG12D OFF”). 2 female mice were pooled for this submission.


title: iKrasG12D 5 weeks ON

description: KrasG12D expression in the pancreatic epithelium was induced in adult iKrasG12D (Ptf1a(aka p48)-Cre;TetO-KrasG12D;Rosa26rtTa/+) mice (8-14 weeks of age) by supplementing 5% sucrose water with doxycycline (0.2 g/L, #D9891, Sigma-Aldrich). After maintaining mice on doxycycline water for 3-4 days, acute pancreatitis was induced via intraperitoneal injection of caerulein (75 μg/kg, #C9026, Sigma-Aldrich) 8 times a day for 2 days. Mice were then aged for 5 weeks after the last day of caerulein, at which point a cohort of mice was randomly selected to switch from doxycycline water to regular water, thus terminating the expression of KrasG12D. After 3 additional days of doxycycline (“5-week KrasG12D ON”) or regular water (“5-week KrasG12D ON + 3-day KrasG12D OFF”), animals were sacrificed and pancreata were collected. 2 male mice were pooled for this submission.


title: iKrasG12D;Trp53R172H/+ 14 weeks ON 1


title: KC PanIN 2

description: KC mice were treated with caerulein i.p. once a day for 5 days ((250 μg/kg, #C9026, Sigma-Aldrich)). Mice were aged for 3 weeks post-caerulein before pancreata were harvested and submitted for sequencing. 2 female mice were pooled in this submission.

value: Ptf1a-Cre; LSL-KrasG12D

value: Jan. 2022 YZ


title: Pdgfra-CreERT2/+ OT

description: Mice were treated with 4 mg/day tamoxifen for 5 days via oral gavage. Three days later, mice were then orthotopically injected with 50k syngeneic KPC cells (cell line 7940b). Tumors were allowed to grow for 3 weeks before harvest. 1 male and 1 female tumor were pooled for this submission.

source_name: Orthotopic pancreas tumor

value: Orthotopic pancreas tumor

value: Jan. 2022 KLD


title: Pdgfra-CreERT2/+;Il33f/f-eGFP OT


title: KC PanIN 1

description: 1 female KC mouse was treated with caerulein i.p. for 1 day (8 hourly injections (75 μg/kg, #C9026, Sigma-Aldrich)). Mouse was aged for 11 weeks-post caerulein; pancreas was harvested and sequenced.


title: Spleen, Naïve B, KO2

city: New Haven

first: Anis

last: Barmada

state: CT

address: 300 Cedar Street

department: Department of Immunobiology

institute: Yale University

description:
Naive_Normalized_Counts.txt
11_282_295_S11

data_processing:
Sequence reads were run using STAR, mapped to the reference genome (mm10), and read counts were extracted and normalized.
Assembly: mm10
Supplementary files format and content: Normalized counts txt files [counts per million (CPM)]

source_name: Spleen

extract_protocol:
Cells were sorted into complete RPMI based on the markers listed in the sample metadata. Cells were spun down and then RNA was extracted using a Qiagen micro or mini kit.
Library construction was completed by the Yale Center for Genomic Analysis following a standard workflow.

treatment_protocol: Mice were immunized with 100L PBS washed SRBC IP and tissues were harvesed at day 28.

value: Spleen

value: Naive B (CD3-/B220+/IgD+)

value: Pik3cg Knockout

value: SRBC Immunization


title: Spleen, Naïve B, WT2

description:
Naive_Normalized_Counts.txt
8_223_354_S8

value: Wild type


title: BM, ASC, WT1

description:
BMPC_Normalized_Counts.txt
13_258_319_S13

source_name: Bone Marrow

value: Bone Marrow

value: Antibody secreting cell (CD138+)


title: BM, ASC, WT3

description:
BMPC_Normalized_Counts.txt
15_234_343_S15


title: Spleen, Naïve B, KO3

description:
Naive_Normalized_Counts.txt
12_270_307_S12


title: BM, ASC, WT2

description:
BMPC_Normalized_Counts.txt
14_246_331_S14


title: Spleen, Naïve B, WT3

description:
Naive_Normalized_Counts.txt
9_211_366_S9


title: Spleen, Naïve B, KO1

description:
Naive_Normalized_Counts.txt
10_199_378_S10


title: Spleen, ASC, WT3

description:
SPPC_Normalized_Counts.txt
3_283_294_S3


title: Spleen, ASC, WT2

description:
SPPC_Normalized_Counts.txt
2_200_377_S2


title: Spleen, ASC, WT1

description:
SPPC_Normalized_Counts.txt
1_212_365_S1


title: Spleen, GC, WT3

description:
GCB_Normalized_Counts.txt
W2_069_124_S1

value: GC B Cell (CD95+/GL7+)


title: iKrasG12D;Trp53R172H/+ 15 weeks ON + 1 week OFF 1

description: iKrasG12D;Trp53R172H/+ (Ptf1a-Cre;TetO-KrasG12D;Rosa26rtTa/+;Trp53R172H/+) mice were provided doxycycline chow (1.0 gm/kg, #F3949, Bio-Serv) to induce KrasG12D. Mice were aged to 14 weeks and then harvested (“14-week KrasG12D ON”) or remained on doxycycline chow to 15 weeks before being switched back to regular diet for an additional week before harvesting pancreata (“15-week KrasG12D ON + 1-week KrasG12D OFF”). 2 male and 1 female mouse were pooled for this submission.


title: Spleen, GC, KO3

description:
GCB_Normalized_Counts.txt
KO3_367_210_S276


title: Spleen, Naïve B, WT1

description:
Naive_Normalized_Counts.txt
7_235_342_S7


title: Spleen, GC, WT1

description:
GCB_Normalized_Counts.txt
W1_381_196_S259


title: Spleen, GC, KO1

description:
GCB_Normalized_Counts.txt
KO1_296_281_S274


title: LN, Lane 2, CITE

description:
10x Genomics, CITE
TotalSeq-CITE-barcodes-to-genotype.csv

data_processing:
The single-cell sequencing data were aligned and processed using 10X CellRanger and CellRanger vdj.
Assembly: mm10 mouse reference genome
Supplementary files format and content: CellRanger output files: gene expression (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) and BCR annotations (filtered_contig_annotations.txt); additionally, table matching cell barcodes to mouse genotype (TotalSeq-CITE-barcodes-to-genotype.csv).

source_name: Lymph node

extract_protocol:
Cells from draining lymph nodes were subjected to pan B cell isolation (Stemcell) negative selection kit with supplemental biotin-IgD antibody to enrich for switched B cells. Enriched cells (70% of total) were mixed back to untouched mixture (30% of total). Mixtures were barcoded with mouse TotalSeqTM-C (BioLegend). Cells were submitted to the Yale Center for Genome Analysis for sequencing following standard protocol.
cDNA libraries for gene expression and BCR sequencing were generated according to manufacturer’s instructions (Chromium Next GEM SingleCell V(D)J Reagent Kits). Each library was then sequenced on an Illumina NovaSeq 6000 platform.

value: Lymph node

value: Immune

value: WT & Pik3cg KO


title: Spleen, GC, KO2

description:
GCB_Normalized_Counts.txt
KO2_379_198_S275


title: LN, Lane 1, CITE


title: LN, Lane 2, BCR

description: 10x Genomics, BCR


title: LN, Lane 2, GEX

description: 10x Genomics, GEX


title: BMP4_6d_rep3

city: Shanghai

first: Sutong

address: No. 500 Zhennan Road, Putuo District

institute: Tongji university

data_processing:
The quality of the raw reads in fastq format were investigated using fastp (version 0.19.7). Paired-end clean reads were aligned to the mm39 genome using HISAT2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Mouse neural stem cells

growth_protocol: NSCs were isolated from the SVZs of adult C57BL/6 mice (2 female mice and 2 male mice were used for one cell isolation experiment) aged 8-9 weeks after euthanasia, which refer to the protocols described elsewhere (Walker and Kempermann, 2014; Leeman et al., 2018).  And then the cells were maintained in vitro in proliferation medium, which was Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 medium (DMEM/F12, Gibco, 11330032) supplemented with 1% penicillin streptomycin glutamine (P/S, Thermo, 10378016), 2% B27 minus vitamin A (Gibco, 12587-010), and the growth factors EGF and bFGF (R&D Systems, 20 ng/ml each).

extract_protocol:
Total RNA was extracted from samples (1×106 cells for one sample) using Trizol, and then the RNA qualification and qualification was determined by RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA was prepared into cDNA and fragmented into 370~420 bp in length. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Final libraries were prepared using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions, and them the library preparations were sequenced on an Illumina NovaSeq 6000 platform (illumine, USA).

treatment_protocol: NSCs obtained after at least three passages were cultured in adherent in the dish treated with poly-L-ornithine (Sigma, P3655) and laminin (Sigma, L2020) in proliferation medium with bFGF/EGF. After 16-18h, the medium were changed into quiescence media (DMEM/F12, 2% B27, 1% P/S, 20ng/ml bFGF (R&D Systems, 3139-FB-025), and 20 ng/ml BMP4 (R&D Systems, 5020-BP-010)) and BMP4-induced media ((DMEM/F12, 2% B27, 1% P/S, and 20ng/ml BMP4 (R&D systems)), and the cells were cultured for another six days

value: Mouse neural stem cells

tag: time


title: BMP4_6d_rep2

tag: cell type


title: bFGF_BMP4_6d_rep2

tag: treatment


title: BMP4_6d_rep1


title: bFGF_BMP4_6d_rep3


title: bFGF_BMP4_6d_rep1


title: bFGF_EGF_0d_rep3

value: bFGF/EGF


title: bFGF_EGF_0d_rep1


title: Spleen, GC, WT2

description:
GCB_Normalized_Counts.txt
W3_357_220_S261