title: CHLA01/SMYD3 E5Del-Myc cell line_RNA-seq rep3

city: St. Petersburg

first: Rudrmani

last: Pokhrel

state: United States

address: 600 Fifth Street S.

department: Oncology

institute: Johns Hopkins All Children’s Hospital

data_processing:
Demultiplexing:  bcl2fastq v2.20
Filtering and QC: FastP v0.20.1
Mapping to Genome: STAR v2.4.2a
Gene Count Matrix:  featureCounts v2.0.1
Differential Analysis: DESeq2 v1.34.0
Genome_build: Human 38 (GRCh38.p13)
Supplementary_files_format_and_content: CSV file of 2D matrix of gene count vs samples

source_name: Medulloblastoma cell line

growth_protocol: CHLA-01-MED (hereafter CHLA01) cell line was purchased from American Type Culture Collection (ATCC). Cells were cultured in DMEM/F-12 medium supplemented with B-27 supplement (Invitrogen, Carlsbad, CA, USA), 20 ng/ml EGF (R&D Systems, Minneapolis, MN, USA) and 20 ng/ml bFGF (R&D Systems, Minneapolis, MN, USA) in a humidified incubator at 37°C in 5% CO2.

extract_protocol: RNA-Seq libraries were prepared using Truseq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA) with 1 ug of total RNA.

tag: cell type

value: Human medulloblastoma cell line

tag: sample type

value: Group 4


title: 5R

status: Public on Oct 31 2022

type: SRA

city: Loughborough

first: Gabriel

last: Castrillo

address: Nr Loughborough

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

library_source: transcriptomic

data_processing:
For the analysis of the RNASeq data, reads were first subjected to quality control and filtering via fastp v0.20.1 (59). The resulting high-quality reads were pseudo-aligned to the Arabidopsis thaliana genome deposited in the Ensembl Plants version 52, using salmon v1.6.0 (60). Gene level summarization from the salmon quantification was performed with the tximport function from the tximport v.1.22.0 R package (50).
Assembly: Ensembl Plants version 52
Supplementary files format and content: Gene level summarization from the salmon quantification

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
RNA was extracted from plant roots following Logemann et al.
RNA libraries were prepared following Finkel et al. with modification

tag: tissue

value: Root

tag: genotype

value: Col 0

tag: treatment


title: cervical cancer-Tanshinone I-rep1

city: YangZhou

first: Shuna

last: Cui

state: JiangSu

address: Jiang Yang Middle Road 136,

department: Medical College of Yangzhou University

country: China

institute: YangZhou university

description:
TanI_1
Replicate 1 of Hela cells treated by Tanshinone I for 5 hours.
Raw_gene_counts_matrix.txt
FPKM_matrix.txt

data_processing:
RNA quality was evaluated and sequenced using Illumina Hiseq X ten platform in GeneChem, raw data from the sequencer were first underwent quality control using FastQC.
Reads are treated using trim_galore, where Illumina adapter sequence and low quality (phred score <20) at the 3’ end were trimmed, and the paired reads were removed if any of the two reads doesn’t meet the minimum length (20bp).
Duplicates in all data samples are removed using Picard. For each sample, we count the reads hitted on each transcript using htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM_matrix.txt: Matrix table with FPKM values for every gene and every sample.
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

organism: Homo sapiens

source_name: human cervical cancer

growth_protocol: HeLa Cells were cultured in the DMEM medium with 10% FBS, penicillin (100 units/ml) and streptomycin (100 µg/ml) in the incubator with 37°C and 5% CO2.

extract_protocol:
Cells were washed with PBS, and Trizol reagent was added. Total RNA of different treatment was isolated by RNeasy Plus Mini Kit according to the manufacturer's instruction (Qiagen, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HeLa Cells were treated with genistein (50 μM) or Tanshinone I (50 μM) and the same amount of solvent control (DMSO) for 5 h, respectively.

tag: cell line

value: HeLa

value: 50 uM Tanshinone I


title: 59R

value: NB


title: du145_DU145PS2B_B09_Foretinib_0.225_24

city: New York City

first: Alessandro

last: Vasciaveo

state: NY

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

country: USA

institute: Columbia University

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Assembly: hg38
Supplementary files format and content: 2 semicolon delinated text files (for 2 cell-lines) with raw gene counts for every gene and every sample

source_name: prostate cancer

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.

value: Foretinib

tag: provider

value: ATCC

tag: vendor id

tag: age

tag: Sex

value: male


title: CHLA01/SMYD3 E5Del-Myc cell line_RNA-seq rep2


title: 58R


title: du145_DU145PS2B_B08_KW2449_0.25_24


title: 57R


title: 62R

value: arf7 arf19


title: 66R


title: CHLA01/SMYD3 E5Del-Myc cell line_RNA-seq rep1


title: 65R


title: 56R


title: 55R


title: 54R


title: 53R


title: CHLA01/SMYD3-Myc cell line RNA-seq rep2


title: du145_DU145PS2B_B06_AZD1480_0.13_24


title: 61R


title: du145_DU145PS2B_B05_Saracatinib_1_24

value: Saracatinib


title: du145_DU145PS2B_B04_Cyclophosphamide_10_24

value: Cyclophosphamide


title: CHLA01/SMYD3-Myc cell line RNA-seq rep1


title: 51R


title: CHLA01/IT1 del cell line_RNA-seq rep3


title: du145_DU145PS2B_B03_Dacarbazine_10_24

value: Dacarbazine


title: 49R


title: CHLA01/IT1 del cell line_RNA-seq rep2


title: 52R


title: 48R


title: du145_DU145PS2B_B02_DMSO__24

value: DMSO


title: CHLA01/SMYD3-Myc cell line RNA-seq rep3


title: 64R


title: du145_DU145PS2B_B01_Melphalan_1_24

value: Melphalan


title: du145_DU145PS2B_B07_Motesanib_1_24

value: Motesanib


title: 47R


title: 4R


title: 45R


title: CHLA01/IT1 del cell line_RNA-seq rep1

value: Human medulloblastoma cell line


title: 46R


title: 44R


title: 43R


title: CHLA01/vo cell line_RNA-seq rep3

value: Group 4


title: 42R

value: Root


title: 41R

value: Col 0


title: du145_DU145PS2B_A12_Megestrol_0.045_24

value: Megestrol


title: du145_DU145PS2B_A11_Axitinib_0.14_24

value: Axitinib


title: CHLA01/vo cell line_RNA-seq rep2


title: 50R


title: 40R


title: du145_DU145PS2B_A10_SB743921_0.075_24


title: 39R


title: CHLA01/vo cell line_RNA-seq rep1


title: 3R

value: NB


title: 38R


title: du145_DU145PS2B_A09_MK2206_1_24


title: 37R


title: 8y_snRNAseq

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

description:
nuclear RNA
same donor as RL1994

data_processing:
cellranger mkfastq with Cellranger v3.1 to generate fastq files as inout for count pipeline.
cellranger count with Cellranger v3.1 to generate feature-barcode matrices of gene expression.
cellranger-atac mkfastq with Cellranger-ATAC v1.2 to generate fastq files as input for count pipeline.
cellranger-atac count with Cellranger-ATAC v1.2 to generate BED-like tabular file with contains frgaments captured by the assay and barcode information in single cell output tables.
Genome_build: hg19
Supplementary_files_format_and_content: For snRNA-seq data: feature-barcode matrices in HDF5 format containing every barcode from the fixed list of known-good barcode sequences that has at least 1 read for raw_feature files, or only containing detected cellular barcodes for filtered_feature files. For snATAC, a BED-like tabular fragment file with each line representing a unique ATAC-seq fragment captured by the assay,  an index for the fragments file as well as a singlecell file containing cell barcodes, QC information and ATAC signal.

source_name: prefrontal cortex, BA9

extract_protocol:
Per sample, 50 mg of frozen brain tissue was lysed and nuclei extracted. Nuclei were then either enriched by DAPI-positive FANS for single cell gene expression library generation or cleaned with a sucrose gradient centrifugation for single cell ATAC library generation.
10X Genomics 3' Single Cell Gene Expression v2/v3 , 10X Genomics Single Cell ATAC
snRNA-seq, snATAC-seq

value: brain


title: 33R


title: 34R


title: du145_DU145PS2B_A06_Bardoxolone Methyl_0.5_24

value: Bardoxolone Methyl

value: ATCC


title: 32R


title: 35R


title: 30R


title: du145_DU145PS2B_A08_Cinacalcet_2_24

value: Cinacalcet

value: male


title: 2m_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: 2y_a_snRNAseq

description:
nuclear RNA
no paired snATAC data

source_name: prefrontal cortex, BA8


title: 31R


title: 2R


title: du145_DU145PS2B_A04_Vorinostat_0.5_24

value: Vorinostat


title: 29R


title: 28R


title: du145_DU145PS2B_A05_FK866_0.00205_24


title: 1m_snRNAseq

description:
nuclear RNA
no paired snATAC data


title: du145_DU145PS2B_A03_Erlotinib_3_24

value: Erlotinib


title: 27R


title: 25R


title: du145_DU145PS2B_A02_DMSO__24

value: DMSO


title: 26R


title: 23R


title: 24R


title: 36R


title: 2y_b_snRNAseq

description:
nuclear RNA
same donor as RL1784


title: du145_DU145PS2B_A01_Mechlorethamine_1_24

value: Mechlorethamine


title: 22R


title: 222R


title: du145_DU145PS2B_A07_Alpelisib_0.37_24

value: Alpelisib


title: 221R


title: 220R


title: 21R


title: du145_DU145PS2A_H12_Dactinomycin_0.00265_24

value: Dactinomycin


title: du145_DU145PS2A_H10_Rigosertib_0.075_24

value: Rigosertib


title: 218R

value: Root


title: 215R


title: du145_DU145PS2A_H9_MK1775_0.115_24


title: du145_DU145PS2A_H11_UNTREATED_0_24

value: UNTREATED


title: du145_DU145PS2A_H8_Amuvatinib_0.02_24

value: Amuvatinib


title: 216R


title: 213R


title: 214R


title: du145_DU145PS2A_H7_BI2536_0.0029_24


title: 211R


title: 212R


title: 210R


title: du145_DU145PS2A_H5_Elesclomol_0.07_24

value: Elesclomol


title: 209R


title: 20R

value: Col 0


title: du145_DU145PS2A_H4_AUY922_0.005_24


title: 207R


title: du145_DU145PS2A_H6_AZD5363_0.5_24


title: 208R


title: E80D81_B

city: Philadelphia

first: Elizabeth

middle: A

last: White

state: PA

address: 3610 Hamilton Walk, 203C Johnson Pavilion, Mail Code 6114

department: Otorhinolaryngology

institute: University of Pennsylvania

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Sequenced reads were filtered to remove adapters and low-quality reads
Clean reads were mapped to hg19 using STAR (v2.5). STAR used  the method of Maximal Mappable Prefix (MMP).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Assembly: hg19
Supplementary files format and content: gene expression quantification table, calculated all genes' FPKM

molecule: polyA RNA

source_name: Primary human forekin keratinocytes

growth_protocol: Primary human keratinocytes stably harboring retroviral expression vectors were grown to 30% confluence in keratinocyte serum-free medium with 0.5 ug/ml puromycin

extract_protocol:
RNA was isolated with Qiagen RNeasy mini kit in White Laboratory and polyA RNA was isolates using oligo dT beads at Novogene Corporation
RNA libraries were prepared for sequencing using standard Illumina protocols at Novogene Corporation

value: Primary human forekin keratinocytes

value: Tranduced with HPV16 E7 E80A/D81A retrovirus (MSCV-P C-FlagHA 16E7 E80A/D81A)

value: Selected with puromycin post retroviral transduction


title: E80D81_C


title: 87R


title: 206R


title: 219R


title: du145_DU145PS2A_H3_Floxuridine_0.5_24

value: Floxuridine

value: ATCC


title: 217R


title: 205R


title: E7_C

value: Tranduced with HPV16 E7 retrovirus (MSCV-P C-FlagHA 16E7)


title: 203R


title: 201R

value: arf7 arf19


title: 204R


title: du145_DU145PS2A_H2_Prednisone_1_24

value: Prednisone

value: male


title: E7_B


title: 202R


title: du145_DU145PS2A_G12_Bosutinib_0.375_24

value: Bosutinib


title: 200R


title: 19R


title: 1R

value: NB


title: du145_DU145PS2A_G11_UNTREATED_0_24


title: GFP_C

value: Tranduced with control retrovirus (MSCV-IP N-HA GFP)


title: du145_DU145PS2A_G10_Flavopiridol_0.06_24

value: Flavopiridol


title: GFP_B


title: 198R

value: Root


title: E80D81_A


title: 197R


title: du145_DU145PS2A_G9_Obatoclax Mesylate_0.1_24

value: Obatoclax Mesylate


title: 194R


title: 195R


title: 192R


title: du145_DU145PS2A_H1_Oxaliplatin_2.5_24

value: Oxaliplatin


title: 193R


title: du145_DU145PS2A_G7_GSK461364_0.005_24


title: 191R


title: 190R


title: du145_DU145PS2A_G6_Navitoclax_0.5_24

value: Navitoclax


title: du145_DU145PS2A_G8_HMN214_0.5_24


title: du145_DU145PS2A_G4_Sonidegib_8_24

value: Sonidegib


title: 186R


title: 187R


title: 189R


title: du145_DU145PS2A_G5_Gossypol_2_24

value: Gossypol


title: 188R


title: 18R

value: Col 0


title: 184R


title: 183R


title: 185R


title: GFP_A

value: Primary human forekin keratinocytes

value: Selected with puromycin post retroviral transduction


title: 196R


title: 182R


title: du145_DU145PS2A_G2_Albendazole_1_24

value: Albendazole

value: ATCC


title: 181R


title: 180R


title: du145_DU145PS2A_G1_Arsenic_0.5_24

value: Arsenic


title: du145_DU145PS2A_F12_Amsacrine_0.11_24

value: Amsacrine

value: male


title: 179R


title: 17R


title: 177R


title: du145_DU145PS2A_F11_DMSO_0_24

value: DMSO


title: 178R


title: 174R

value: arf7 arf19

value: NB


title: du145_DU145PS2A_F10_Entinostat_0.12_24

value: Entinostat


title: du145_DU145PS2A_F9_Epigallocatechin_0.5_24

value: Epigallocatechin


title: 173R

value: Root


title: 170R


title: 171R


title: 176R


title: 175R


title: du145_DU145PS2A_F8_Tivantinib_0.5_24

value: Tivantinib


title: du145_DU145PS2A_G3_Bicalutamide_10_24

value: Bicalutamide


title: 172R


title: 169R


title: du145_DU145PS2A_F5_-_0_24


title: 167R


title: du145_DU145PS2A_F6_UNTREATED_0_24

value: UNTREATED


title: 16R

value: Col 0


title: 165R


title: 166R


title: 168R


title: 164R


title: du145_DU145PS2A_F3_Finasteride_5.5_24

value: Finasteride


title: du145_DU145PS2A_F7_Brivanib_10_24

value: Brivanib


title: 161R


title: 163R


title: du145_DU145PS2A_F2_Thalidomide_8.5_24

value: Thalidomide


title: 162R


title: 160R


title: du145_DU145PS2A_F1_Carmustine_1.5_24

value: Carmustine

value: ATCC


title: 158R


title: 15R


title: du145_DU145PS2A_E12_Idarubicin_0.02_24

value: Idarubicin


title: 157R


title: du145_DU145PS2A_E11_DMSO_0_24

value: male


title: du145_DU145PS2A_F4_Omacetaxine_0.015_24

value: Omacetaxine


title: 155R


title: 154R


title: 159R


title: 152R


title: RNAseq_MOLM13_sgROSA_Venetoclax_Replicate_3

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Illumina Casava software was used for base calling.
Reads were aligned to the human transcriptome using RSEM followed by mapping to the human (Hg19) genome using Bowtie and TopHat.
RNA splicing was quantified using MISO.
Assembly: Hg19
Supplementary files format and content: Matrix of normalized (TPM) gene expression counts.

source_name: Acute Myelogenous Leukemia

growth_protocol: MOLM13 cells were grown under standard in vitro conditions in RPMI-1640 medium supplemented with fetal calf serumn and cultured at 37 °C with 5% CO2.

extract_protocol:
RNA was extracted from cells of interest using an RNeasy kit (Qiagen, Frederick, MD) and quantified using a NanoDrop 8000 (ThermoFisher Scientific).
A minimum of 500 ng of high quality RNA (as determined by Agilent Bioanalyzer) per sample or replicate was used for library preparation. Poly(A)-selected, stranded Illumina libraries were prepared with a modified TruSeq protocol and then sequenced on the Illumina HiSeq 2000.

treatment_protocol: Small molecule inhibitors, or DMSO vehicle control, were added to MOLM13 cells at the following concentratios for 48 hours prior to collection for RNA-seq anaylsis: SM09419 (100nM) and/or Venetoclax (10nM).

tag: cell line modification

tag: drug treatment duration

value: 48 hours

tag: drug treatment

value: Venetoclax (10nM)


title: RNAseq_MOLM13_sgROSA_Venetoclax_Replicate_2


title: 150R


title: 151R


title: du145_DU145PS2A_E10_YM155_0.015_24


title: du145_DU145PS2A_E9_Neratinib_0.225_24

value: Neratinib


title: du145_DU145PS2A_E8_Linifanib_1_24

value: Linifanib


title: 149R

value: Root


title: RNAseq_MOLM13_sgRBM10-3_Venetoclax


title: 14R


title: RNAseq_MOLM13_sgRBM10-2_Venetoclax


title: du145_DU145PS2A_E6_UNTREATED_0_24


title: du145_DU145PS2A_E5_AZD2014_0.35_24


title: 148R


title: 156R


title: RNAseq_MOLM13_sgRBM10-1_Venetoclax


title: 147R


title: RNAseq_MOLM13_sgROSA_DMSO_Replicate_3

value: DMSO vehicle


title: 146R


title: 153R


title: RNAseq_MOLM13_sgROSA_DMSO_Replicate_2


title: du145_DU145PS2A_E4_Rosiglitazone_2_24

value: Rosiglitazone


title: du145_DU145PS2A_E3_Altretamine_10_24

value: Altretamine


title: RNAseq_MOLM13_sgROSA_Venetoclax_Replicate_1


title: RNAseq_MOLM13_sgROSA_DMSO_Replicate_1


title: du145_DU145PS2A_E2_Fludarabine_3_24

value: Fludarabine


title: RNAseq_MOLM13_sgRBM10-3_DMSO


title: 144R

value: Col 0


title: du145_DU145PS2A_E1_Pipobroman_10_24

value: Pipobroman


title: 142R


title: du145_DU145PS2A_E7_PD0325901_0.015_24


title: RNAseq_MOLM13_sgRBM10-2_DMSO


title: 140R


title: du145_DU145PS2A_D11_Disulfiram_0.015_24

value: Disulfiram


title: 13R


title: 145R


title: RNAseq_MOLM13_sgRBM10-1_DMSO


title: RNAseq_MOLM13_Venetoclax_Replicate_3

value: Parental Cell Line


title: RNAseq_MOLM13_Venetoclax_Replicate_2


title: du145_DU145PS2A_D9_Dinaciclib_0.005_24

value: Dinaciclib

value: ATCC


title: 139R


title: du145_DU145PS2A_D10_KX2391_0.03_24

value: male


title: RNAseq_MOLM13_Venetoclax_Replicate_1


title: du145_DU145PS2A_D8_BGJ398_8_24


title: 143R


title: du145_DU145PS2A_D7_PKC412_0.23_24


title: 137R


title: RNAseq_MOLM13_Vehicle_Replicate_2


title: 136R


title: 138R


title: RNAseq_MOLM13_Vehicle_Replicate_3


title: du145_DU145PS2A_D6_DMSO_0_24

value: DMSO


title: 135R


title: 141R


title: du145_DU145PS2A_D12_Daunorubicin_0.03_24

value: Daunorubicin


title: du145_DU145PS2A_D5_Selumetinib_10_24

value: Selumetinib


title: RNAseq_MOLM13_SM09419+Venetoclax_Replicate_3

value: 48 hours

value: SM09419 (100nM) + Venetoclax (10nM)


title: 134R

value: Root


title: du145_DU145PS2A_D4_Bosentan_1_24

value: Bosentan


title: RNAseq_MOLM13_SM09419+Venetoclax_Replicate_2


title: rhizobia, T2, rep2

city: Jena

first: Clabe

last: Wekesa

state: State

address: Hans-Knöll-Str. 8

country: Germany

institute: MPI for Chemical Ecology

data_processing:
Removal of low quality reads, trimming of adaptors trimmomatic
Assembly of reads to Rhizobium phaseoli genome with bowtie2
Counting reads overlapping the genes bedtools
Performing differential expression with DESeq2
Mapping DEGs to KEGG and COGs databases
Assembly: GCA_001664385.1
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: comma-delimited text files include differential expression for each gene

organism: Rhizobium phaseoli

source_name: whole cell

extract_protocol:
RNA was extracted using Trizol reagent
Library for RNA-seq was prepared as follows: The mRNA was randomly fragmented by the NEBNext® Magnesium RNA Fragmentation Module followed by cDNA synthesis with SuperScript IV Reverse Transcriptase kit. The second strand was synthesized using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: Plants were treated with 300 mM NaCl

value: whole cell

value: bacteroids

value: wild type

value: 300 mM NaCl


title: rhizobia, T1, rep1


title: rhizobia, T3, rep3


title: rhizobia, C3, rep3

value: 0 mM NaCl


title: du145_DU145PS2A_D2_UNTREATED_0_24

value: UNTREATED


title: RNAseq_MOLM13_SM09419+Venetoclax_Replicate_1

value: Parental Cell Line


title: RNAseq_MOLM13_SM09419_Replicate_3


title: 131R

value: Col 0


title: rhizobia, C2 rep2


title: du145_DU145PS2A_D1_Thiotepa_3.5_24

value: Thiotepa

value: ATCC


title: RNAseq_MOLM13_SM09419_Replicate_1


title: RNAseq_MOLM13_SM09419_Replicate_2


title: du145_DU145PS2A_C12_Tofacitinib_0.305_24

value: Tofacitinib

value: male


title: 12R


title: 132R


title: 130R


title: du145_DU145PS2A_C11_Azathioprine_0.25_24

value: Azathioprine


title: 129R


title: M-BMDM_3h

city: qingdao

first: qiaoling

last: song

address: Xiang Gang East Road NO.23

institute: Ocean University of China

data_processing:
After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach.
The differential expression analysis was performed using the DESeq2 with p value ≤ 0.05, DEGs with |log2FC|>1, which was considered to be significantly different expressed genes).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: BMDM

growth_protocol: Bone marrow were isolated and routinely generated by 7-day GM-CSF or M-CSF treatment.

extract_protocol:
Total RNA was isolated by using a TRIzol Reagent according to the manufacturer’s instructions (Invitrogen), genomic DNA was removed using DNase I (TaKara), and
1 μg of this RNA was used for high-throughput sequencing using Illumina NovaSeq 6000 sequencers.

treatment_protocol: GM-BMDMs or M-BMDMs were treated with IL6 for 3 or 24 h.

tag: strain

value: 8 weeks

value: bone marrow

value: M-BMDM

value: IL6 for 3h


title: M-BMDM_24h

value: IL6 for 24h


title: 128R

value: Root


title: 133R


title: RNAseq_MOLM13_Vehicle_Replicate_1

value: 48 hours

value: DMSO vehicle


title: M-BMDM

value: control


title: du145_DU145PS2A_C9_Alisertib_0.17_24

value: Alisertib


title: du145_DU145PS2A_D3_Leucovorin_2_24

value: Leucovorin


title: 127R

value: Col 0


title: rhizobia, C1, rep1

value: whole cell

value: bacteroids

value: wild type

value: 0 mM NaCl


title: GM-BMDM_3h

value: GM-BMDM


title: du145_DU145PS2A_C8_JNJ26854165_0.155_24

value: ATCC

value: male


title: 126R


title: du145_DU145PS2A_C7_Bafetinib_8.5_24

value: Bafetinib


title: BM (bone marrow cells)

source_name: bone marrow cells

value: 8 weeks

value: bone marrow

value: BM


title: GM-BMDM


title: du145_DU145PS2A_C6_DMSO_0_24

value: DMSO


title: 125R

value: Root


title: du145_DU145PS2A_C10_GDC0941_0.5_24


title: 123R


title: du145_DU145PS2A_C4_Clarithromycin_1_24

value: Clarithromycin


title: 121R


title: du145_DU145PS2A_C2_UNTREATED_0_24

value: UNTREATED


title: 122R


title: 120R


title: 11R


title: DS4

city: shanghai

first: li

last: zihao

address: dongchuan road 800

institute: shanghai jiao tong university

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.
Assembly: mm9
Supplementary files format and content: fpkm

source_name: colonrectum

extract_protocol:
colonrectum were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: colitis mice model was induced by DSS treatment for 7d, while Sulfasalazine or Berberine via gavage administration for 6d

value: DSS treatment for 7d and Sulfasalazine treatment for 6d


title: DS3


title: DB6

value: DSS treatment for 7d and Berberine treatment for 6d


title: du145_DU145PS2A_B12_Busulfan_0.295_24

value: Busulfan


title: 119R

value: Col 0


title: DB7


title: du145_DU145PS2A_C1_Hydroxyurea_10_24

value: Hydroxyurea


title: DB5


title: DS2


title: du145_DU145PS2A_B11_Teniposide_0.045_24

value: Teniposide


title: 118R


title: 124R


title: hcar1-4-/- PA4h rep2

city: New York

first: Yanan

last: Ma

state: New York

address: 430 east 67st street

department: Cell Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The output data (FASTQ files) were mapped to the zebrafish genome GCz10 (UCSC) using the rnaStar aligner that mapped reads genomically and resolved reads across splice junctions.
A two pass -mapping method was used in which the reads were mapped twice. The first mapping pass used a list of known annotated junctions from Ensembl. Novel junctions found in the first pass were then added to the known junctions, and a second mapping pass was done (on the second pass the RemoveNoncanoncial flag was used).
After mapping, the output SAM files were post processed using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorted the file and converted it to the compressed BAM format.
The expression count matrix was then computed from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq).
The raw count matrix generated by HTSeq was then processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq), which was used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: GCz10 (UCSC)
Supplementary files format and content: counts_scaled_DESeq.txt: Tab-delimited text file

organism: Danio rerio

source_name: whole larvae

growth_protocol: Adult wt casper zebrafish and larvae were maintained according to institutional animal healthcare guidelines with the approval of the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
~40 2.5-3 dpf zebrafish for each sample, mRNA were isolated using Trizol reagent (Life technologies) according to manufacturer's protocol. After Quant-It quantification and quality control of Agilent BioAnalyzer, 500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instruction provided by TruSeq Stranded mRNA Library Prep Kit (Illumina). Samples were barcoded and run on a HiSeq 2500 in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v4 (Illumina). An average of 42 million paired reads was generated per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.
50 bp pair-end barcode length generated an average of 42 million paired reads per sample and sequenced on Illumina Hi-Seq 2500 system (MSKCC Integrated Genomics Operation core facility).

treatment_protocol: Wt Pseudomonas aeruginosa (PA14) were injected into the otic vesicle of 2.5-3dpf zebrafish larvae for 2 h or 4 h. Uninjected zebrafish larvae were served as control. ~40 larvae from each group were euthanized for total mRNA extraction before or after 2h and 4h post-infection.

value: wt casper

value: whole larvae

tag: developmental stage

tag: infection

value: PA14, 4hr


title: hcar1-4-/- PA4h rep3


title: du145_DU145PS2A_C5_Azacitidine_0.02_24

value: Azacitidine

value: ATCC

value: male


title: hcar1-4-/- PA4h rep1


title: 116R


title: du145_DU145PS2A_C3_Gefitinib_0.5_24

value: Gefitinib


title: du145_DU145PS2A_B10_SNX2112_0.02_24


title: 199R

value: arf7 arf19


title: hcar1-4+/+ PA4h rep3

description: control siblings


title: du145_DU145PS2A_B8_KW2449_0.25_24


title: 115R

value: Root


title: du145_DU145PS2A_B7_Motesanib_1_24

value: Motesanib


title: hcar1-4+/+ PA4h rep2

description: control siblings


title: hcar1-4+/+ PA4h rep1

description: control siblings


title: du145_DU145PS2A_B6_AZD1480_0.13_24


title: 114R

value: NB


title: du145_DU145PS2A_B5_Saracatinib_1_24

value: Saracatinib


title: 112R


title: hcar1-4-/- PA2h rep3

value: PA14, 2hr


title: du145_DU145PS2A_B3_Dacarbazine_10_24

value: Dacarbazine


title: 117R

value: Col 0


title: hcar1-4-/- PA2h rep1


title: hcar1-4-/- PA2h rep2


title: du145_DU145PS2A_B2_DMSO_0_24

value: DMSO


title: du145_DU145PS2A_B4_Cyclophosphamide_10_24

value: Cyclophosphamide


title: du145_DU145PS2A_B9_Foretinib_0.225_24

value: Foretinib


title: 10R


title: 111R


title: hcar1-4+/+ PA2h rep3

description: control siblings

value: wt casper

value: whole larvae


title: hcar1-4+/+ PA2h rep2

description: control siblings


title: du145_DU145PS2A_B1_Melphalan_1_24

value: Melphalan


title: 109R


title: du145_DU145PS2A_A12_Megestrol_0.045_24

value: Megestrol

value: ATCC


title: hcar1-4+/+ PA2h rep1

description: control siblings


title: 108R


title: A18w_Mcph1KO_rep1

city: Shenzhen

first: Cao

last: Qiang

address: No. 66 Gongchang Road, Guangming District, Shenzhen

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Filter sequencing adapters and low-quality reads using Trimmomatic (v0.39).
The clean reads were mapping to the GENCODE reference trancriptome (GRCm38.p6 M23 release) and quantifying with Salmon (v1.4.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: cerebral cortex

growth_protocol: standard growth condition

extract_protocol:
Every tissue in our study were chopped into small pieces, and half of homogenate from one tissues were used to extract the genomic DNA using the DNeasy Blood & Tissue Kits (Qiagen), and half of homogenate from one tissues were used to extract the total RNA using the Total RNA Extraction Kit (Omega).
In brief, a total of 1ug RNA per sample was used as input material, and then sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. All libraries were constructed using the TruSeq SBS v3-HS kit before sequencing to investigate the global transcriptome of the control group using Illumina HiSeq 2500 (Illumina, Inc.).

value: cerebral cortex

value: Mcph1 knockout

value: male


title: A18w_Mcph1KO_rep2


title: A18w_WT_rep2

value: wild-type


title: du145_DU145PS2A_A11_Axitinib_0.14_24

value: Axitinib


title: 110R

value: Root


title: 107R


title: A18w_WT_rep1


title: du145_DU145PS2A_A10_SB743921_0.075_24


title: 106R


title: hcar1-4-/- no infection rep3


title: hcar1-4-/- no infection rep2


title: 105R


title: A6w_Mcph1KO_rep1


title: A6w_Mcph1KO_rep2


title: hcar1-4+/+ no infection rep3

description: control siblings


title: du145_DU145PS2A_A9_MK2206_1_24


title: du145_DU145PS2A_A8_Cinacalcet_2_24

value: Cinacalcet


title: A6w_WT_rep2


title: hcar1-4-/- no infection rep1


title: hcar1-4+/+ no infection rep2

description: control siblings


title: du145_DU145PS2A_A6_Bardoxolone Methyl_0.5_24

value: Bardoxolone Methyl


title: du145_DU145PS2A_A7_Alpelisib_0.37_24

value: Alpelisib


title: 102R


title: 103R


title: A6w_WT_rep1


title: 104R


title: P4_Mcph1KO_rep2


title: primary cortical neurons, exo-ogd3

city: Guangzhou

first: Yousheng

last: Wu

address: 601 Huangpu Avenue West

institute: the First Affiliated Hospital of Jinan University

data_processing:
ssss
Supplementary files format and content: FPKMs

source_name: primary cortical neurons, exo-ogd

extract_protocol:
RNA was harvested using Trizol.
EpiTM mini longRNA-seq kit (Epibiotek, E1802) was used for library preparation according to the instructions.

value: embryonic cortical neurons

value: WT

value: OGD/R


title: P4_Mcph1KO_rep1


title: 101R


title: du145_DU145PS2A_A5_FK866_0.00205_24


title: du145_DU145PS2A_A4_Vorinostat_0.5_24

value: Vorinostat


title: 100R


title: primary cortical neurons, exo-ogd2


title: P4_WT_rep2


title: primary cortical neurons, exo-ogd1


title: primary cortical neurons, exo-con3

source_name: primary cortical neurons, exo-con

value: control


title: primary cortical neurons, exo-con2


title: hcar1-4+/+ no infection rep1

description: control siblings

value: wt casper

value: whole larvae


title: du145_DU145PS2A_A1_Mechlorethamine_1_24

value: Mechlorethamine

value: ATCC


title: E17.5_Mcph1KO_rep1

value: cerebral cortex

value: Mcph1 knockout


title: primary cortical neurons, exo-con1


title: E17.5_WT_rep2

value: wild-type

value: male


title: du145_DU145PS2A_A3_Erlotinib_3_24

value: Erlotinib


title: du145_DU145PS1B_H10_Bortezomib_0.015_24

value: Bortezomib


title: E17.5_WT_rep1


title: du145_DU145PS1B_H12_Cabazitaxel_0.00065_24

value: Cabazitaxel


title: du145_DU145PS2A_A2_DMSO_0_24

value: DMSO


title: du145_DU145PS1B_H9_Trifluridine_1.5_24

value: Trifluridine


title: mESC_WT_rep2

value: mouse embryonic stem cells


title: du145_DU145PS1B_H8_Temozolomide_10_24

value: Temozolomide


title: du145_DU145PS1B_H7_Exemestane_1.5_24

value: Exemestane


title: mESC_WT_rep1


title: P4_WT_rep1


title: E17.5_Mcph1KO_rep2


title: du145_DU145PS1B_H6_Ifosfamide_6.5_24

value: Ifosfamide


title: du145_DU145PS1B_H11_UNTREATED_0_24

value: UNTREATED


title: du145_DU145PS1B_H5_Tamoxifen_1_24

value: Tamoxifen


title: du145_DU145PS1B_H4_Estramustine_3.5_24

value: Estramustine


title: Placenta 3, cytotrophoblasts, PT2385, Day4

city: Woluwé-Saint-Lambert

first: Arthur

middle: Henri

last: Colson

address: Avenue Hippocrate, 54

department: Institut de recherche expérimentale et clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
Fastq files were processed using a standard RNAseq pipeline, including Trimmomatic-0.38 (68) to remove low quality reads
hisat2-2.1.0 was used to align reads to the human genome (GRCh38)
Gene expression levels were evaluated using featureCounts from subread-2.0.0 (70) and Homo_sapiens.GRCh38.94.gtf.
Differential expression analyses were performed with the  DESeq2 Bioconductor package v1.32.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with raw counts values for each Sample

source_name: term placenta

growth_protocol: Primary cytotrophoblasts were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 and 2.5% O2 at 37C

extract_protocol:
Primary cytotrophoblasts were isolated from three different human placentas by using Dispase II digestion and Percoll gradient separation.
RNA was harvested using PureLink RNA Mini Kit (Invitrogen) according to the manufacturer's protocol.
RNA libraries for RNA-seq was prepared by the Genewiz company (Azenta, Chelmsford, MA, USA)

treatment_protocol: PT2385 treatment was added at a concentration of 10 µmol/L the day after isolation. Culture medium containing the treatment was changed every day.

value: term placenta

value: primary cells

value: stem cells

value: WT

value: PT2385 10 µmol/L


title: Placenta 3, cytotrophoblasts, DMSO, Day4


title: du145_DU145PS1B_H3_Abiraterone_10_24

value: Abiraterone

value: ATCC

value: male


title: du145_DU145PS1B_G12_Epirubicin_0.065_24

value: Epirubicin


title: Placenta , cytotrophoblasts, DMSO, Day4

value: DMSO


title: Placenta 1, cytotrophoblasts, DMSO, Day4


title: Placenta 1, cytotrophoblasts, PT2385, Day4


title: Placenta 2, cytotrophoblasts, PT2385, Day4


title: TI

city: London

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

description:
ES3 mESCs were transduced with ZFP819 and ZFP809-expressing lentiviral vectors (pRRLSIN.cPPT.PGK-ZFP.WPRE vectors with a triple HA tag).
ZFP819_common.bed

library_source: genomic

data_processing:
RNA-Seq and CUT&RUN fastq files were trimmed for quality using TrimGalore v0.4.1
For RNA-Seq samples, alignment of trimmed reads to mm10 version of the mouse genome was performed with Tophat 2.1.0 using the --max-multihits 100 option. The number of read counts per gene and repeat family was calculated using the multi option from Tecount. Differential expression analysis was performed with DESeq2. For further details see Fernandes et al., 2022.
For CUT&RUN samples, trimmed reads were aligned with STAR with the following parameters: --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06. Genomic coverage in form of bigwig files was calculated using the genomecov tool from bedtools using 10000000 / number_of_mapped_reads as a scaling factor.
For ChIP-Seq samples, reads were mapped to the mm10 version of the mouse genome using Bowtie2. ChIP-seq enriched peaks were called by MACS2 (v.2.1.2), and the common peaks were merged using bedtools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic coverage normalised to number of mapped reads. Excel spreadsheet with results of differential expression analysis. Bed files with ChIP-Seq peaks

molecule: genomic DNA

source_name: mESC

growth_protocol: ES3 mESCs were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 100 U/ml penicillin/streptomycin, 10% fetal calf serum (FCS, Life Technologies), 2mM L-glutamine (Gibco, Thermo Fisher Scientific), 1mM Sodium pyruvate (Sigma), 1x MEM non-essential amino acids (Gibco, Thermo Fisher), 0.1mM  2-Mercaptoethanol (Life Technologies) and 1,000 units/ml Leukaemia inhibitory factor (LIF, Chemicon) and grown at 5% CO2 at 37 °C. mESC lines were split 1:4 every 2 days using accutase or trypsin.

extract_protocol:
RNA-seq - Total RNA was extracted using RNeasy Micro kit columns (Qiagen) and DNase treated according to the manufacturer’s instructions (Ambion AM1907). RNA was quality checked on a 4200 Tapestation using the RNA ScreenTape assay (Agilent Technologies, Wokingham, UK) and the RNA concentration measured using a Qubit RNA Broad Range kit (Life Technologies, Paisley, UK)
CUT&RUN - We followed the EpiCypher® CUTANATM CUT&RUN Protocol (v1.6) (https://www.epicypher.com/resources/protocols/cutana-cut-and-run-protocol/). Briefly, CUT&RUN was performed using 100,000 sorted GFPBright cells (per antibody/sample combination). Cells were washed twice [20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, 1× protease inhibitors (cOmplete™, Mini, EDTA-free, Roche)], attached to Concanavalin A beads (BioMag®Plus, Generon) which were pre-activated in activation buffer (20mM HEPES pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Sample and bead slurry was resuspended in antibody buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1× protease inhibitors, 0.01% w/v digitonin, 2mM EDTA) containing primary antibody. 1ug of anti-H3K9me3 (Abcam, ab8898) or anti-H3K27ac (Abcam, ab4729) was incubated overnight at 4°C with gentle shaking. IgG control Ab (Millipore, 12-370) alone was used in parallel. The samples were washed 3x in cold digitonin buffer (20 mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1× Roche complete protease inhibitors, 0.01% digitonin). pA-MNase (2.5μl per tube, CUTANA™ pAG-MNase, Epicypher) was added incubated with the bead-cell slurry at room temperature for 10min. The beads were washed twice and resuspended in cold digitonin buffer. The pA-MNase was activated by addition of 2mM CaCl2 (final) and incubating at 4°C for 2h. The reaction was quenched using stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50μg/ml glycogen, 50μg/ml RNase A), vortexing and incubating for 10 min at 37°C. A magnetic rack was used to separate cells and beads from the supernatant which was purified with a MinElute PCR Purification Kit (Qiagen).
ChIP - ES3 mESCs were transduced with ZFP819 and ZFP809-expressing lentiviral vectors (pRRLSIN.cPPT.PGK-ZFP.WPRE vectors with a triple HA tag). Cells were washed twice (in PBS + 2% FCS), counted to normalize by cell number, cross-linked (10 min rotation in 1% formaldehyde), quenched with glycine (at 125 mM on ice), washed three times (PBS), and snap-frozen at 107 cells per tube. Cells were resuspended in sequential ChIP lysis buffers and then in 900ul of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors). Where a Covaris sonicator was used, 900ul was sonicated in one covaris glass tube with the settings: 20% duty cycle, intensity 5, 200 cycles/burst, 30 min. For sonication with a Bioruptor Pico, 300ul aliquots per 1.5ml tube were sonicated1. Immunoprecipitations were performed in duplicates as described2 using an HA Ab (Biolegend, 901501) and DNA extracted (Qiagen MinElute PCR purification kit, Cat. 28004) for PCR and sequencing. See Supplementary Information for primers.  1. Tie, C.H. et al. KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control. EMBO Rep 19(2018).  2. Robbez-Masson, L. et al. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res (2018).
RNA-seq - 500 ng per sample was processed using KAPA’s stranded RNA HyperPrep RiboErase kit and sequenced on a NextSeq 500 instrument (Illumina Cambridge, Chesterford, UK) after pooling libraries in equimolar quantities, using a 2x 151 bp paired-end run, resulting in over 15 million reads per sample.
CUT&RUN - Illumina sequencing libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (New England BioLabs). Enrichment of DNA fragments was achieved by PCR (12 cycles). Libraries pooled in equimolar quantities were sequenced on Novaseq6000 for 150 paired-end reads.
ChIP-seq - Libraries were prepared following the ChIP-Seq library preparation protocol (Illumina, IP-102-1001). Ligation products were purified on 2% E Gels Size Select (Invitrogen; fragments of 200 bp recovered), followed by enrichment of DNA fragments by PCR (18 cycles). Sequencing was performed with Illumina HiSeq 2500 in 100-bp single-end reads.

treatment_protocol: mESCs were transduced with shRNA expressing lentiviral vectors. Puromycin selection was performed 2 days post transduction overnight (and control cells verified to die) and samples harvested 5 days post selection. Cells tranduced with GFP shRNA expressing lentiviral vectors were sorted on day 2 post transduction and harvested 5 days later.

tag: transduction

tag: antibodies

tag: full name


title: ZFP819_IP1

value: HA Ab (Biolegend, 901501)


title: ZFP819_IP2


title: du145_DU145PS1B_G11_UNTREATED_0_24


title: du145_DU145PS1B_G10_Panobinostat_0.01_24

value: Panobinostat


title: HepG2, R1274W, input

city: Huntsville

first: Chris

last: Partridge

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

data_processing:
Fastq files were obtained from Illumina software and Discovery Life Sciences sequencing center pipeline.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.3.4.3.
Peaks were called using SPP v.2.2.4 and IDR v.2.0.4.2 at .05.
Assembly: hg38
Supplementary files format and content: regionPeak

extract_protocol:
Crosslinking: 1% formaldehyde, 10 minutes, room temperature. See Meadows et al. (2020) "Epitope tagging ChIP-seq of DNA binding proteins using CETCh-seq"
ChIP-seq libraries were prepared using the ENCODE standardized protocol. 5-50 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Libraries were validated and quantified using KAPA library quantification kit.

tag: chip antibody


title: ZFP809_IP1

description:
ES3 mESCs were transduced with ZFP819 and ZFP809-expressing lentiviral vectors (pRRLSIN.cPPT.PGK-ZFP.WPRE vectors with a triple HA tag).
ZFP809_common.bed


title: du145_DU145PS1B_G9_Ixazomib_0.035_24

value: Ixazomib


title: HepG2, R688H, input


title: du145_DU145PS1B_H2_Decitabine_0.5_24

value: Decitabine


title: du145_DU145PS1B_G7_Methotrexate_0.01_24

value: Methotrexate


title: du145_DU145PS1B_G8_Lenvatinib_0.5_24

value: Lenvatinib


title: du145_DU145PS1B_G6_Topotecan_0.065_24

value: Topotecan


title: Wild-type clon 3 time 2

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

description: mESC WT, 2 days in N2B27

data_processing:
RNA-seq processing:
Read adapters and polyA tails were removed with bbduk.sh, following the Lexogen recommendations. Processed reads were analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19 (--library-type fr-secondstrand in TopHat), allowing two mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM20.GRCm38.Ensembl95). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: ESC from mouse blastocysts

growth_protocol: mESCs were grown over feeders in LIF-containing DMEM. Medium was changed every day

extract_protocol:
Samples were collected at day 0, 2 and 7 of the differentiation protocol. RNA was extracted with miRVana RNA isolation kit (Ambion)
Total RNA samples were used (500 ng on average). Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
Quantseq 3’UTR

treatment_protocol: Prior extraction, ESCs were grown on gelatin-coated plates at low density to remove feeders. For differentiation induction, LIF-containing medium was replaced with N2B27 with growing factors EGF snd FGF2. Medium was changed every 2 days. At day 6, cells were seeded on laminin-coated plates at high density and growth factors were removed

tag: cell type

value: embryonic stem cells

value: Neural Differentiation media 2 days

tag: clon/replicate


title: Wild-type clon 3 time 0

description: mESC WT not differentiated

tag: treatment

value: LIF-containing ESC media


title: HepG2, CETCh-seq, input

tag: cell line


title: Astro_DIV14_IRKO_Ins rep4

city: Old Westbury

first: Ying-Tao

last: Zhao

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing:
The RNA-seq data analyses were performed as previously described (Johnson et al., 2017; Moon & Zhao, 2021). Reads in FASTQ files were aligned to mouse reference genome (mm10) using STAR read aligner (STAR 2.7.7a). The numbers of reads aligned to the exon regions of each gene were quantified by a Perl script. The normalization and comparison of RNA-seq were performed using edgeR. Genes with average count-per-million < 0.5 were filtered out. The absolute value of log2 fold change (log2FC) greater than 1.5 and false discovery rate (FDR) less than 0.05 were set as the thresholds to determine significantly differentially expressed genes (DEGs). Data plotting was carried out using the R version 4.0.4. The DESeq2 (Love, Huber, & Anders, 2014) was used to perform the principal component analysis (PCA). The colorRampPalette in mixOmics was used to compute the distances between variables to plot the clustering image map (CIMs, heatmap). Pathway enrichment analysis was performed using g:Profiler (version_e106_eg53_p16 _65fcd97) and was carried out to detect the most enriched Gene Ontology (GO), including Biological Process, Cellular Component, Molecular Function, KEGG, and Reactome. The custom background used in g:profiler comprised genes expressed with the Benjamini-Hochberg FDR algorithm was used with a significance threshold of 0.05. The gene ratio was computed by the intersection size divided by the query size. The gene ratio and intersection size were used as input to generate a dot plot for enriched GO terms. The autophagy pathway analysis of the DEGs was carried out using the KEGG database (KEGG:04140; Autophagy: animal) to generate heat maps.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each Sample

source_name: Brain

growth_protocol: Primary cortical astrocyte cultures were prepared from IRf/f, IGF1Rf/f or IR/IGF1R double floxed newborn pups as previously described (19). Briefly, cortices were surgically dissected and digested in Hibernate-A media supplemented with 4 mg/ml papain (Sigma) and 33 U/ml DNase I (Sigma) on a shaker at 37°C for 30 min. Dissociated cells were plated on a T75 flask and cultured in DMEM/F12 (Gibco) plus 10% FBS and 1x pen/strep (Gibco). Contaminating non-astrocytes were depleted by vigorously shaking the following day. Culture media was changed every 3 days. Upon confluency, astrocytes were trypsinized and replated onto 6-well plates (Corning) or 8-chamber slides (ibidi).

extract_protocol:
Total RNA was extracted from primary cultured control and IRKO astrocytes treated with 100 nM insulin, IGF-1 or vehicle using QIAzol reagent (Qiagen). RNA quality and quantification were verified using a 2100 Agilent Bioanalyzer.
Total RNA samples (2 μg, RNA integrity score > 7) were submitted for library preparation and next-generation sequencing by Novogen. Briefly, mRNAs were purified from total RNAs using poly-T oligo-conjugated magnetic beads. Non-stranded cDNA libraries were prepared and subjected to sequencing (paired-end 150bp).

treatment_protocol: To induce flox allele recombination, IRf/f, IGF1Rf/f, and double floxed astrocytes were infected with adenovirus encoding Cre:GFP (1 x 109 GC/ml) overnight, and cultured for an additional 5 days before experiments. To generate the control cells, the same floxed astrocytes were infected with adenovirus encoding GFP alone. To assess transcriptional regulation, primary IRKO, IGF1RKO and double knockout (DKO) astrocytes, along with the appropriated single or double IR/IGF1R floxed control astrocytes were serum starved overnight with DMEM/F12 medium containing 0.1% BSA, followed by 100 nM insulin, 100 nM IGF-1 or vehicle treatment for 6 h. To examine the protein expression after insulin and IGF-1 treatment, astrocytes were serum starved for 4 h, followed by 100 nM insulin, 100 nM IGF-1 or vehicle treatment overnight. To prevent rapid degradation of proteins through autophagy, cells were co-treated with 100 nM Bafilomycin A1.

tag: tissue

value: Brain

value: Primary astrocytes

value: Astrocytes

tag: genotype

value: IR KO

value: Ins


title: Astro_DIV14_IRKO_Ins rep2


title: Astro_DIV14_IRKO_Ins rep1


title: Wild-type clon 1 time 7

description: mESC WT, 7 days in N2B27

value: Neural Differentiation media 7 days


title: du145_DU145PS1B_G5_Nilotinib_2_24

source_name: prostate cancer

value: Nilotinib

tag: provider

value: ATCC

tag: vendor id

tag: age

tag: Sex

value: male


title: Wild-type clon 1 time 2

description: mESC WT, 2 days in N2B27


title: Wild-type clon 1 time 0

description: mESC WT not differentiated


title: Astro_DIV14_IRKO_IGF1 rep3


title: 113R

city: Loughborough

first: Gabriel

last: Castrillo

address: Nr Loughborough

institute: University of Nottingham

data_processing:
For the analysis of the RNASeq data, reads were first subjected to quality control and filtering via fastp v0.20.1 (59). The resulting high-quality reads were pseudo-aligned to the Arabidopsis thaliana genome deposited in the Ensembl Plants version 52, using salmon v1.6.0 (60). Gene level summarization from the salmon quantification was performed with the tximport function from the tximport v.1.22.0 R package (50).
Assembly: Ensembl Plants version 52
Supplementary files format and content: Gene level summarization from the salmon quantification

source_name: Root

extract_protocol:
RNA was extracted from plant roots following Logemann et al.
RNA libraries were prepared following Finkel et al. with modification

value: Root

value: Col 0

value: NB


title: Astro_DIV14_IRKO_IGF1 rep1


title: du145_DU145PS1B_G2_Vismodegib_10_24

value: Vismodegib


title: Cdc14b KO clon 3 time 2

description: mESC Cdc14b KO, 2 days in N2B27


title: P2

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: hg19
Supplementary files format and content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: hepatocellular carcinoma patient

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: patient diagnosis

value: hepatocellular carcinoma

value: normal adjacent liver tissue


title: Astro_DIV14_IRKO_Ctrl rep4

value: Ctrl


title: P3


title: Astro_DIV14_IRKO_IGF1 rep4


title: du145_DU145PS1B_G1_Enzalutamide_10_24

city: New York City

first: Alessandro

last: Vasciaveo

address: 1130 Saint Nicholas Ave., 910

institute: Columbia University

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Assembly: hg38
Supplementary files format and content: 2 semicolon delinated text files (for 2 cell-lines) with raw gene counts for every gene and every sample

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Enzalutamide


title: du145_DU145PS1B_G4_Pentostatin_1_24

value: Pentostatin


title: Cdc14b KO clon 3 time 7

description: mESC Cdc14b KO, 7 days in N2B27

value: embryonic stem cells


title: Cdc14b KO clon 3 time 0

description: mESC Cdc14b KO not differentiated

value: LIF-containing ESC media


title: P1


title: Astro_DIV14_IRKO_Ctrl rep3

value: Brain

value: Primary astrocytes

value: Astrocytes

value: IR KO


title: N3


title: PLK1 [2_2]

type: genomic

first: Peng

last: Yuchong

address: The First Affiliated Hospital, Guangdong Pharmaceutical University, 19 Nonglinxia Road, Yuexiu District, Guangzhou, Guangdong, China

department: Clinical Pharmacy of the First Affiliated Hospital

institute: Guangdong Pharmaceutical University

description:
SAMPLE 2_2
Genome-wide DNA methylation profiling analysis after PLK1 knockdown.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation BeadChip using standard Illumina protocol.

scan_protocol: Put the processed chip into a scanner, use laser to excite the fluorescent group of the single-base extension product on the chip, and the scanner obtains the fluorescence emitted by the fluorescent group and generates a high-resolution picture.

data_processing: The data thus obtained is directly imported into GenomeStudio software for analysis, so as to obtain the methylation data of each sample.

label: not provided

source_name: PLK1 knockdown (si-PLK1)

label_protocol: Standard Illumina Protocol.

growth_protocol: DU145 cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin and streptomycin.

extract_protocol: Genomic DNA was extracted and purified from DU145 cell samples using Kit according to standard instructions.

treatment_protocol: DU145 cells were transfected every 3 days with the siRNA, and the genomic DNA was isolated from DU145 cells after 6 days of depletion for bisulfite conversion. Three biological replicates per sample.

tag: sirna


title: UHRF1 [3_2]

description:
SAMPLE 3_2
Genome-wide DNA methylation profiling analysis after UHRF1 knockdown.

source_name: UHRF1 knockdown (si-UHRF1)


title: du145_DU145PS1B_F12_Ponatinib_0.135_24

value: Ponatinib

value: ATCC


title: du145_DU145PS1B_F11_DMSO_0_24

value: DMSO

value: male


title: du145_DU145PS1B_F10_Docetaxel_0.00165_24

value: Docetaxel


title: Cdc14b KO clon 1 time 7

description: mESC Cdc14b KO, 7 days in N2B27

value: Neural Differentiation media 7 days


title: Astro_DIV14_IRKO_Ctrl rep1


title: N2

value: hepatocellular carcinoma


title: du145_DU145PS1B_F9_Trametinib_0.035_24

value: Trametinib


title: Astro_DIV14_IRKO_Ctrl rep2

value: Ctrl


title: NC [1_1]

description:
SAMPLE 1_1
Genome-wide DNA methylation profiling analysis.

source_name: Normal (si-CON)

value: si-CON


title: Astro_DIV14_IRflox_Ins rep4

value: IR floxed

value: Ins


title: Cdc14b KO clon 1 time 2

description: mESC Cdc14b KO, 2 days in N2B27

value: embryonic stem cells

value: Neural Differentiation media 2 days


title: Cdc14b KO clon 1 time 0

description: mESC Cdc14b KO not differentiated

value: LIF-containing ESC media


title: Astro_DIV14_IRflox_Ins rep3

value: Brain

value: Primary astrocytes

value: Astrocytes


title: du145_DU145PS1B_F8_Cytarabine_0.18_24

value: Cytarabine

value: ATCC


title: UHRF1 [3_3]

description:
SAMPLE 3_3
Genome-wide DNA methylation profiling analysis after UHRF1 knockdown.


title: PLK1 [2_3]

description:
SAMPLE 2_3
Genome-wide DNA methylation profiling analysis after PLK1 knockdown.


title: PLK1 [2_1]

description:
SAMPLE 2_1
Genome-wide DNA methylation profiling analysis after PLK1 knockdown.


title: Cdc14a KO clon 3 time 2

description: mESC Cdc14a KO, 2 days in N2B27


title: Astro_DIV14_IRflox_Ins rep2


title: ZFP809_IP2

tag: strain

value: HA Ab (Biolegend, 901501)


title: Base,F7,E2,scRNAseq

city: Cambridge

first: Vincent

last: Knight-Schrijver

address: Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way

institute: University Of Cambridge

description:
SINHA_E2_s1
Second sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

library_source: transcriptomic single cell

data_processing:
Demultiplexed using bcl2fastq by sequencing CRUK.
Mutiple fastq files for I1, R1 and R2 reads were concatenated into a single file and aligned using Illumina CellRanger 6.1 with default parameters.
Filtered matrices were read in R and processed, retaining only cells with between 1000 and 15000 UMIs, over 300 uniquely expressed genes, or under 15 % UMIs within mitochondrial features.
Red Blood Cells were removed using a two-compartment Gaussian Mixture Model on the mean cellular expression of haemoglobin and erythrocyte-associated gene features, following by clustering and RBC cluster removal.
Doublets were detected and removed after QC steps using scrublet with default parameters.
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed data files are provided in two forms. Firstly the filtered output for each foetal sample resulting from alignment in CellRanger 6.1, prior to any filtering or data processing steps  (*barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz).
Supplementary files format and content: Secondly, the sub-sampled and integrated object containing both foetal, and adult cells, as an .rds file including raw counts, log-normalised counts, integrated object dimemsion reduction embeddings and residuals matrix, and annotations produced during the analysis.

source_name: Heart

extract_protocol:
Tissue was dissociated using 6.6 mg/ml Bacillus Licheniformis protease, 5 mM CaCl2 and 20 U/ml DNase I, where the mixture was triturated on ice for 20 s every 5 minutes until clumps of tissue were no longer visible.
Chromium Single Cell 3' Library Construction Kit v3 and v3.1 (10x Genomics)

value: Heart

value: Primary Tissue

value: F

tag: region

value: Base

tag: developmental stage_(days)


title: Astro_DIV14_IRKO_Ins rep3

value: IR KO


title: Cdc14a KO clon 3 time 7

description: mESC Cdc14a KO, 7 days in N2B27

value: Neural Differentiation media 7 days


title: Wild-type clon 3 time 7

description: mESC WT not differentiated


title: Cdc14a KO clon 1 time 7

description: mESC Cdc14a KO, 7 days in N2B27


title: du145_DU145PS1B_F6_UNTREATED_0_24

value: UNTREATED

value: male


title: Cdc14a KO clon 3 time 0

description: mESC Cdc14a KO not differentiated

value: embryonic stem cells


title: Astro_DIV14_IRflox_Ins rep1

value: IR floxed

value: Ins


title: du145_DU145PS1B_F7_Etoposide_0.5_24

value: Etoposide


title: du145_DU145PS1B_F5_Vandetanib_1.5_24

value: Vandetanib


title: Astro_DIV14_IRflox_IGF1 rep3

value: Brain

value: Primary astrocytes

value: Astrocytes


title: Base,F6,E8,scRNAseq

description:
SINHA_E8_s1
First sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds


title: du145_DU145PS1B_F4_Pazopanib_10_24

value: Pazopanib

value: ATCC


title: NC [1_3]

description:
SAMPLE 1_3
Genome-wide DNA methylation profiling analysis.

value: si-CON


title: Cdc14a KO clon 1 time 0

description: mESC Cdc14a KO not differentiated

value: LIF-containing ESC media


title: du145_DU145PS1B_F3_Mitotane_10_24

value: Mitotane


title: Base,F6,E8,s2,scRNAseq

description:
SINHA_E8_s2
Second sequencing run

value: Heart

value: Primary Tissue

value: F

value: Base


title: Astro_DIV14_IRflox_IGF1 rep4


title: Astro_DIV14_IRflox_IGF1 rep2


title: Base,F4,F7,scRNAseq

description:
SINHA_F7_s1
Second sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds


title: Apex,F6,F8,scRNAseq

description:
SINHA_F8_s1
First sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

value: Apex


title: Cdc14a KO clon 1 time 2

description: mESC Cdc14a KO, 2 days in N2B27

value: embryonic stem cells

value: Neural Differentiation media 2 days


title: NC [1_2]

description:
SAMPLE 1_2
Genome-wide DNA methylation profiling analysis.


title: Cdc14ab KO clon 3 time 7

description: mESC Cdc14ab KO, 7 days in N2B27

value: Neural Differentiation media 7 days


title: Astro_DIV14_IRflox_IGF1 rep1

value: IR floxed


title: Apex,F4,G7,scRNAseq

description:
SINHA_G7_s1
Second sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds


title: Cdc14ab KO clon 3 time 2

description: mESC Cdc14ab KO, 2 days in N2B27


title: du145_DU145PS1B_F1_Irinotecan_0.3_24

value: Irinotecan

value: male


title: Base,F3,F4,s2,scRNAseq

description:
SINHA_F4_s2
Second sequencing run

value: M


title: Astro_DIV14_IRflox_Ctrl rep4

value: Brain

value: Primary astrocytes

value: Astrocytes

value: Ctrl


title: Astro_DIV14_IRflox_Ctrl rep3


title: Cdc14ab KO clon 1 time 7

description: mESC Cdc14ab KO, 7 days in N2B27


title: du145_DU145PS1B_E11_DMSO_0_24

value: DMSO

value: ATCC


title: du145_DU145PS1B_E12_Pomalidomide_0.21_24

value: Pomalidomide


title: Base,F3,F4,scRNAseq

description:
SINHA_F4_s1
First sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

value: Heart

value: Primary Tissue


title: Cdc14ab KO clon 1 time 2

description: mESC Cdc14ab KO, 2 days in N2B27


title: du145_DU145PS1B_E10_Vinorelbine_0.005_24

value: Vinorelbine


title: Base,F2,A1,scRNAseq

description:
SINHA_A1_s1
Second sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

value: Base


title: Astro_DIV14_IRflox_Ctrl rep1


title: Apex,F3,G4,scRNAseq

description:
SINHA_G4_s1
First sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

value: Apex


title: Astro_DIV14_IRKO_IGF1 rep2

value: IR KO


title: Astro_DIV14_IRflox_Ctrl rep2

value: IR floxed


title: du145_DU145PS1B_F2_Letrozole_2_24

value: Letrozole


title: du145_DU145PS1B_G3_Temsirolimus_0.09_24

value: Temsirolimus

value: male


title: du145_DU145PS1B_E7_Mercaptopurine_0.24_24

value: Mercaptopurine


title: Apex,F2,B1,scRNAseq

description:
SINHA_B1_s1
Second sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

value: M


title: du145_DU145PS1B_E9_Cobimetinib_0.5_24

value: Cobimetinib


title: Base,F1,C8,scRNAseq

description:
SINHA_C8_s1
First sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

value: F


title: du145_DU145PS1B_E5_Mithramycin_0.18_24

value: Mithramycin


title: du145_DU145PS1B_E6_UNTREATED_0_24

value: UNTREATED

value: ATCC


title: Apex,F1,D8,scRNAseq

description:
SINHA_D8_s1
First sequencing run
Adult_Foetal_Integrated_Hearts_VKS2022.rds

value: Heart


title: snATAC Isl A0019

city: La Jolla

first: Paola

last: Benaglio

state: CA

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: University of California San Diego

description: snATAC-seq of islet A0019 (non-diabetic)

data_processing:
10x Genomics Cell Ranger ATAC v1.1 and multiplet removal script (version 1.1) were used to process 10x fastq files for each sample and perform alignment to the hg19 reference genome. BAM files were filtered for PCR duplicates, converted into tagAlign files, and intersected with a reference set of islet ATAC-seq peaks. Each experiment was clustered separately using scanpy following the procedure described in Chiou et al. 2021 (PMID: 33795864).
Fitered assays from different samples were combined; and the top 50 PCs were obtained. Harmony was used to batch correct PCs for experiments followed by UMAP dimensionality reduction and clustering using the Leiden algorithm (Resolution = 0.5), and sub-clustered using the Louvain algorithm (Resolution = 1.5). Low-quality cells from the merged clusters were iteratively removed and manual doublet removal was performed on sub-clusters with above average high usable read depth or those that expressed multiple marker genes. Cell type of each cluster was assigned based on chromatin accessibility at promoter regions of known marker genes. These sampels were used as reference to imporove clistering and removed from downstream analysis of this publication.
Assembly: hg19
Supplementary files format and content: List of final barcodes and cell type assignments of the snATAC experiments

source_name: Pancreatic islets

growth_protocol: Human islet samples were enriched using a dithizone stain and cultured in CMRL 1066 supplemented with 10% FBS, 1X pen-strep, 8mM glucose, 2mM L-glutamine, 1mM sodium pyruvate, 10mM HEPES, and 250ng/mL Amphotericin B.

extract_protocol:
Approximately 1,000 islet equivalents (~1,000 cells per IEQ) were resuspended in 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water) and homogenized using 1ml glass dounce homogenizer with a tight-fitting pestle for 15 strokes. Homogenized islets were incubated for 10 min at 4°C and filtered with 30 µm filter (CellTrics). Nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf) and washed twice with Wash buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, and 1% BSA (Proliant 7500804) in molecular biology-grade water). Nuclei were pelleted and resuspended in 30 µL of 1X Nuclei Buffer (10x Genomics). Nuclei were counted using a hemocytometer, and 15,360 nuclei were used for tagmentation.
Single nucleus ATAC-seq libraries were generated using the (Chromium Chip E Single Cell ATAC kit (10x Genomics, 1000086) and indexes (Chromium i7 Multiplex Kit N, Set A, 10x Genomics, 1000084) following manufacturer instructions. Final libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NovaSeq6000 (Illumina) with following read lengths: 50 + 8 + 16 + 50 (Read1 + Index1 + Index2 + Read2).

tag: source id

value: no treatment

tag: ethnicity

value: Caucasian

tag: bmi

tag: islet index

tag: islet purity


title: EPSC2C12-4_S8_L001 [EPSC-3]

city: Baton Rouge

first: John

middle: P

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner v2.5.1 program.
The expression levels of genes were determined using Cufflinks v2.2.1and presented as FPKM
Differential expression analysis was done using Cuffdiff v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPM for all samples and genes

source_name: C2C12_EPS stimulated

growth_protocol: C2C12 cells (ATCC, Manassas, VA, USA, passage 4-8) were grown in high glucose DMEM (4.5 g/L D-glucose) supplemented with 10% FBS and 1% penicillin-streptomycin (100 U/mL). Prior to 80% confluence, the cells were plated on 0.1% gelatin coated twelve-well plates. Upon full confluence, the medium was switched to differentiation medium comprised of high glucose DMEM supplemented with 2% horse serum and 1% penicillin-streptomycin. Differentiation medium was replenished daily with 75% fresh medium. Cells were deemed ready for stimulation after 5 days of differentiation into contractile myotubes.

extract_protocol:
RNA was extracted from the C2C12 cell pellet using an RNAeasy-mini kit (Qiagen).
Illumina TruSeq Stranded Total RNA kit

treatment_protocol: A Grass S88 Dual Output Square Pulse Stimulator (Warwick, RI) set at Stimulus Isolation Unit mode was used to drive an electrical current through the electrodes at 1 Hz, 6 millisecond pulse width (0.6% duty cycle), and 2.75 V/mm. An uncoupling in-line capacitor (250 µF) blocked Direct Current and a Double Pull Double Throw (DPDT) mechanical relay was used to switch the electrical field polarity at 0.5 Hz to limit electrophoretic effects

tag: cell line

tag: cell type

value: differentiated skeletal muscle myotubes

tag: treatment

value: EPS stimulated

tag: passage

value: Passage 4-8


title: EPSC2C12-3_S7_L002 [EPSC-2]


title: EPSC2C12-4_S8_L002 [EPSC-3]


title: du145_DU145PS1B_E4_Dabrafenib_1.5_24

value: Dabrafenib

tag: provider

tag: vendor id


title: snATAC Isl C0025

description: snATAC-seq of islet C0025 (non-diabetic)

tag: age

tag: Sex

value: White


title: EPSC2C12-3_S7_L001 [EPSC-2]


title: du145_DU145PS1B_E3_Capecitabine_10_24

value: Capecitabine


title: EPSC2C12-2_S6_L002 [EPSC-1]


title: snATAC Isl C0026

description: snATAC-seq of islet C0026 (non-diabetic)

value: Hispanic/Latino


title: du145_DU145PS1B_H1_Anastrozole_10_24

value: Anastrozole

value: male


title: UHRF1 [3_1]

description:
SAMPLE 3_1
Genome-wide DNA methylation profiling analysis after UHRF1 knockdown.

tag: sirna


title: du145_DU145PS1B_E2_Cladribine_0.5_24

value: Cladribine


title: du145_DU145PS1B_E8_Raloxifene_0.01_24

value: Raloxifene


title: 16E6-E7-B-IL1B

city: Philadelphia

first: Elizabeth

last: White

address: 3610 Hamilton Walk, 203C Johnson Pavilion, Mail Code 6114

institute: University of Pennsylvania

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Sequenced reads were filtered to remove adapters and low-quality reads
Clean reads were mapped to hg19 using STAR (v2.5). STAR used  the method of Maximal Mappable Prefix (MMP).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Assembly: hg19
Supplementary files format and content: gene expression quantification table, calculated all genes' FPKM

source_name: Primary human forekin keratinocytes

extract_protocol:
RNA was isolated with Qiagen RNeasy mini kit in White Laboratory and polyA RNA was isolated using oligo dT beads at Novogene Corporation
RNA libraries were prepared for sequencing using standard Illumina protocols at Novogene Corporation

treatment_protocol:
Tranduced with two oncogene-expressing retroviruses (MSCV-IP N-HA 16E6 and MSCV-neo C-V5 16E7)
Selected with puromycin and neomycin post retroviral transduction
Treated with 0.5 ng/ml IL-1B in media for 3h prior to harvest
Before harvest, cells were refed with keratinocyte serum-free medium (untreated) or with the same medium containing 0.5 ng/ml IL-1B, and incubated for 3 hours.

value: primary human foreskin keratinocytes (HFK)

value: HPV16 E6/E7, IL-1B


title: 16E6-E7-C-IL1B


title: Cdc14ab KO clon 1 time 0

description: mESC Cdc14ab KO not differentiated

value: embryonic stem cells

value: LIF-containing ESC media

tag: clon/replicate


title: EPSC2C12-2_S6_L001 [EPSC-1]


title: TMRM_Low3

first: Meng

state: Guangdong

address: Zhongshan 2nd Road

data_processing:
RNA seq reads were aligned to mouse genome GRCm38 and gene annotation from the Ensembl database. For read alignment and expression quantification, low quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.5.0, Babraham Bioinformatics). The remaining pair-end reads were mapped to the reference genome by Salmon (v0.03.1, COMBINE-lab) with ENCODE options. The uniquely mapped reads were counted and transformed to transcripts per kilobase millionreads (TPM)
Assembly: GRCm38
Supplementary files format and content: TMRM_Raw_Counts.txt.gz with raw counts matrices

source_name: bone marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8 weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Low input RNA seq was performed according to published scRNA seq protocols with modifications (Picelli et al., 2014). Briefly, FACS-sorted 1500 Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) (3-5 µL) of each sample were transferred into 40 µL cell lysis buffer prepared by adding 2 µL of RNase inhibitor to 38 µL of a 0.25% (v/v) Triton X-100 solution. Quickly vortex the tube to mix, and then purify RNA using 80 µL VAHTS RNA Clean Beads (N412, Vayzme), following reverse transcription with 5 µL purified RNA and 15 µL RT mix of each sample. cDNA purified with VAHTS DNA Clean Beads (N411, Vazyme) was used to perform PCR enrichment with 13 cycles of amplification. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit (Q3285, Guangzhou IGE biotechnology ltd) after purification. TruePrepTM DNA library Prep Kit V2 (TD503, Vazyme) was used to prepare RNA seq library following the manufacturer’s protocol. Libraries were sequenced as paired 150 bp using NovaSeq-PE150.

tag: strain

tag: tissue

value: bone marrow

value: 6-8 weeks

tag: genotype

value: wild type


title: du145_DU145PS1B_E1_Regorafenib_5_24

value: Regorafenib

value: ATCC


title: 16E6-E7-A-IL1B


title: EPSC2C12-1_S5_L002 [EPSC-0]

value: differentiated skeletal muscle myotubes

value: EPS stimulated

value: Passage 4-8


title: TMRM_Low2


title: du145_DU145PS1B_D12_Bleomycin_0.275_24

value: Bleomycin


title: 16E6-E7-C-untreated

treatment_protocol:
Tranduced with two oncogene-expressing retroviruses (MSCV-IP N-HA 16E6 and MSCV-neo C-V5 16E7)
Selected with puromycin and neomycin post retroviral transduction
Refed with media only at time of treatment
Before harvest, cells were refed with keratinocyte serum-free medium (untreated) or with the same medium containing 0.5 ng/ml IL-1B, and incubated for 3 hours.

value: HPV16 E6/E7, no IL-1B


title: EPSC2C12-1_S5_L001 [EPSC-0]


title: du145_DU145PS1B_D11_Sunitinib_0.045_24

value: Sunitinib

value: male


title: 16E6-E7-B-untreated


title: TMRM_Low1


title: ControlC2C12-4_S4_L002 [CTRL-3]

source_name: C2C12_non-EPS stimulated

value: non-EPS stimulated


title: ControlC2C12-4_S4_L001 [CTRL-3]


title: du145_DU145PS1B_D10_Fulvestrant_0.03_24

value: Fulvestrant


title: 16E6-E7-A-untreated

value: primary human foreskin keratinocytes (HFK)


title: TMRM_High3


title: TMRM_High2


title: du145_DU145PS1B_D9_Ruxolitinib_10_24

value: Ruxolitinib


title: TMRM_High1


title: ControlC2C12-3_S3_L002 [CTRL-2]


title: GFP-GFP-C-IL1B

treatment_protocol:
Tranduced with two control retroviruses (MSCV-P GFP C-FlagHA and MSCV-neo GFP C-HA)
Selected with puromycin and neomycin post retroviral transduction
Treated with 0.5 ng/ml IL-1B in media for 3h prior to harvest
Before harvest, cells were refed with keratinocyte serum-free medium (untreated) or with the same medium containing 0.5 ng/ml IL-1B, and incubated for 3 hours.

value: control transduction, IL-1B


title: N1

tag: patient diagnosis

value: hepatocellular carcinoma


title: ControlC2C12-3_S3_L001 [CTRL-2]


title: ControlC2C12-2_S2_L002 [CTRL-1]


title: du145_DU145PS1B_D8_Ceritinib_0.5_24

value: Ceritinib


title: GFP-GFP-A-IL1B


title: RNA-Seq - Cl13D30+aPDL1

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

data_processing:
scRNA-seq sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier (UMI) counting and aggregating sequencing runs were performed using 10x Cell Ranger pipeline (3.0.2) and mm10 genome.
Downstream scRNA-seq analysis was performed in R (version 4.0.2) using Seurat (version 4.0.4).
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered gene-barcode matrices containing only cellular barcodes

source_name: P14 CD8 T cells from LCMV Clone13 infection+anti PDL1 treatment

extract_protocol:
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells.
The scRNAseq libraries were generated using 10x Genomics Chromium Single Cell 3’ Library (v2) according to the manufacturer’s protocol.
scRNA-seq

treatment_protocol: PD1 blockade was performed with 5 treatments of 200ug aPD-L1 antibody (10F.9G2, BioXCell) i.p. every 3 days starting 16 days after infection with LCMV Cl13. Analysis was performed one day after final treatment. For control treatments, phosphate-buffered saline (PBS) was administered i.p.

value: P14 CD8 T cells

tag: background strain


title: GFP-GFP-B-IL1B


title: GFP-GFP-C-untreated

treatment_protocol:
Tranduced with two control retroviruses (MSCV-P GFP C-FlagHA and MSCV-neo GFP C-HA)
Selected with puromycin and neomycin post retroviral transduction
Refed with media only at time of treatment
Before harvest, cells were refed with keratinocyte serum-free medium (untreated) or with the same medium containing 0.5 ng/ml IL-1B, and incubated for 3 hours.

value: control transduction, no IL-1B


title: du145_DU145PS1B_D7_Gemcitabine_0.00255_24

treatment_protocol: Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.

value: Gemcitabine

value: ATCC


title: ControlC2C12-2_S2_L001 [CTRL-1]

value: differentiated skeletal muscle myotubes


title: du145_DU145PS1B_D6_DMSO_0_24

value: DMSO


title: RNA-Seq - Cl13D15

source_name: P14 CD8 T cells from LCMV Clone13 infection 15 days post infection

value: No


title: du145_DU145PS1B_D5_Olaparib_1_24

value: Olaparib


title: GFP-GFP-B-untreated


title: du145_DU145PS1B_D4_Procarbazine_2_24

value: Procarbazine


title: ControlC2C12-1_S1_L002 [CTRL-0]

value: Passage 4-8


title: GFP-GFP-A-untreated


title: ControlC2C12-1_S1_L001 [CTRL-0]

value: non-EPS stimulated


title: RNA-Seq - Cl13D8

source_name: P14 CD8 T cells from LCMV Clone13 infection 8 days post infection


title: RNA-Seq - ArmD30

source_name: P14 CD8 T cells from LCMV Armstrong infection 30 days post infection


title: du145_DU145PS1B_D3_Nelarabine_10_24

value: Nelarabine

value: male


title: RNA-Seq - ArmD8

source_name: P14 CD8 T cells from LCMV Armstrong infection 8 days post infection


title: F_F_159_NC_NT

first: Tatiana

last: Kisseleva

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA 1.18.64 with default parameters
Sequenced reads were mapped to the Mouse Genomes Project GRCm38_68.fa reference genome using STAR v2.5.1a with default parameters
Read quantification was performed with RSEM v1.3.0 and Ensembl annotation Mus_musculus.GRCm38.68.gtf
Genome_build: GRCm38.68
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts for each gene accession number and sample

source_name: Liver

extract_protocol:
Total RNA was isolated using Purelink RNA Mini Kit (Life Technologies)
Illumina Stranded Total RNA (Illumina 20020597)

value: Liver

tag: injury model

value: DEN

value: chow


title: F_F_158_NC_NT


title: du145_DU145PS1B_D2_UNTREATED_0_24

source_name: prostate cancer

value: UNTREATED


title: HiChIP EndoC untreat 72h

description:
HiChIP of islet EndoC_betaH1 treatment: untreated for 72h
HiChIP_interactions_EndoC-BH1_cells.xlsx

data_processing:
Data was processed using the MAPS v2.0 pipeline from Arima Genomics using hg19 as the reference genome and H3K27ac ChIP-seq peaks in EndoC-βH1 cells from a published study (PMID: 30650367). Interactions between 5kb windows containing a H3K27ac peak in both ends were considered significant at FDR<0.10.
Assembly: hg19
Supplementary files format and content: Matrix tables with raw gene or peak counts for every gene/peak and every sample
Supplementary files format and content: Co-accessible sites are provided for beta cells and annotated with gene promter within a 5kb window
Supplementary files format and content: List of islet candidate regulatory elements coordinates annotated with cell type and cytokine response
Supplementary files format and content: List of final barcodes and cell type assignments of the snATAC experiments
Library strategy: HiChIP

source_name: EndoC_betaH1 cell line

growth_protocol: EndoC-βH1 cells were cultured at 9×104 cells/cm2 of cell culture surface area pre-coated with ECM (Sigma) and Fibronectin (Sigma). Cell culture media containing DMEM (Gibco), 2% BSA (Sigma), 3.5× 10-4% 2-mercaptoethanol (Gibco), 0.12% Nicotinamide (Calbiochem), 5.5 ng/mL transferrin (Sigma), 6.7pg/mL Sodium Selenite (Sigma) and 1% Penicillin-Streptomycin (Gibco) were refreshed every 2 days. Cells were passaged weekly using 0.25% Trypsin-EDTA, which was quenched with an equal volume of FBS and two volumes of IMDM media (Gibco).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 minutes with shaking at room temperature, followed by a 5-minute quenching step with 1.25 M glycine/PBS. Cross-linked EndoC-βH1 cells in both control and cytokine-treated conditions were washed three times with ice-cold PBS and collected from the dish with a cell scraper. Cells were then pelleted, and flash frozen with liquid nitrogen.
HiChIP assays were performed by Arima Genomics using the HiC+ protocol with a H3K27ac antibody, and libraries were sequenced on an Illumina NovoSeq with 150 bp paired end reads.

treatment_protocol: 10 million EndoC-βH1 cells were treated with either control (0.1% BSA) or cytokines (0.5 ng/mL IL1β, 1 ng/mL TNFα and 10 ng/mL IFNγ) for 72 hours.

value: no treatment

tag: treatment duration

tag: experiment label

value: untreat


title: RNA-Seq - ArmD15

source_name: P14 CD8 T cells from LCMV Armstrong infection 15 days post infection

tag: cell type

value: P14 CD8 T cells


title: du145_DU145PS1B_D1_Lenalidomide_1.5_24

tag: treatment

value: Lenalidomide

tag: cell line

value: ATCC


title: du145_DU145PS1B_C12_Paclitaxel_0.00225_24

value: Paclitaxel

tag: provider


title: RNA-Seq - Cl13D30

source_name: P14 CD8 T cells from LCMV Clone13 infection 30 days post infection

value: No


title: HiChIP EndoC 3cyt-hi 72h

description:
HiChIP of islet EndoC_betaH1 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
HiChIP_interactions_EndoC-BH1_cells.xlsx


title: dHEP_164_NC_NT


title: du145_DU145PS1B_C11_Afatinib_0.185_24

value: Afatinib

tag: vendor id


title: dHEP_165_NC_NT


title: snATAC Isl.15337453 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
"Bulk-like" matrices of read counts, but are derived from single cell data.
snATAC-seq of islet SAMN15337453 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Coaccessible_sites_untreated_beta_cells.tsv
Coaccessible_sites_cytokine-treated_and_untreated_beta_cells.tsv
stellate.snATAC_count.matrix.txt
endothelial.snATAC_count.matrix.txt
delta.snATAC_count.matrix.txt
alpha.snATAC_count.matrix.txt
acinar.snATAC_count.matrix.txt
beta.snATAC_count.matrix.txt
snATAC_barcodes_and_metadata.csv

data_processing:
Processing. 10x Genomics Cell Ranger ATAC v1.1 and multiplet removal script (version 1.1) were used to process 10x fastq files for each sample and perform alignment to the hg19 reference genome. BAM files were filtered for PCR duplicates, converted into tagAlign files, and intersected with a reference set of islet ATAC-seq peaks. Each experiment was clustered separately using scanpy following the procedure described in Chiou et al. 2021 (PMID: 33795864). Demuxlet was used to deconvolute the two-samples snATAC pool using genotyping data from Illumina Infinium Omni 2.5-8 array imputed into the HRC r1.1 panel.
Clustering. The filtered assays were merged and combined with 3 existing islet snATAC datasets previously processed using the same method; and the top 50 PCs were obtained. Harmony was used to batch correct PCs for experiments followed by UMAP dimensionality reduction and clustering using the Leiden algorithm (Resolution = 0.5), and sub-clustered using the Louvain algorithm (Resolution = 1.5). Low-quality cells from the merged clusters were iteratively removed and manual doublet removal was performed on sub-clusters with above average high usable read depth or those that expressed multiple marker genes. Cell type of each cluster was assigned based on chromatin accessibility at promoter regions of known marker genes. The remaining cells excluding samples used for reference were used for downstream analysis.
Differential chromatin accessibility in islet cell types. Accessible sites the individual cell types were identified as described in Chiou et al. 2021 (PMID: 33795864) and then used to annotate the consensus set of peaks identified in bulk islet ATAC using bedtools intersect. Duplicate-removed BAM files from each assay were used to generate a bulk-like matrix of read counts mapping to the consensus islet peaks in each cell type using featureCounts. Each celltype matrix was filtered for an average read depth of 1 per sample/condition and DESeq2 was used to identify differentially accessible sites between cytokine treated and untreated samples with the donor as covariate.
Co-accessibility. Cicero (version 1.4.4), was used to calculate co-accessibility between pairs of snATAC peaks in either untreated beta cells, cytokine-treated beta cells or merged treated-untreated beta cells, following the method described in Chiou et al. 2021 (PMID: 33795864). To annotate co-accessibility links between distal and promoter peaks, we annotated peaks within a 5kb window of a transcription start site (+/- 2.5 kb from GENCOVEv19 TSS).
Assembly: hg19
Supplementary files format and content: Matrix tables with raw gene or peak counts for every gene/peak and every sample
Supplementary files format and content: Co-accessible sites are provided for beta cells and annotated with gene promter within a 5kb window
Supplementary files format and content: List of islet candidate regulatory elements coordinates annotated with cell type and cytokine response
Supplementary files format and content: List of final barcodes and cell type assignments of the snATAC experiments

extract_protocol:
Cells were collected from culture and homogenized in permeabilization buffer consisting of 5% BSA, 0.2% IGEPAL-CA630, 1mM DTT, and 1X cOmplete EDTA-free protease inhibitor (Sigma) in 1X PBS. Isolated nuclei were resuspended in 1X TDE1 buffer (Illumina) and quantified using a Countess II Automated Cell Counter (Thermo).
Islet nuclei were adjusted to a concentration of approximately 3000 nuclei/uL. We targeted 5000 nuclei per assay for use in the 10X Genomics Chromium Single Cell ATAC assay, v1 chemistry. Sequencing was performed at the UCSD Institute for Genomic Medicine on an Illumina NovaSeq using a specific paired-end 10X ATAC run configuration with reads of 50bp.
snATAC-seq

treatment_protocol: For cytokine-treated samples, human cytokines were added to the culture media for the indicated duration and concentration as follows: for high doses, 10ng/mL and IFN-g, 0.5ng/mL IL-1B (2 cytokines), with 1ng/mL TNF-α where indicated (3 cytokines); for low doses, 0.2ng/mL IFN-g and 0.01ng/mL IL-1B (2 cytokines), with 0.02ng/mL TNF-α where indicated (3 cytokines).

value: Pancreatic islets

tag: source id


title: RNA-Seq - Naïve

source_name: P14 naïve CD8 T cells


title: dHEP_155_NC_NT


title: du145_DU145PS1B_C10_Leuprolide_0.075_24

value: Leuprolide

tag: age

tag: Sex