title: MCF7 cells; Y537S mutant ER; Vehicle (DMSO); biol rep 2

value: Y537S mutant ER

value: Vehicle (DMSO)


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous) and Capecitabine (150mg/kg/d oral); 10 d; biol rep 3

status: Public on Jun 01 2024

type: SRA

city: Boston

first: Rinath

last: Jeselsohn

state: MA

address: 450 Brookline Ave.

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
The VIPER pipeline was used for alignment, quality control, and downstream analysis.
Alignment to the hg19 human genome was done using STAR v2.7.0f followed by transcript assembly using cufflinks v2.2.1.
Quality control steps were done using STAR v2.7.0f and RseQC v2.6.4.
Assembly: hg19
Supplementary files format and content: comma-delimited text file containing raw counts (via STAR) for each sample
Supplementary files format and content: comma-delimited text file containing FPKM values (via Cufflinks) for each sample

molecule: total RNA

organism: Homo sapiens

source_name: PDX1526 model

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy kit with DNase digestion. RNA concentrations were measured by NanoDrop, and the quality of RNA was determined by a Bioanalyzer. RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina). Samples were sequenced on an Illumina Nextseq500.
RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: When tumors reached 150-200 mm3, mice were randomized into 4 arms (N=5-8): control (drug vehicle), fulvestrant 5mg/mouse/week subcutaneous, capecitabine 150mg/kg/daily oral and fulvestrant 5mg/mouse + capecitabine 150 mg/kg. Capecitabine was administered in a cycle consisting of 14 days on, 7 days off and again 7 days on. Fulvestrant vehicle was 10% ethanol and castor oil, while capecitabine vehicle was 10% Dimethylsulfoxide (DMSO), 40% polyethylene glycol, 2.5% Tween-80, and 47.5% normal saline.

tag: tissue

value: PDX1526 model

tag: cell type

tag: genotype

tag: treatment

value: Fulvestrant (5mg/mouse/week subcutaneous) and Capecitabine (150mg/kg/daily oral)

tag: time

value: 10 days


title: MCF7 cells; WT ER; Fulvestrant (10nM) and 5FU (1000 nM); biol rep 2

source_name: Breast

extract_protocol:
Then, cells were harvested (as duplicates) for downstream RNA analysis. Total RNA was extracted using the QIAGEN RNeasy kit with DNase digestion. RNA concentrations were measured by NanoDrop, and the quality of RNA was determined by a Bioanalyzer. RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina). Samples were sequenced on an Illumina Nextseq500.
RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina).

value: Breast

tag: cell line

value: Breast cancer cell line

value: WT ER

value: Fulvestrant (10nM) and 5FU (1000 nM)

value: 12 hours


title: NUFS208859

city: Seongnam-si

first: Dong Min

last: Shin

address: 700, Daewangpangyo-ro, Bundang-gu

country: South Korea

institute: Theragen Bio

data_processing:
Sequecne Reads were trimmed for adaptor sequence / low-quality sequence using cutadapt (version : 2.8, parameter : quality-cutoff (20), minimum-length (50))
Trimmed Sequence reads were mapped to reference genome
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options  with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Gene expression estimation was performed by RSEM v.1.3.1 considering the direction of the reads which are corresponding to the library protocol using option --strandedness. To improve the accuracy of the measurement, “--estimate-rspd” option was applied. All other options were set to default values. To normalize sequencing depth among samples, FPKM and TPM values were calculated.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes TPM for each sample

molecule: polyA RNA

source_name: Ovarian cancer

extract_protocol:
RNA was harvested using Rnaesay mini plus kit (Qiazen).
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA).

value: Ovarian cancer


title: NUFS163769


title: PBMC, ACS2

city: Hangzhou

first: Zhicheng

last: Pan

address: 79 Qingchun Road

department: Department of Cardiology

country: China

institute: The First Affiliated Hospital, Zhejiang University School of medicine

data_processing:
Sequencing data were filtered and trimmed using Cutadapt (v1.14), and then aligned to a reference transcriptome using Hisat2 (v2.0.5, default parameters). Transcripts were assembled using the StringTie (v1.3.1c) tool, and expression levels were calculated using the Ballgown tool (v2.8.4). Circular RNAs are identified and quantificated using CIRCexplorer2 (v2.2.6).
Assembly: hg19
Supplementary files format and content: Expression_Gene.txt (tab-delimited text file include FPKM values for each sample)
Supplementary files format and content: Expression_circRNA.txt (tab-delimited text file include raw counts for each sample)

source_name: PBMC

extract_protocol:
Total RNA was extracted from the PBMC samples using the Total RNA Extraction Reagent (Vazyme biotech co., Ltd, R401), according to the manufacturer’s instructions. The integrity of the extracted RNA was assessed through agarose gel electrophoresis, while the quantity and quality were evaluated using the NanoDrop ND-1000.
For library construction, 1 μg of the total RNA was utilized. To remove rRNA, the RiboZero Magnetic Gold Kit (Epicentre, an Illumina Company) was employed. Subsequently, the KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used to construct the RNA-sequencing library. All procedures were conducted following the manufacturer’s instructions

value: PBMC

tag: condition

value: ACS


title: A4_1_20OH2D3

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

data_processing:
Raw FASTQ files were aligned to reference genome using STAR version 2.7.1a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using Cufflinks version 2.2.1 using parameters --library-type fr-firststrand -G -L
All 10 samples were merged using Cuffmerge (from above Cufflinks) using parameters -g -s
Differential expression was calculated using Cuffdiff (from above Cufflinks) using parameters --library-type fr-firststrand -L
Assembly: Gencode GRCh38 p7 Release25
Supplementary files format and content: tab-delimited text file containing FPKM values for each gene in each sample

source_name: WM164 melanoma line

growth_protocol: The cells were cultured using DMEM media supplemented with 10% serum (fetal bovine serum while growing cells and charcoal-treated serum during incubation with vitamin D compounds), 1% antibiotics and 5 µg/mL insulin (Sigma-Aldrich, St. Louis, MO, USA). Cells were cultured in 75 cm2plastic filtered flasks (TPP–Techno Plastic Products AG, Trasadingen, Switzerland) in an incubator at 37 °C with 5% CO2.

extract_protocol: RNA was isolated using Absolutly RNA Miniprep Kit  (Stratagen) . Approximately 120 ng/ul of each sample was sent for RNAseq analysis. BGI@CHOP genomics company sequenced the samples on Illumina HiSeq TM, analyzed, and sent us the results.

treatment_protocol: VDR-KO or scramble WM164 cells were plated onto 100 mm2Petri dishes and treated with 1,25(OH)2D3, 25(OH)D3, 20(OH)D3, 1,20(OH)2D3 or ethanol (control) in triplicates.  Cells were incubated in 10% charcoal-treated serum for 24 h. Cells were further harvested and RNA isolated using Absolutly RNA Miniprep Kit  (Stratagen)

value: WM164 melanoma line

value: VDR knockout


title: NUFS175472


title: PBMC, ACS3


title: A3_25OHD3


title: NUFS146568


title: A1_EtOH_control

value: ethanol 0.1percent


title: PBMC, ACS1


title: MCF7 cells; Y537S mutant ER; Vehicle (DMSO); biol rep 1


title: MCF7 cells; WT ER; 5FU (1000 nM); biol rep 2


title: PBMC, SA3

value: SA


title: MCF7 cells; WT ER; 5FU (1000 nM); biol rep 1


title: A2_1_25OH2D3


title: MCF7 cells; WT ER; Fulvestrant (10nM) and 5FU (1000 nM); biol rep 1


title: MCF7 cells; WT ER; Fulvestrant (10nM); biol rep 2

value: Fulvestrant (10nM)


title: NUFS116442


title: SW780, RC48, rep3

city: Tianjin

first: Jingxian

last: Li

address: Pingjiang Road 23#, Hexi District, Tianjin

institute: Tianjin institute of urology

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The limma was used to perform differential expression analysis.limma: Adjusted Pvalue <= 0.05
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: bladder cancer

extract_protocol:
RNA was harvested using Trizol reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA librares were prepared for sequencing using the standard BGI protocols.

value: bladder cancer


title: NUFS122160


title: SW780, RC48, rep2


title: PBMC, SA1


title: NUFS115586


title: SW780, RC48, rep1


title: NUFS114596


title: SW780, Control, rep3

value: Control


title: NUFS111474


title: PBMC, Ctrl3

value: Ctrl


title: PBMC, Ctrl2


title: MCF7 cells; WT ER; Vehicle (DMSO); biol rep 2

value: Vehicle (DMSO)


title: PBMC, SA2


title: MCF7 cells; WT ER; Vehicle (DMSO); biol rep 1

value: Breast


title: NUFS095273


title: NUHE831286


title: SW780, Control, rep1


title: 12570_RA_PCW17_RNA

city: Bern

first: Marco

last: Osterwalder

address: Murtenstrasse 24

department: DBMR

country: Switzerland

institute: Universiy of Bern

data_processing:
Single-end reads were subjected to quality filtering and adaptor trimming using cutadapt_v1.1 (‘-m 25 -q 25’). Tophat v2.0.6 was used to align RNA-seq reads to the mouse reference genome (hg19) and the reads mapping to UCSC known genes were determined by HTSeq (Anders 2015).
Assembly: hg19
Supplementary files format and content: bigWig files were generated using bedtools from bedGraph files derived from read mapping with HTSeq (Anders 2015)

source_name: fetal right atrium, total RNA

extract_protocol:
RNA was isolated from homogenized tissue using the TRIzol Reagent (Thermo Fisher Scientific). RNA samples were DNase-treated with the TURBO DNA-free Kit (Thermo Fisher Scientific), and then RNA quality was assessed via 2100 Bioanalyzer (Agilent) and an RNA 6000 Nano Kit (Agilent).
RNA-seq libraries were generated via the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat kit (Illumina), according to manufacturer protocols.
RNA-seq, libraries were subjected to additional purification steps to remove remaining high molecular weight products.

value: right atrium

tag: developmental stage

tag: library type

value: Stranded (first-strand synthesis)


title: ETP-ALL_patient_56284

city: Moscow

first: Elena

last: Zerkalenkova

address: Samora Mashela str., 1

country: Russia

institute: Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology

data_processing:
Sequencing data was aligned to the reference using STAR aligner (ver. 2.10.7b)
Fusion transcripts were called using Arriba (ver. 2.4.0)
Read counts were calculated using salmon (ver. v1.10.1)
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file containing fusions called by Arriba
Supplementary files format and content: tab-delimited text file containing discarded fusions called by Arriba
Supplementary files format and content: tab-delimited text file containing TPM counted by salmon

source_name: bone marrow blasts

extract_protocol:
RNA was extracted with InnuPrep kit (AnalytikJena, Jena, Germany). 1 ug of total RNA was taken for library preparation.
Nextera UltraII Directional RNA kit (NEB, Ipswich, MA, USA) according to manufacturers' instructions

value: bone marrow blasts

value: disease oneset

tag: relapse status

value: no relapse


title: MCF7 cells; WT ER; Fulvestrant (10nM); biol rep 1

value: Breast cancer cell line

value: WT ER

value: 12 hours


title: NUFS076685

value: Ovarian cancer


title: 12570_RV_PCW17_RNA

source_name: fetal right ventricle, total RNA

value: right ventricle


title: ctr1d polyA Rep2

city: Melbourne

first: Attila

last: Horvath

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description: OligodT purified poly(A) selected RNA was used for cDNA library preparation

data_processing:
Paired-end illumina reads were aligned with hisat 2.1.0,allowing introns with a maximum length of 2,000 nt (‘--max.intronlen 2000’).
Aligned bam files were then sorted and indexed using samtools 1.3.1
Strand-specific bigwig tracks were generated using bamCoverage to the pombe genome (ASM294v2) with the parameter ‘—binSize 1’.
Assembly: ASM294v2
Supplementary files format and content: Bigwig tracks were generated after normalisation by the sum of the raw signals of chromosome I and II multiplied by 100 million.

organism: Schizosaccharomyces pombe

source_name: S. pombe grown in YEA liquid culture to an OD600 of 0.8

growth_protocol: S. pombe strains used for the study were grown in YEA liquid culture to an OD of 0.8 - 2.2 according to experiment performed.

extract_protocol:
RNA was isolated using TriReagent (Sigma-Aldrich, T9424) and precipitated using 2-propanol (Sigma-Aldrich). 10ug of this isolated RNA was used for DNase treatment using NEB DNase 1 (M0303), and purified using the RNA Clean and Concentrator Kit (Zymo Research, R1015/R1017).
1 ug of RNA samples were OligodT purified (NEB, E7490) and the recovered poly(A) selected RNA was used for cDNA library preparation using NEBNext Ultra II directional RNA library kit (NEB, E7760) following manufacturers library preparation protocol.

value: h+, HIS, leu1-32, ade6-210, ura4-D18, ctr1(SPAC140.04)delta::kanMX6


title: ETP-ALL_patient_55216


title: ETP-ALL_patient_55019


title: NUFS061036


title: SW780, Control, rep2


title: 12570_LA_PCW17_RNA

source_name: fetal left atrium, total RNA

value: left atrium


title: PBMC, Ctrl1

value: PBMC


title: Wild Type polyA Rep1


title: 12570_LV_PCW17_RNA [re-analysis]

description: GSM3605148 (12570_LV_PCW17_RNA)

source_name: fetal left ventricle, total RNA

value: left ventricle


title: ETP-ALL_patient_44144

value: relapsed


title: ETP-ALL_patient_51082


title: NUFS060930


title: MS2-RsaG_R1

city: Strasbourg

first: Isabelle

last: Caldelari

address: rue René Descartes

country: France

institute: CNRS

description: MS2 affinity purified RNA

data_processing:
Basecalling pipeline: 1. HiSeq Control Software 2.2.38; 2. RTA 1.18.61.0; 3. CASAVA-1.8.2
Adapter sequences and poor quality reads removed with Trimmomatic
Reads alignement on the HG001 genome (GenBank assembly accession: GCA_001900185.1) using BOWTIE2 (very sensitive end-to-end protocol with maximum 4 mismatches allowed).
Reads per feature counted with HTseq. The protocol chosen is interception non-empty, with reverse strand interpretation.
Differential analysis with DEseq2 (n=2)
Genome_build: GCA_001900185.1
Supplementary_files_format_and_content: Tables obtained by DEseq2 reporting the Fold Changes, p-values and p-adj-values

organism: Staphylococcus aureus

source_name: Bacterial cells

growth_protocol: Bacteria were grown in Brain Heart Infusion (BHI) medium for 5 hours, then 0.5% glucose-6-phosphate was added for another hour of incubation at 37°C. Erythromycin at 10 ug/ml final concentration was added to the medium for plasmid selection.

extract_protocol:
Bacterial cells were resuspended in lysis Buffer (20 mM Tris-HCl pH 8, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and broken using the FastPrep apparatus. Crude extract were loaded on a MS2-MBP coated column and purified by affinity chromatography. Eluted RNA were extracted with phenol/chloroform :isoamylalcohol prior to RNAseq analysis.
DNase I (0.1 U/ml) treatment was performed 1h at 37°C. The reactions mixtures were then purified by phenol/chloroform/isoamylalcohol and subsequent ethanol precipitation. RNA pellets were re-suspended in sterile milliQ water. RNA quality and quantity assessments were performed on Agilent Nano Chip on the Bioanalyzer 2100. RNAs were treated to deplete abundant rRNAs, and the cDNA libraries were performed using the ScriptSeq complete kit (bacteria) from Illumina. The libraries were sequenced using Illumina MiSeq with a V3 Reagent kit (Illumina), which preserves the information about the orientation of the transcripts and produces reads of 150 nts, which map on the complementary strand. Each RNA-seq was performed at least in duplicates.

tag: strain

value: HG001 delta-rsaG

tag: plasmid

value: pCN51-P3 MS2-RsaG


title: irradiated HaCaT cells, LBP treatment,repeated experiment group 3

city: Chendu

first: Si

middle: jing

last: Jiang

state: Sichuan

address: 32# W. Sec 2, 1st Ring Rd

department: Stomatology department

institute: Sichuan Provincial People's Hospital

description:
"FY" means group with irradiated cells with LBP pretreatment
FY3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The  adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence using Hisat2 tools.
Assembly: The project used the specified genome as a reference for sequence alignment and subsequent analysis. The reference genome download address:ftp://ftp.ensembl.org/pub/release-103/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.The first column represents the gene ID, and the remaining columns represent the amount of expression of the gene in different samples
Supplementary files format and content: text files include gene counts for each Sample.The first column represents the gene ID; The last column indicates the length of the gene, and the remaining columns indicate the alignment of genes in different samples    to the number of fragments on the gene.

source_name: mucosa

growth_protocol: HaCaT cells were maintained in RPMI 1640 Medium supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol at 3 h after irradiation
The cDNA fragments were amplified by PCR, and products were purified by Ampure XP Beads. The double stranded PCR products were heated denatured and circularized by the splint oligo sequence to get the final library.

treatment_protocol: HaCaT cells were pretreated with LBP or vehicle for 24h before 12 Gy radiation.

value: mucosa

value: HaCaT

value: WT

value: LBP pretreatment, irradiation


title: RFP, RMC-6272, 24h, replicate 2

city: San Francisco

first: Sourav

last: Bandyopadhyay

state: CA

address: 1450 3rd Street

department: Department of Bioengineering and Therapeutic Sciences

institute: University of California San Francisco

data_processing:
the ribosome profiling reads were first trimmed using cutadapt (v2.3) to remove the linker sequence AGATCGGAAGAGCAC
The fastx_barcode_splitter script from the Fastx toolkit was then used to split the samples based on their barcodes. Since the reads contain unique molecular identifiers (UMIs), they were collapsed to retain only unique reads. The UMIs were then removed from the beginning and end of each read (2 and 5 Ns, respectively) and appended to the name of each read using umitools (v0.3.3).
Bowtie2 (v2.3.5) was then used to remove reads that map to ribosomal RNAs and tRNAs, and the remainder of reads were then aligned to mRNAs (we used the isoform with the longest coding sequence for each gene as the representative)
Subsequent to alignment, umitools was used to deduplicate reads. The RNA-seq reads were directly aligned to the same mRNA reference using bowtie2.
The translation efficiencies, i.e. the ratio between the RPF and RNA read counts per gene, were compared using Ribolog.
Supplementary files format and content: tab-delimited text file including normalized read counts for each Sample after filtering out low count transcripts

growth_protocol: MCF-7 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Please refer to this paper for details: McGlincy NJ, Ingolia NT. Transcriptome-wide measurement of translation by ribosome profiling. Methods 2017; 126: 112-129.
Please refer to this paper for details: McGlincy NJ, Ingolia NT. Transcriptome-wide measurement of translation by ribosome profiling. Methods 2017; 126: 112-129.

treatment_protocol: Cells were treated with 20 nM RMC-6272, 20 nM everolimus, or DMSO for indicated time.

value: breast cancer cells


title: NUFS076959


title: NUFS057918


title: NUFS060426


title: RFP, RMC-6272, 24h, replicate 1


title: ctr1d polyA Rep1


title: ETP-ALL_patient_37940

value: bone marrow blasts

value: disease oneset

value: no relapse


title: irradiated HaCaT cells,vehicle,repeated experiment group 3

description:
"FW" means group with irradiated cells without LBP pretreatment
FW3

value: irradiation


title: RFP, everolimus, 24h, replicate 2

value: everolimus


title: irradiated HaCaT cells, LBP treatment,repeated experiment group 2

description:
"FY" means group with irradiated cells with LBP pretreatment
FY2


title: MES28 cells, shMCT1-2

city: Chapel Hill

first: Daqi

address: 450 West Dr

institute: Univerity of North Carolina at Chapel Hill

data_processing:
RNA sequencing was performed using BGISEQ-500 platforms. FASTQ sequencing reads were trimmed using Trim Galore (RRID:SCR_011847), and transcript quantification was performed using Salmon with the quasi-mapping mode
Assembly: hg38
Supplementary files format and content: MES28_MCT1_core_table_gene.txt includes FPKM values for 4 of total 12 Samples
Supplementary files format and content: MES28_KU70_core_table_gene.txt includes FPKM values for 4 of total 12 Samples
Supplementary files format and content: MES28_KU70_WT_MU_core_table_gene.txt includes FPKM values for 4 of total 12 Samples

source_name: glioblastoma

extract_protocol:
Total RNA was extracted with Trizol reagent (Takara) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: glioblastoma

value: glioma stem cells


title: irradiated HaCaT cells, LBP treatment,repeated experiment group 1

description:
"FY" means group with irradiated cells with LBP pretreatment
FY1


title: ETP-ALL_patient_43846


title: NUFR827541

value: Ovarian cancer


title: ETP-ALL_patient_28408


title: RFP, everolimus, 24h, replicate 1


title: PDX1526; Y537S mutant ER; Vehicle (DMSO); 10 d; biol rep 3

value: PDX1526 model

value: Y537S mutant ER

value: Vehicle (DMSO)

value: 10 days


title: irradiated HaCaT cells,vehicle,repeated experiment group 2

description:
"FW" means group with irradiated cells without LBP pretreatment
FW2

value: mucosa


title: NUFR758685


title: RFP, RMC-6272, 4h, replicate 2

value: 4 h


title: NUFS057592


title: CHiC_H_E115-WT

library_source: genomic

data_processing:
Sequencing was performed to have comparable depth among tissue samples and reads were mapped to the reference genome GRCm38/mm10, filtered and de-duplicated using HiCUP pipeline v0.8.1. The pipeline was set up with Bowtie2 v2.4.5 for short read mapping. Juicer command line tools v1.9.9 was used for the generation of binned contact maps from valid and unique read pairs with MAPQ ≥ 30. Normalization and diagonal filtering was performed using the Cooler v0.8.11 matrix balancing tool with options “--mad-max 5 --min-nnz 10 --min-count 0 --ignore-diags 2 --tol 1e-05 --max-iters 200 --cis-only”. For binning and normalization, only the genomic region chr3:65196079-68696078 (mm10) that represents the targeted interval was considered and read pairs mapping to this interval were retained and shifted by the offset of 65,196,078 bp using custom chrom.sizes files. Balanced maps were exported at 5kb resolution with corrected coordinates (transformed back to original values). Subtraction maps were directly generated from Cooler balanced HiCmaps using hicCompareMatrices tool (HiCExplorer v3.7.2) with option “--operation diff”. Hi-C maps were visualized from .cool files using pyGenomeTracks.
Normalized inter-domain insulation scores(Crane et al. 2015)and TAD boundaries were determined using FAN-C(Kruse et al., 2020)(v.0.9.26-b2-beta) with ‘fanc insulation -w 15000 25000 35000 50000 75000 100000 130000’ and‘fanc boundaries --min-score 0.21’, respectively, from input .cool matrices. Tissue-differential insulation scores and boundary values were calculated using ‘fanc compare -c difference’and‘fanc boundaries --min-score 0.21’.
For virtual Capture-C, to better visualize individual interactions of target regions, a 5kb viewpoint centered on the coordinates of each genomic element of interest was used. Capture-C-like profiles were generated as described (Paliou et al., 2019) from filtered unique read pairs (hicup.bam files) which also served as input for CHi-C maps. Read-pairs were mapped based on MAPQ ≥ 30 and relative position of the two reads inside and outside the viewpoint, respectively. After quantitation of reads outside of the viewpoint (per restriction fragment), read counts were distributed into 3kb bins with proportional distribution of read counts in case of overlap with more than one bin. Each binned profile was smoothened by averaging over a running window of 5 bins and scaled by 10^3 / sum of all its counts on chr3 (Paliou et al., 2019). Peak profiles were generated using custom Java code based on htsjdk v2.12.0 (https://samtools.github.io/htsjdk/). The viewpoint and neighboring +/-5kb regions were excluded from computation of the scaling factor. The following genomic interval was used as Virtual Capture-C viewpoint: chr3:66,978,288-66,983,288 (centering Shox2 TSS). BigwigCompare tool (deepTools v3.5.1) was further used to generate relative subtraction Capture-C-like profiles.
Assembly: GRCm38/mm10
Supplementary files format and content: hic output files containing binned contact maps from unique read pairs (MAPQ ≥ 30) were generated by Juicer command line tools v1.9.9 (Durand 2016).
Supplementary files format and content: cool files containing balanced contact matrices generated with the hicConvertFormat tool (HiCExplorer v3.7.2) from native .hic out-puts.

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic Heart

growth_protocol: Embryonic forelimbs, mandibular processes, and hearts of wildtype embryos at E11.5 (48-52 somite-stage) were microdissected in cold PBS and subjected to tissue dissociation.

extract_protocol:
Tissues were homogenized using a Dounce tissue grinder and fixed with 2% formaldehyde (37%) for 10 min. The reaction was quenched using 1.25M Glycine and pellets were snap-frozen for storage at -80°C. For nuclei isolation pellets were resuspended in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor). After on wash with PBS samples were digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was sheared and after adaptor ligation and amplification of sheared DNA fragments, libraries were hybridized to custom-designed SureSelect beads (SureSelectXT Custom 0.5-2.9Mb library) and indexed following Agilent’s instructions. Multiplexed libraries were sequenced using a Illumina HiSeq 4000 (50bp paired-end).
3C-library, hybridization to custom-designed SureSelect beads (Agilent)

value: Embryonic Heart

value: FVB

tag: embryonic day

value: WT


title: ETP-ALL_patient_24345

value: bone marrow blasts


title: irradiated HaCaT cells,vehicle,repeated experiment group 1

description:
"FW" means group with irradiated cells without LBP pretreatment
FW1

value: HaCaT


title: NUFR758296


title: HaCaT cells, LBP treatment, repeated experiment group 1

description:
"KY" means group with non-irradiated cells with LBP pretreatment
KY1

value: LBP pretreatment


title: Tet-FLAG-FOXM1c-hTERT-RPE1 no dox RNA-seq, rep 3

city: Chicago

first: Sakshi

last: Khurana

state: IL

address: SQBRC Room 7-400, 303 E Superior St.

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description:
R_586nd3
htseq.normCounts.txt
htseq.fpkms.txt

data_processing:
Data was processed using the Ceto pipeline (https://github.com/ebartom/NGSbartom)
Base calls were performed using bcl2fastq2.17.1.14 for NextSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with Trimmomatic and then reads were aligned to hg19 with Tophat
Read counts and differential gene expression profiling analysis was conducted using EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKMS for each sample

extract_protocol:
Qiagen Rneasy Kit
1ug RNA was used as input, using NEBNext polyA isolation kit and Ultra II RNA library kit following manufacturer protocol

treatment_protocol: 1ug/mL doxycycline evey 24 hours for 48 hours

value: epithelial


title: RFP, RMC-6272, 4h, replicate 1

value: breast cancer cells


title: HaCaT cells,vehicle,repeated experiment group 1

description:
"KW" means group with non-irradiated cells without LBP pretreatment
KW1

value: non


title: RFP, everolimus, 4h, replicate 2

value: everolimus


title: ETP-ALL_patient_14441

value: disease oneset

value: no relapse


title: RFP, DMSO, 4h, replicate 1

value: DMSO (control)


title: NUFR741676

value: Ovarian cancer


title: NUFR735161


title: ETP-ALL_patient_24113

value: relased


title: NUFM727316


title: NUFR741825


title: RNA, RMC-6272, 24h, replicate 2


title: RFP, everolimus, 4h, replicate 1


title: Tet-FLAG-FOXM1c-hTERT-RPE1 no dox RNA-seq, rep 2

description:
R_586nd2
htseq.normCounts.txt
htseq.fpkms.txt


title: Tet-FLAG-FOXM1c-hTERT-RPE1 no dox RNA-seq, rep 1

description:
R_586nd1
htseq.normCounts.txt
htseq.fpkms.txt


title: RFP, DMSO, 4h, replicate 2


title: HaCaT cells,vehicle,repeated experiment group 2

description:
"KW" means group with non-irradiated cells without LBP pretreatment
KW2

value: mucosa


title: NUFR712461


title: Tet-FLAG-FOXM1c-hTERT-RPE1 dox RNA-seq, rep 1

description:
R_586d1
htseq.normCounts.txt
htseq.fpkms.txt

value: FOXM1 overexpression

value: doxycycline


title: RNA, RMC-6272, 24h, replicate 1


title: Tet-FLAG-FOXM1c-hTERT-RPE1 dox RNA-seq, rep 3

description:
R_586d3
htseq.normCounts.txt
htseq.fpkms.txt


title: NUFS432757


title: RNA, everolimus, 24h, replicate 2


title: NUHF355367


title: HaCaT cells, LBP treatment,repeated experiment group 2

description:
"KY" means group with non-irradiated cells with LBP pretreatment
KY2


title: Tet-FLAG-FOXM1c-hTERT-RPE1 dox RNA-seq, rep 2

description:
R_586d2
htseq.normCounts.txt
htseq.fpkms.txt


title: NUFM700896


title: OVCAR5CDDPsshGPX44249_3

first: Daniela

last: Matei

address: 420 E. Superior St.

institute: Northwestern University Feinberg School of Medicine

data_processing: RNA sequencing library of OVCRA5 Pt-R shGPx4 vs. shCTRL OC cells were analyzed using BioJupies https://www.cell.com/cell-systems/fulltext/S2405-4712(18)30432-0. TF PPI pathways enrichments was analyzed using Enrichr https://maayanlab.cloud/Enrichr/.

source_name: ovarian cancer

growth_protocol: OVCAR5 Pt-R shctrl and shGPX4 ovarian cancer cells were maintained in RPMI-1640 with L-glutamine (Corning, Cat# 10-040-CV) plus 10% FBS, 1% GlutaMAX, and 1% penicillin-streptomycin. OVCAR4 and OVCAR4 Pt-R cells were maintained in RPMI-1640 with L-glutamine (Corning, Cat# 10-040-CV) plus 10% FBS, and 1% penicillin-streptomycin.

extract_protocol: Total RNA was extracted with TRI Reagent (Sigma, Cat# T9424). DNA contamination in the samples was removed by using a RNeasy MinElute Cleanup Kit (QIAGEN) with RNase-Free DNase Set (QIAGEN). mRNA was isolated from 1 µg of total RNA with a NEBNext Poly(A) mRNA Magnetic Isolation Module, which was used for preparing RNA sequencing libraries with the NEBNext Ultra II RNA library prep kit and protocol from Illumina (New England Biolabs Inc., Ipswich, MA). Library quality was verified using a BioAnalyzer (Agilent Technologies), and then sequenced on an Illumina NextSeq500 system with single-end, 75-bp read length settings. For quality control, raw fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14) with single-end trimming mode, Phred score cutoff of 20 and minimum sequence length cutoff of 20 bp (62). After checking quality with the FastQC tool, raw sequencing reads were aligned to human genome build hg38 using STAR v.2.5.2 (https://github.com/alexdobin/STAR) with standard settings. Mapped reads were converted to raw counts with HTSeq (https://htseq.readthedocs.io/en/master/), normalized to library size, and analyzed for DEGs by edgeR (Bioconductor). The log2(fold-change) andP-value of total normalized counts and DEG counts were then analyzed by GSEA, Ingenuity Pathway Analysis (IPA, QIAGEN). Data are deposited in the NCBI gene expression omnibus

value: ovarian cancer

value: platinum resistant OVCAR5

tag: disease

tag: transfection

value: GPX4 sh


title: NUFM727015


title: Stromal cells (CD45-, EPCAM -) of colon from 26Gy irradiated mice 8, 2 weeks post irradiation

city: Fontenay-Aux-Roses

first: Fabien

last: Milliat

address: 31 avenue de la division Leclerc

institute: IRSN

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, bar coded processing, gene counting and agregation were made using the Cell Ranger Software (Pipeline Version cellranger-6.0.2 10X gennomics) with the Chemistry Single Cell 3' v3 and the transcriptome version mm10-2020-A
Assembly: mm10-2020-A
Supplementary files format and content: table-separated values and matrix files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: colon

extract_protocol:
2 weeks after IR, mice were euthanized, and colon tissues collected. Single-cell suspensions were prepared and CD45+, EPCAM+ cells were negatively selected using CD45 an,d EPCAM+  MicroBeads and viability (at least 70% of cell viability ) was checked before encapsulation.
Cells were encapsulated using the 10x Chromium Controller system and a Chromium Single Cell 3ʹ single Index Kit v3 or Next GEM Single Cell 3ʹ Dual Index Kit v3.1. Reverse transcription and libraries were prepared according to the manufacturer's instruction.

treatment_protocol: Male C57BL/6JRj mice were exposed to irradiation at 26 GY focus on the colorectal area, under anesthesia (using a medical linear accelerator (Elekta synergy® platform); Colon from age matched control mice are used in the project.

value: colon

tag: age

value: 12 weeks-old

value: stromal populations

value: Irradiated (2 weeks post IR)


title: Stromal cells (CD45-, EPCAM -) of colon from 26Gy irradiated mice 4, 2 weeks post irradiation

description: 10X Genomics


title: Stromal cells (CD45-, EPCAM -) of colon from 26Gy irradiated mice 3, 2 weeks post irradiation

description: 10X Genomics


title: Stromal cells (CD45-, EPCAM -) of colon from 26Gy irradiated mice 6, 2 weeks post irradiation

description: 10X Genomics


title: Stromal cells (CD45-, EPCAM -) of colon from 26Gy irradiated mice 7, 2 weeks post irradiation

description: 10X Genomics


title: NUFM726919


title: Stromal cells (CD45-, EPCAM -) of colon from 26Gy irradiated mice 2, 2 weeks post irradiation

description: 10X Genomics


title: RNA, everolimus, 24h, replicate 1

value: breast cancer cells

value: WT


title: NUFM677260


title: NUFM700692


title: RNA, RMC-6272, 4h, replicate 2

value: 4 h


title: OVCAR5CDDPsshGPX44249_1


title: OVCAR5CDDPshctrl_3

value: control


title: Stromal cells (CD45-, EPCAM -) of colon from 26Gy irradiated mice 1, 2 weeks post irradiation

description: 10X Genomics


title: RNA, RMC-6272, 4h, replicate 1


title: KD1092, KD, replicate 2, scRNAseq

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Re-analysis of GSM6042980

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
RNA samples of mononuclear/polymorphnuclear cells are harvested by Tri-zol (Invritrogen, Inc. Faraday Avenue, Carlsbad, CA). (500 μl Tri-zol/600 μl cell lyses buffer for each 1 × 105 cell)
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3’ Gel Bead and Library Kit (now sold as P/N 120262, 1000009, 120267, 10x Genomics). GEM-RT was performed in a Veriti 96-Well Thermal Cycler 2020/7/29 Version1 (Applied Biosystems; Model#: 9902)at 53 °C for 45 min, 85 °C for 5 min, and held at 4 °C.

value: WBC

value: peripheral blood

tag: disease state

value: Kawasaki disease


title: OVCAR5CDDPsshGPX44249_2

tag: tissue


title: NUFM606828

source_name: Ovarian cancer

value: Ovarian cancer


title: RNA, everolimus, 4h, replicate 1

tag: cell type

value: everolimus


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 8

description: 10X Genomics

value: 22 weeks-old

value: Control


title: NUFM601559


title: OVCAR5CDDPshctrl_1

value: ovarian cancer

value: platinum resistant OVCAR5


title: RNA, everolimus, 4h, replicate 2

tag: genotype


title: NUFM601391


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 9

description: 10X Genomics

value: colon

tag: treatment


title: NUFS244596


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 6

description: 10X Genomics


title: H2BFWT_Input2

city: Hong Kong

first: Toyotaka

last: Ishibashi

address: Rm6260, Academic Building, HKUST, Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

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 hg19 whole genome using bowtie2 version 2.4.2  with default parameters in Galaxy.
Duplicate molecules were marked with MarkDuplicates with default paprameters.
Peak calling was achieved with MACS2 call peak Version 2.1.1.20160309 with default parameters.
Assembly: hg19
Supplementary files format and content: peak bed file

source_name: Testis

extract_protocol:
FFPE human testis blocks within the normal region were cut into 10-μm thickness sections. Paraffin was removed and tissue sections were rehydrated with a series of xylene and ethanol/water solution.  Tissue sections were removed from the slides and kept in a resuspension buffer for 30 min at room temperature with rotation. The supernatant was removed and the pellet was resuspended in 1 mL of a buffer (50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2) with 10 units/ml MNase (Worthington). The reaction was incubated at 37°C for 9 min and stopped by adding 15 mM of EDTA. After keeping the samples at 40°C for 1 h, Thermolabile Proteinase K (NEB, P8111S) was added to 0.08 unit/ml. After maintaining the reaction at 37°C for 6 min, it was inactivated at 65°C for 15 min. The chromatin was further fragmented with sonication. The supernatant was kept after centrifugation at 21, 000 g for 5 min at 4°C. Three volumes of Ch-IP buffer (30 mM Tris-HCl, pH 7.5, 50 mM NaCl, 3 mM EDTA, and 0.1 mM PMSF) were added to the supernatant. Antibody against H2BFWT (25 μg), which was raised from the synthesized peptide (amino acids, 37-50, SKQRKRGRHGPRRC) was added to the supernatant and incubated for 16 h at 4°C with rotation. 15 μl ChIP-grade protein A/G Plus Agarose (Thermo Scientific, 26159) was blocked by BSA for 16 h at 4°C. The beads and antibody-incubated sample were mixed and further incubated for 3 h at 4 °C. After centrifugation at 2 000 g for 2 min at 4 °C, the pellet was washed sequentially with 1 ml washing buffer A/B/C (50/100/150 mM NaCl, 50 mM Tris-HCl, pH 7.5, 1% TritonX-100, 5 mM EDTA). TE buffer containing 200 mM NaCl was added to the beads with a further incubation at 65°C for 20 hrs for de-crosslinking. Proteinase K (NEB, P8107S) was added to 80 ng/μl with incubation at 45 °C for 3 h before DNA extraction with a regular PCR clean-up kit.
DNA libraries were prepared with Smarter Thruplex DNAseq Kit (Clontech, R400674) following Abclonal StepWise Plus DNA Lib Prep Kit protocal for illumina DNA sequencing library construction with amplification for 10-13 circles.

value: Testis

value: 18 years old

value: Donor with testicular cancer and tissue used within normal region.


title: H2BFWT_ChIP2

tag: antibody

value: The antibody used for this data set was raised in rabbits based on a synthesized peptide using the H2BFWT peptide sequence (36-49 aa, SKQRKRGRHGPRRC, Shanghai Youke Biotechnology). Antibody was purified with Protein G.


title: RNA, DMSO, 4h, replicate 2

tag: cell line

value: breast cancer cells

value: WT

value: DMSO (control)

tag: time


title: OVCAR5CDDPshctrl_2

value: control


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 7

description: 10X Genomics

value: stromal populations


title: NUFM308591

data_processing:
Sequecne Reads were trimmed for adaptor sequence / low-quality sequence using cutadapt (version : 2.8, parameter : quality-cutoff (20), minimum-length (50))
Trimmed Sequence reads were mapped to reference genome
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options  with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Gene expression estimation was performed by RSEM v.1.3.1 considering the direction of the reads which are corresponding to the library protocol using option --strandedness. To improve the accuracy of the measurement, “--estimate-rspd” option was applied. All other options were set to default values. To normalize sequencing depth among samples, FPKM and TPM values were calculated.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes TPM for each sample

extract_protocol:
RNA was harvested using Rnaesay mini plus kit (Qiazen).
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA).


title: RNA, DMSO, 4h, replicate 1

value: 4 h


title: OMM2.3-Combined

city: Shanghai

first: Minyue

last: Xie

state: China

address: No. 227, South Chongqing Road

institute: School of Medicine, Shanghai Jiao Tong University

data_processing:
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.
Supplementary_files_format_and_content:  xls files include FPKM values for each Sample

growth_protocol: The cell line OMM2.3 were cultured in 1630 (Gibco,USA) supplemented with 10% certified heat-inactivated fetal bovine serum (FBS; Gibco, USA), penicillin (100 U/ml) and streptomycin (100μg/ml) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
OMM2.3 cells samples 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: treated with CCCP and/or DHA

value: Ocular melanoma cells/uveal region

value: CCCP + DHA


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 5

description: 10X Genomics

value: 12 weeks-old


title: NUFM308157

first: Dong Min

address: 700, Daewangpangyo-ro, Bundang-gu

institute: Theragen Bio

value: Ovarian cancer


title: KD1278-1, KD-CAL, replicate 1, scRNAseq

value: WBC

value: peripheral blood

value: Kawasaki disease and coronary artery lesions


title: OMM2.3-DHA

value: DHA


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 4

description: 10X Genomics

value: colon

value: Control


title: H2BFWT_ChIP1

value: Testis

value: 30 years old

value: Donor with testicular cancer and tissue used within normal region.

value: The antibody used for this data set was raised in rabbits based on a synthesized peptide using the H2BFWT peptide sequence (36-49 aa, SKQRKRGRHGPRRC, Shanghai Youke Biotechnology). Antibody was purified with Protein G.


title: NUFM308050


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 3

description: 10X Genomics


title: NUFM246963


title: OMM2.3-CCCP

value: CCCP


title: rls6_3

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Filtered reads  (> 17 nucleotides) were mapped to the Arabidopsis genome (TAIR10) with with Bowtie2 (Langmead and Salzberg, 2012).
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include read count values for each sample

organism: Arabidopsis thaliana

source_name: 26-d-old rbp-ko-2, grown under LD conditions

growth_protocol: The Arabidopsis plants were grown on soil for 25 days under long-day conditions (16 h light, 8 h dark)

extract_protocol:
Total plant RNA was extracted from 25-d-old plants grown under LD condition using the Trizol reagent (Invitrogen, Carlsbad, USA) and dissolved in RNase-free H2O. To make siRNA library, 30 μg RNA was mixed with equal volume of 2× RPA loading buffer (10 ml of 98% formamide, 200 µl 2 mM EDTA, 10 mg bromophenol blue, 10 mg xylene cyanol) and denatured at 94℃ for 3 min. RNA samples were separated on 15% TBE-PAGE by running at 120 v for 2 h at 4℃, the gel was then stained with 5 µl of Syber Gold (Invitrogen, S11494) for 5 min in 50 ml of 1× TBE buffer (89 mM Tris base, 89 mM boric acid, 1 mM EDTA, pH 8.0). The gel band corresponding to 17-30 nt sRNA was cut and ground in a low-bind 1.5-ml tube with a RNase-free pestle in 500 μl of 0.3 M NaCl. Then the tube was incubated at -80℃ for 30 min at 4℃ overnight with slow rotation.  The gel slurry was filtered through a Spin-X filter (Corning, Cat. 8162) by centrifugation at 20,000 ×g for 1 min at 4℃. The flow through was transferred to two 1.5-ml tubes, each contain 250 μl flow through and was added with  625 µl ethanol, 25 µl NaAc (3 M, pH=5), 1 µl glycogen (Invitrogen, Cat. 10814010). After keeping at -80℃ for 4 h, sRNA was pelleted by centrifugation at 20,000 ×g for 30 min at 4℃. The pellets was washed with 80% ethanol for two times and dissolved in 7 µl of RNase-free H2O.
NEBNext® Small RNA library prep kit (E7300)


title: rls6_2


title: NUFM311629

city: Seongnam-si

last: Shin


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 2

description: 10X Genomics

value: stromal populations


title: OMM2.3-Control

value: control


title: NUFM246510


title: prors1 (LUC)_3

source_name: 26-d-old rbp-ko-1, grown under LD conditions

value: prors1 (LUC)


title: rls6_1


title: NUFM244327


title: NUFM244488


title: NUEV623430


title: H2BFWT_Input1


title: Stromal cells (CD45-, EPCAM -) of colon from control mice 1

description: 10X Genomics


title: prors1 (LUC)_1


title: prors1 (LUC)_2


title: NUEV623157


title: Col-0 (LUC)_3

source_name: 26-d-old Col-0, grown under LD conditions

value: Col-0 (LUC)


title: Col-0 (LUC)_2


title: NUEV593591


title: NUEV593430


title: NUEV597083


title: NUEV592875


title: Stim-4

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using STAR v 2.7.1a under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Splicing analysis was done using rMATS v. 4.1.1
Assembly: mm39
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

source_name: CD8+ T cell

extract_protocol:
QIAGEN miRNEasy Micro Kit
SMARTerUltra-lowPOLYA-V4

value: CD8+ T cell

value: OT-I


title: Sample3_GFPpos

city: Bethesda

first: Lingling

last: Miao

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: National Institutes of Health

data_processing:
Reads from each sample underwent trimming to remove adapters and low-quality bases using Trimmomatic software. Subsequently, the processed reads were aligned to the reference Mouse mm10 genome utilizing STAR software. Gene expression quantification was performed using RSEM.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files at gene level

source_name: Epidermis

extract_protocol:
Neonatal epidermal cells were disscociated from Sox2-GFP reporter mice. Subsequently, cells were stained for SCA1, CD49F , and DAPI, followed by sorting to isolate GFP-positive Merkel cells and GFP-negative SCA1-positive CD49F-positive basal epidermalis keratinocytes. RNA extraction was carried out using the RNeasy® Plus Micro Kit from Qiagen.
Library preparation was accomlished using the TruSeq Stranded Total RNA Library Prep – RS-122-2201 kit from Illumina.
cDNA libraries were pooled together, and sequencing was performed on the HiSeq2500 platform, employing paired-end reads with a length of 125 base pairs.

value: Epidermis

value: Merkel cells


title: CMS_HOx80_rep7

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 8.2.7

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Cultured primary cells, resident lung mesenchymal stromal cells

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: Pulmonary MSCs are isolated from tracheal aspirates of preterm infants and taken into culture (passage 2-6). For the functional studies 200.000 cells per well are seeded and treated for 72h (treatment group RNA 24h, Group 1-8, see below).

extract_protocol: peqGOLD Total RNA Kit

treatment_protocol: MSCs were treated with DMEM-Medium (including 20% FCS, PenStrep and Gentamycin). Starting with a confluency of 50% 200.000 cells per well are seeded and the following experimental procedures are applied for 24h: no treatment (control), rhythmic shear stretch (CMS), exposure to 40% oxygen alone (Hox40), exposure to 80% oxygen alone (Hox80), combination of shear stretch and oxygen 40% (CMS+Hox40), combination of shear stretch and oxygen 80% (CMS+Hox80).

tag: group

value: pulmonary mesenchymal stem cells (MSC)


title: CMS_HOx80_rep6


title: Sample3_GFPneg2

value: Basal keratinocytes


title: CMS_HOx80_rep8


title: CMS_HOx80_rep4


title: CMS_HOx80_rep5


title: Naïve-4


title: NUEV592477

value: Ovarian cancer


title: CMS_HOx80_rep1


title: Torin-3


title: NUEV592273


title: NUEV591821


title: Stim-3


title: Sample2_GFPpos


title: Sample2_GFPneg2


title: NUEV591210


title: Naïve-3


title: CMS_HOx80_rep2


title: Torin-4


title: Col-0 (LUC)_1


title: NUEV590992


title: Sample2_GFPneg1


title: Sample3_GFPneg1


title: CMS_HOx40_rep8


title: NUEV590831


title: Sample1_GFPneg2


title: Stim-2


title: Naïve-2


title: NUEV590293


title: Torin-1


title: Sample1_GFPneg1


title: CMS_HOx40_rep5


title: CMS_HOx40_rep6


title: CMS_HOx40_rep4


title: CMS_HOx80_rep3


title: CMS_HOx40_rep3


title: NUEV587998


title: Stim-1


title: microglia-repopulated condition (cortex) #4

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing:
Bulk RNAseq analysis: On average we received 30 million paired ends for each of the replicates. RNAseq libraries were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The Enrichment Analysis for Gene Ontology was performed by topGO. The heatmaps were generated using pheatmap function in R.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mice brain cortex

growth_protocol: C57BL/6J male mice were purchased from Jax lab. Male mice at 10 to 20 weeks of age were used for experiments unless stated otherwise. All experiments were approved by the Institutional Animal Care and Use Committee of the University of Virginia. For control group, mice were treated with control food. For PLX group, mice were treated with PLX3397 for 9days. For repopulation group, mice were first treated PLX3397 food for 9 days and then change back to control food for 9 days.

extract_protocol:
Brain cortex were extracted for bulk RNA sequencing.
Library was constructed at UVA Genome Analysis and Technology Core.

treatment_protocol: Fifteen mice were used for RNA-Seq experiments. Five mice were treated with PLX food and five mice were treated with control food. Five mice were used for repopulation. Treatment duration is 9 days.

value: mice brain cortex


title: microglia-repopulated condition (cortex) #5


title: Naïve-1


title: NUEV569105


title: Tra2bKO_B2

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using STAR v 2.7.1a under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Splicing analysis was done using rMATS v. 4.1.1 and Whippet v. 1.6
Assembly: mm39 (rMATs)
Assembly: mm10 (Stringtie, Whippet)
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

source_name: Spleen and lymph nodes

value: Spleen and lymph nodes


title: microglia-repopulated condition (cortex) #3


title: Sample1_GFPpos


title: NUEV579573


title: microglia-repopulated condition (cortex) #2


title: Tra2bKO_B1


title: NUEV552965


title: NUEV590132


title: Naïve_N8


title: CMS_HOx40_rep1


title: microglia-repopulated condition (cortex) #1


title: CMS_HOx40_rep2


title: HOx80_rep8


title: Microglia depletion (cortex) #5


title: Naïve_N7


title: Microglia depletion (cortex) #4


title: NUEV529277


title: Naïve_N6


title: NUEV519775


title: HOx80_rep6


title: Microglia depletion (cortex) #3


title: HOx80_rep5


title: Naïve_N5


title: HOx80_rep4


title: HOx80_rep7


title: Naïve_N4


title: Naïve_N3


title: NUEV550754


title: Microglia depletion (cortex) #1


title: NUEV494032


title: HOx40_rep8


title: Naïve_N2


title: NUEV418634


title: HOx80_rep3


title: Microglia depletion (cortex) #2


title: HOx80_rep2


title: Naïve_N1


title: Control mouse (cortex) #4


title: NUEV352170


title: HOx80_rep1


title: Control_C8


title: HOx40_rep7


title: Control mouse (cortex) #3


title: HOx40_rep5


title: NUEV351922


title: Control_C7


title: Control mouse (cortex) #2


title: NUEV351728


title: NUEV489377


title: NUEV434997


title: Control mouse (cortex) #5


title: NUEV351524


title: Control mouse (cortex) #1


title: Control_C6


title: Control_C5


title: NUEV342614


title: ST3

first: Chuandong

last: Wang

address: 320 Yueyang Road

institute: SJTU

data_processing:
Trimmomatic and Cutadapt software were used to remove the sequencing connections and low-quality sequences from the original sequencing data to obtain clean data.
Blastn (2.9.0+) was used for comparison and the read count number was obtained based on the quantitative result.
miRDeep2 software was used to normalize reads counts and obtain CPM (Reads Count Per Million) values.
Assembly: mm10
Supplementary files format and content: raw_counts includes raw counts for each sample

source_name: Bone

growth_protocol: BMSCs were maintained inDMEM supplemented with 10% fetal bovine serum and 1% antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Tissue RNA Purification Kit PLUS kit (#EZB-RN001-plus) was used to extract total RNA from the cell.
Perform 3 'end connector connections, reverse transcription primer hybridization, 5' end connector connections, cDNA single strand synthesis, library amplification, and other processing on the sample. After quality inspection and purification, a library that meets the Illumina platform sequencing requirements was finally obtained.

treatment_protocol: The serum-free test (ST) group cells were cultured in a serum-free medium for 24 h, and the general medium (GM) group cells were cultured in a medium containing 10% fetal bovine serum for 24 h

value: Bone

value: bone mesenchymal stem cells

value: primary cell

value: WT

value: Serum-free medium


title: ST2


title: Control_C4


title: NUEV342456


title: HOx40_rep3


title: Control_C3


title: ST1


title: HOx40_rep2


title: NUEV321338


title: Control_C2


title: GM3

value: General medium


title: NUEV318307


title: GM2


title: NUEV320250


title: Control_C1


title: HOx40_rep6


title: HOx40_rep1


title: CMS_rep15

value: CMS


title: PEKO_4

source_name: Lung

value: Lung


title: GM1


title: Control_4

value: CD8+ T cell


title: NUEV316433


title: NUEV316026


title: Matrigel/rhBMP2+Palovarotene

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

description: 10x Genomics

data_processing:
Cell Ranger (version 3.0.2) was used to de-multiplex reads, followed by extraction of cell barcode and unique molecular identifiers (UMIs).
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Ectopic mass cells

extract_protocol:
Ectopic tissue masses were harvested on day 5 from initial implantation, minced and dissociated into single cell suspension
cDNA libraries of cells from each group were generated by Chromium controller (10X Genomics Inc.), barcoded and purified as described by the manufacturer, and sequenced using a 2x150 pair-end configuration on an Illumina HiSeq platform
10X Single Cell 3' v3

value: 6-8 weeks old

value: Ectopic mass cells


title: CX3CR1+CD74+_Postn

city: 市辖区

first: zaiqi

last: xie

state: 徐汇区

address: 上海市徐汇区岳阳路320号

institute: chinese academy of science

description: CD74_Vhicle_vs_CD74_Postn RNAseq.xlsx

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using Hisat2
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx file with raw gene counts for every gene and every sample

source_name: Periosteum

growth_protocol: Single periosteum cell suspension was isolated from 4w male C57BL/B6 mice. To sort Cx3cr1+ACE+/- and Cx3cr1+CD74+/- periosteum resident macrophages, cell suspension were incubated with anti-CD45+, anti-Cx3cr1+, anti-ACE+ or anti-CD74+ antibody for 30 minutes, after washing with PBS, cell sorting was conducted using Aria Sorp (BD Bioscience).

extract_protocol:
Cells were collected 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.
Libraries were prepared according to Illumina's instructions

treatment_protocol: Sorted cells were cultured in DMEM containing 10% FBS, 1% penicillin/streptomycin and 10ng/ml M-CSF, and treated with rmPostn (500ng/ml) or vehicle (PBS) for 24h.

value: Periosteum

value: post natal day 28

value: Wild type

value: Postn


title: PEKO_3

value: OT-I


title: HOx40_rep4

value: pulmonary mesenchymal stem cells (MSC)


title: CMS_rep16


title: NUEV314329

value: Ovarian cancer


title: CX3CR1+CD74+_Vhicle

address: 上海市徐汇区岳阳路320号

description: CD74_Vhicle_vs_CD74_Postn RNAseq.xlsx

value: Vhicle


title: Control_3


title: NUEV314046


title: CMS_rep11


title: NUEV313515


title: PEKO_2


title: CX3CR1+ACE+_Postn

address: 上海市徐汇区岳阳路320号

description: ACE_Vhicle_vs_ACE_Postn RNAseq.xlsx


title: CMS_rep13


title: CMS_rep12


title: CMS_rep10


title: NUEV312206


title: CX3CR1+ACE+_Vhicle

address: 上海市徐汇区岳阳路320号

description: ACE_Vhicle_vs_ACE_Postn RNAseq.xlsx


title: Control_2


title: NUEV289078


title: PEKO_1


title: CX3CR1+CD74- PRMs

address: 上海市徐汇区岳阳路320号

description: CD74_ctrl_vs_CD74_postn RNAseq.xlsx

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using Hisat2
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx file contain counts for each sample

tag: subset


title: NUEV282941


title: NUEV230957


title: Naïve-2

source_name: Spleen+lymph nodes

value: Spleen+lymph nodes


title: CMS_rep7


title: Naïve-1


title: CX3CR1+ACE+ PRMs

address: 上海市徐汇区岳阳路320号

description: ACE_Negtive_vs_ACE_Positve RNASeq.xlsx


title: CMS_rep9


title: SNU-1-palbociclib-treat2

first: Chunchao

last: Zhu

state: shanghai

address: Pujian road 160, shanghai

institute: Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

data_processing:
CLC Genomics Workbench v 11.0.1
Seouence reads were trimmed for adaptor secuenceow-oualtvy secuence usina CLC genomic benchwork (parameter- Quality imit 0.05)
Trimmed secuence reads were mapoed to GrCW38m10 usino clc aeromic bercwok oarameters-mismat cost 2 inserion ost 3 deleto cost 3lenot fracior 08 simiariy feacion: 00
Read count extraction and normalization were performed using CL C genomic benchwork
Assembly: mm10
Supplementary files format and content: tab.delimited text fle includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Stomach

extract_protocol:
RNA was harvested usina Rneasy mini plus kit (Qlagen).3 uo of total PNA was used for the construction of seguencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufa cturer's protocols.

value: Stomach

value: gastric cancer (GC) cell line

value: Palbociclib


title: CMS_rep5

value: CMS


title: CMS_rep8


title: CMS_rep6


title: T4-1


title: NUEV230513


title: CMS_rep4


title: CMS_rep3


title: CMS_rep2


title: SNU-1-palbociclib-treat1


title: SNU-1-control2

value: none (control)


title: N4-2

value: CD8+ T cell


title: CMS_rep1


title: Control_1

value: Lung


title: CX3CR1+ACE- PRMs

address: 上海市徐汇区岳阳路320号

description: ACE_Negtive_vs_ACE_Positve RNASeq.xlsx


title: NUEV212988


title: NUEV212410


title: N4-1


title: T4-2


title: NUEV230832


title: NUEV230638


title: CD4Sf3b1M3

city: Duarte,

first: Yun

last: Shi

address: 1500 E Duarte Rd

institute: City of Hope

data_processing:
Partek Flow build version 11.0.24.0414
Sequence reads were trimmed using end min quality level (Phred score equal to 34) from both 3' and 5' ends
Sequence reads were aligned to GRCm39/mm39 using STAR v2.7.8a with validation of quality through prealignment and postalignment quality assurance (QA)/quality control (QC) using Partek Flow
Aligned reads were subject to quantify to mm39 using the Parteck E/M algorithm then annote using Ensembl Transcripts replease 108 and normalization to counts per million(CPM) with 0.0001 added to each gene
Assembly: GRCm39/mm39
Supplementary files format and content: A tab-delimited text file including raw counts for all samples.

source_name: Spleen

growth_protocol: RPMI 1640 medium (Corning Inc.) containing 2 mM l-glutamine, 50 µM β-mercaptoethanol, penicillin (100 U/ml), streptomycin (100 mg/ml), and 10% FBS (Corning Inc.)

extract_protocol:
RNA extraction with the RNeasy Mini Kit (QIAGEN)，1.0 ug of total RNA was used for the constrction of sequecing libraries.
RNA  libraries for RNA-seq were prepared using with kapa RNA hyperprep kit with riboerase kit  following manufacture's protocols.

treatment_protocol: TGF-β,hamster anti-CD3 , hamster anti-CD28 ,anti-IFNγ and anti-IL-4 treatment for 36 h

value: Spleen

value: T cell

value: CD4 T cell

value: Sf3b1 mutation


title: CX3CR1+CD74+ PRMs

address: 上海市徐汇区岳阳路320号

description: CD74_ctrl_vs_CD74_postn RNAseq.xlsx

value: Periosteum

value: post natal day 28

value: Wild type


title: CMS_HOx40_rep7

value: pulmonary mesenchymal stem cells (MSC)


title: AGS-palbociclib-treat2

value: AGS


title: NUEV205076

source_name: Ovarian cancer

value: Ovarian cancer


title: CD4Sf3b1M2

value: TGF-β,hamster anti-CD3 , hamster anti-CD28 ,anti-IFNγ and anti-IL-4 treatment


title: SNU-1-control1

value: Stomach

value: gastric cancer (GC) cell line


title: CMS_rep14

value: CMS


title: control_rep14

value: control


title: CD4Sf3b1M1


title: AGS-palbociclib-treat1

value: Palbociclib


title: control_rep15


title: control_rep16


title: AGS-control2

value: none (control)


title: NUEV200752


title: CD4W3

value: Spleen

value: WT


title: NUEV200956


title: CD4W2

value: T cell

value: CD4 T cell


title: CD4W1


title: 12570_PCW17_RA_input

city: Bern

first: Marco

last: Osterwalder

address: Murtenstrasse 24

institute: Universiy of Bern

description: input chromatin

data_processing:
Single-end reads were obtained by quality filtering and adaptor trimming using cutadapt_v1.1  with parameter ‘-m 25 -q 20’ and were mapped to the reference genome NCBI37/hg19 using Bowtie version 2.0.2.0 (Langmead 2009) with parameter ‘-m 1 -v 2 -p 16’. Duplicates were removed with samtools and MACS (Zhang 2008) (version 1.4.2) with parameter ‘-mfold = 10,30 -nomodel -p 0.0001’ was used for peak calling.
Assembly: hg19
Supplementary files format and content: Normalized bigWig files were generated using bedtools (bedGraphToBigWig).
Supplementary files format and content: Peak files were generated using MACS (Zhang 2008).

source_name: fetal right atrium, input ChIP

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 19212405) with some modifications. Briefly, frozen tissue was pulverized with a mortar and pestle, resuspeneded in PBS, and cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp.  Chromatin was inclubated for 2h at 4 C with 5 µg of antibody. Protein A and G Dynabeads (Invitrogen) were then added to this chromatin/antibody mixture for 30 minutes at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 37 C for one hour. Samples were treated  with Proteinase K at 37 C and reverse-crosslinked overnight. Finally, the DNA was purified on Zymo ChIP clean and concentrate columns (Zymo Research) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared using the Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2000.

value: right atrium

tag: developmental stage

tag: chip antibody

value: untreated


title: AGS-control1


title: control_rep13


title: Wildtype mouse 397, brain tissue (cortex), replicate 2

city: Rockville

first: May Christine

middle: V

last: Malicdan

address: 5625 Fisher's Ln

department: National Human Genome Research Institute

data_processing:
Reads were aligned to the mm10 reference genome using the HISAT alignment software.
Read counts and differential expression analysis were generated using the DESeq2 R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: Brain, cortex

extract_protocol:
Brain tissues were were snap frozen in liquid nitrogen immediately after harvesting. Frozen samples were then sent to Azenta Life Sciences (Chelmsford, MA) for RNA extraction, library preparation, and sequencing.
PolyA-selected Libraries were prepared by Azenta Life Sciences (Chelmsford, MA).

value: Brain, cortex

value: Wildtype

value: 18 months old


title: control_rep11

value: pulmonary mesenchymal stem cells (MSC)


title: 12570_PCW17_RA_H3K27ac

description: Chromatin IP against H3K27ac

source_name: fetal right atrium, H3K27ac ChIP

value: anti-H3K27ac (Active motif, 39133)


title: NUEV177074

value: Ovarian cancer


title: 12570_PCW17_LA_input

description: input chromatin

source_name: fetal left atrium, input ChIP

value: left atrium


title: control_rep10


title: NUEV201292


title: Wildtype mouse 397, brain tissue (cortex), replicate 1


title: NUEV169552


title: NUEV177454


title: control_rep12


title: control_rep9


title: NUEV169394


title: control_rep7


title: 12570_PCW17_LA_H3K27ac

description: Chromatin IP against H3K27ac

source_name: fetal left atrium, H3K27ac ChIP


title: NUEV188672


title: NUEV166476


title: Wildtype mouse 397, brain tissue (cerebellum), replicate 1

source_name: Brain, cerebellum

value: Brain, cerebellum


title: 12570_PCW17_RV_H3K27ac

description: Chromatin IP against H3K27ac

source_name: fetal right ventricle, H3K27ac ChIP

value: right ventricle


title: NUEV166713


title: Wildtype mouse 391, brain tissue (cortex), replicate 1


title: Wildtype mouse 19352, brain tissue (cortex), replicate 2

value: 3 months old


title: 12570_PCW17_LV_input [re-analysis]

description:
input chromatin
GSM3606020 (12570_PCW17_input)

source_name: fetal left ventricle, input ChIP

value: left ventricle


title: NUEV119469


title: Wildtype mouse 19352, brain tissue (cortex), replicate 1


title: Wildtype mouse 391, brain tissue (cerebellum), replicate 1


title: islet cells from 7-day old PpyCre/+; Rosa26tdTomato; LSL-Tag-3

city: Maebashi

first: Yuko

last: Nakagawa

state: Gunma

address: 3-39-15 Showa-machi

department: Institute for Molecular & Cellular Regulation

country: Japan

institute: Gunma University

data_processing:
After trimming with fastp (version 0.21.0), reads were mapped to the Mus musculus genome assembly (Genome Reference Consortium GRCm38, UCSC version mm10) and read counts were obtained using STAR (version 2.5.3a)-RSEM (version 1.3.3).
For each sample, at least 47 M uniquely mapped reads were obtained.
Differentially Expressed Genes (DEGs) between two groups were detected using TCC-iDEGES-edgeR pipeline on R (https://www.R-project.org/, version 4.0.3) packages TCC (version 1.30.0) and edgeR (version 3.32.1).
Genes with adjusted p-value (q.value) <0.05 were defined as significant DEGs.
The EnhancedVolcano (version 1.8.0) and clusterProfiler (version 3.18.1) packages of R were used for volcano plot depiction and gene ontology enrichment analyzes, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: pancreatic islet

growth_protocol: Cells were dispersed from pancreatic islets isolated from 7-day old PpyCre/+; Rosa26tdTomato/+ (control) and PpyCre; Rosa26tdTomato; LSL-TAg mice to obtain control and transformed Ppy-lineage cells (n = 3 mice per group) respectively. Isolation of pancreatic islets was performed as described previously (Saitou, D. et. al., PLOS ONE, 2022).

extract_protocol:
RNA was harvested using SMART-Seq® HT Kit (Takara R400748).
RNA libraries for RNA-seq preparation were performed using SMART-Seq® HT Kit (Takara R400748) following manufacture's protocols .

value: pancreatic islet

value: PpyCre/+; Rosa28tdTomato; LSL-Tag


title: Wildtype mouse 397, brain tissue (cerebellum), replicate 2


title: scRNAseq

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

description: 10x Genomics

data_processing:
using Cell Ranger (version 3.1.0; 10X Genomics, Pleasanton, CA. USA)
Assembly: ZebraFishGRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
Thirty hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: neuron

value: zebrafish embryo

tag: strain

value: mixed

value: 30 hours post-fertilization


title: 12570_PCW17_RV_input

description: input chromatin

source_name: fetal right ventricle, input ChIP

value: untreated


title: islet cells from 7-day old PpyCre/+; Rosa26tdTomato; LSL-Tag-1

value: PpyCre/+; Rosa26tdTomato; LSL-Tag


title: islet cells from 7-day old PpyCre/+; Rosa26tdTomato; LSL-Tag-2

value: PpyCre/+; Rosa27tdTomato; LSL-Tag


title: NUEV119265

data_processing:
Sequecne Reads were trimmed for adaptor sequence / low-quality sequence using cutadapt (version : 2.8, parameter : quality-cutoff (20), minimum-length (50))
Trimmed Sequence reads were mapped to reference genome
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options  with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Gene expression estimation was performed by RSEM v.1.3.1 considering the direction of the reads which are corresponding to the library protocol using option --strandedness. To improve the accuracy of the measurement, “--estimate-rspd” option was applied. All other options were set to default values. To normalize sequencing depth among samples, FPKM and TPM values were calculated.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes TPM for each sample


title: control_rep3

source_name: Cultured primary cells, resident lung mesenchymal stromal cells

value: control

value: pulmonary mesenchymal stem cells (MSC)


title: CEL210312AN_WT_48h

description: 10x Genomics

extract_protocol:
Forty-eight hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: 48 hours post-fertilization


title: control_rep2


title: control_rep4


title: Wildtype mouse 19352, brain tissue (cerebellum), replicate 2

value: Wildtype


title: NUEV117197

extract_protocol:
RNA was harvested using Rnaesay mini plus kit (Qiazen).
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA).

value: Ovarian cancer


title: Wildtype mouse 19352, brain tissue (cerebellum), replicate 1

value: Brain, cerebellum


title: control_rep1


title: islet cells from 7-day old PpyCre/+; Rosa26tdTomato/+-3

value: PpyCre/+; Rosa28tdTomato/+


title: control_rep6


title: NUEV107552


title: 12570_PCW17_LV_H3K27ac [re-analysis]

description:
Chromatin IP against H3K27ac
GSM3605947 (12570_PCW17_H3K27ac)

source_name: fetal left ventricle, H3K27ac ChIP

value: left ventricle

value: anti-H3K27ac (Active motif, 39133)


title: control_rep5


title: Wildtype mouse 19311, brain tissue (cortex), replicate 1

value: Brain, cortex

value: 3 months old


title: CEL210312AN_WT_22h

description: 10x Genomics

extract_protocol:
Twenty-two hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: neuron

value: zebrafish embryo

value: 22 hours post-fertilization


title: NUEV119867


title: islet cells from 7-day old PpyCre/+; Rosa26tdTomato/+-2

value: pancreatic islet

value: PpyCre/+; Rosa27tdTomato/+


title: CEL210312AN_WT_14h

description: 10x Genomics

extract_protocol:
Fourteen-hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: mixed

value: 14 hours post-fertilization


title: NUEV107288


title: Wildtype mouse 19311, brain tissue (cerebellum), replicate 1


title: NUBW594378


title: islet cells from 7-day old PpyCre/+; Rosa26tdTomato/+-1

value: PpyCre/+; Rosa26tdTomato/+


title: Fish4 zTLR4bb-sg2

city: New York

first: Ting-Hsiang

last: Huang

state: New York

institute: Memorial Sloan Ketteting Cancer Center

description:
Fish4
zTLR4bb-sg2

data_processing:
The results of the amplicon were aligned and percent of indels at the target site was quantified using R version 4.0.5 and CrispRVariants 1.18.0 as previously described (Linsay et. al. 2016).
Assembly: GRCz10
Library strategy: CRISPR-Seq

source_name: melanoma

growth_protocol: Tumors generated by TEAZ were dissected out from randomly picked fish.

extract_protocol:
Mince the tumor tissue into small sizes with a razor and transfer the pieces immediately to a 15 ml conical tube containing tissue digestion buffer. After tissue dissociation, suspension cells were filtered through a 70 mm strainer to remove tissue debris followed by counterstaining with Hoechst 33342. After FACS, tdTomato and Hoechst double positive melanomas were lysed for phenol-chloroform based whole genome extraction. To validate gene editing using CRISPR-seq, primer pairs were set to flank 200-280 bp of the sequence that should encompass mutation sites within 100 bp from the beginning or end of it.
The sequence was amplified from 50-100 ng of genomic DNA using Phusion High-Fidelity DNA Polymerase master mix PCR protocol.

value: melanoma

tag: knockout


title: Lyst-Knockout mouse 397, brain tissue (cortex), replicate 1

value: Lyst-Knockout

value: 18 months old


title: SLAMseq_CB6644_MYC_ER_OHT_R3

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

data_processing:
GRAND SLAM (version 2.0.5g, Jürges et al., 2018, Bioinformatics)
Trimming of 5' 10 nt UMI, and 3' Adapter
STAR alignment to the mm10 reference sequence
Differential gene expression analysis using DESeq2 (version 1.36.0)
Assembly: mm10
Supplementary files format and content: .tsv/.csv file containing the results of differential gene expression analysis

growth_protocol: KPC-AID-Ruvbl1 and KPC-MYC-ER cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.

extract_protocol:
total RNA was extracted using miRNeasy kit (Qiagen)
QuantSeq 3' mRNA-Seq Library Prep Kit (FWD)
OTHER: SLAMseq

treatment_protocol: KPC-AID-Ruvbl1 cells were treated with 1 µM 5-Ph-IAA for 3 or 15 h respectively followed by 2 h of labelling with 800 µM 4sU. KPC-MYC-ER cells were treated with 1 µM CB-6644 for 20 h followed by 4 h treatment with 4-OHT and 2 h of labelling with 400 µM 4sU.

value: KPC

value: pancreatic ductal adenocarcinoma

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, MYC-ER

value: 200 nM 4-OHT 4 h


title: NTAC809803

first: Dong Min

value: Ovarian cancer


title: Fish3 zTLR4bb-sg2

description:
Fish3
zTLR4bb-sg2


title: Lyst-Knockout mouse 397, brain tissue (cerebellum), replicate 1

value: Brain, cerebellum


title: SLAMseq_CB6644_MYC_ER_OHT_R2


title: SLAMseq_CB6644_MYC_ER_OHT_R1


title: Lyst-Knockout mouse 390, brain tissue (cortex), replicate 2

value: Brain, cortex


title: Fish2 zTLR4bb-sg2

description:
Fish2
zTLR4bb-sg2


title: Lyst-Knockout mouse 390, brain tissue (cortex), replicate 1


title: SLAMseq_CB6644_MYC_ER_OHT_4sU_minus


title: Fish1 zTLR4bb-sg2

description:
Fish1
zTLR4bb-sg2


title: Fish4 zTLR4bb-sg1

description:
Fish4
zTLR4bb-sg1


title: Lyst-Knockout mouse 390, brain tissue (cerebellum), replicate 2


title: SLAMseq_CB6644_MYC_ER_Ctrl_R2

value: Ctrl


title: 4046527654


title: Lyst-Knockout mouse 390, brain tissue (cerebellum), replicate 1


title: 4046527553


title: SLAMseq_CB6644_MYC_ER_Ctrl_R3


title: Lyst-Knockout mouse 19351,  brain tissue (cortex), replicate 3

value: 3 months old


title: SLAMseq_CB6644_MYC_ER_Ctrl_R1


title: Fish4 zTLR4ba-sg2

description:
Fish4
zTLR4ba-sg2


title: Fish3 zTLR4ba-sg2

description:
Fish3
zTLR4ba-sg2


title: Fish3 zTLR4bb-sg1

description:
Fish3
zTLR4bb-sg1


title: 4046526256


title: SLAMseq_CB6644_MYC_ER_Ctrl_4sU_minus


title: NTAC809487


title: Human skin fibroblasts, si-TAGLN-2

first: Jia

last: Zhou

state: --- Select One ---

address: 639 Zhizaoju Road, Shanghai

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skin

growth_protocol: Human skin fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
For gene silencing, human pathological scar fibroblasts were transfected with 100 nM siRNA using Lipofectamine RNAiMAX reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's experimental protocol.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Skin

value: Fibroblasts

value: TAGLN knockdown


title: Human skin fibroblasts, si-TAGLN-3


title: Fish2 zTLR4ba-sg2

description:
Fish2
zTLR4ba-sg2


title: SLAMseq_CB6644_MYC_ER_CB6644_R3


title: Lyst-Knockout mouse 19351,  brain tissue (cortex), replicate 2


title: NTAC809292

last: Shin

institute: Theragen Bio


title: Lyst-Knockout mouse 19351,  brain tissue (cerebellum), replicate 3


title: SLAMseq_CB6644_MYC_ER_CB6644_R2


title: Human skin fibroblasts, si-TAGLN-1


title: Fish1 zTLR4ba-sg2

description:
Fish1
zTLR4ba-sg2


title: control_rep8

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

extract_protocol: peqGOLD Total RNA Kit

value: control

value: pulmonary mesenchymal stem cells (MSC)


title: Human skin fibroblasts, si-NC-3

value: WT


title: Fish4 zTLR4ba-sg1

description:
Fish4
zTLR4ba-sg1

value: melanoma


title: Human skin fibroblasts, si-NC-2


title: Lyst-Knockout mouse 19351, brain tissue (cerebellum), replicate 1

value: Lyst-Knockout


title: Lyst-Knockout mouse 19351, brain tissue (cerebellum), replicate 2


title: SLAMseq_CB6644_MYC_ER_CB6644_R1

value: KPC


title: Fish3 zTLR4ba-sg1

description:
Fish3
zTLR4ba-sg1


title: SLAMseq_CB6644_MYC_ER_CB6644_OHT_R3

value: pancreatic ductal adenocarcinoma


title: Human skin fibroblasts, si-NC-1


title: Fish3 zAcaa2-sg2

description:
Fish3
zAcaa2-sg2


title: SLAMseq_CB6644_MYC_ER_CB6644_OHT_R2

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, MYC-ER


title: Fish4 zAcaa2-sg2

description:
Fish4
zAcaa2-sg2


title: Lyst-Knockout mouse 19351,  brain tissue (cortex), replicate 1


title: Naïve-4

first: Anthony

last: Vella

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using STAR v 2.7.1a under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Splicing analysis was done using rMATS v. 4.1.1
Assembly: hg38
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

source_name: Health Donor PBMCs

extract_protocol:
QIAGEN miRNEasy Micro Kit
SMARTerUltra-lowPOLYA-V4

value: Health Donor PBMCs

value: CD8+ T cell


title: WAC23_HET_F

city: Davis

first: Karol

last: Cichewicz

address: 1544 Newton Ct

department: Center for Neuroscience

institute: UC Davis

data_processing:
Alignment with STAR (version 2.5.4b)
Gene counts were generated using featureCounts
Assembly: GRCm38/mm10
Supplementary files format and content: CSV gene counts

source_name: Forebrain

extract_protocol:
Total RNA was extracted using Ambion RNAqueous Total RNA Isolation Kit (cat# AM1912)
Illumina poly-A-enriched mRNA libraries

value: Forebrain

value: HET


title: WAC24_WT_F


title: SLAMseq_CB6644_MYC_ER_CB6644_OHT_R1


title: Tra2bPE-4

institute: UConn Health


title: WAC22_HET_M


title: SLAMseq_CB6644_MYC_ER_CB6644_4sU_minus


title: Fish2 zAcaa2-sg2

description:
Fish2
zAcaa2-sg2


title: Fish1 zAcaa2-sg2

description:
Fish1
zAcaa2-sg2


title: Control-4


title: SLAMseq_CB6644_MYC_ER_CB6644_OHT_4sU_minus


title: KPC_allograft_screen_preexperiment_Ctrl_100k

description: PCR amplified gDNA

data_processing:
Fastq files were generated on Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
Bowtie1 (version 1.2.2) alignment (option -v 0) to the shRNA oligonucleotide reference
Counting of alignment per shRNA (bash script)
Differential enrichment (DESeq2)
Assembly: NA, fastq files were aligned to a custom reference containing the shRNA oligonucleotide sequences
Supplementary files format and content: .csv file containing raw read counts per shRNA sequence

source_name: tumor

growth_protocol: KPC cells were grown in DMEM supplemented with 10 % FCS and 1% Penicillin/Streptomycin. 100,000 KPC cells were orthotopically transplanted into the pancreata of C57BL/6J mice in 50 µl PBS/Matrigel (1:1)

extract_protocol:
Cells/Tumors were lysed in lysis buffer (10 mM TRIS/HCl, pH 8, 100 mM NaCl, 10 mM EDTA, 0.5 % SDS, 400 µg/ml proteinase K) at 56 °C overnight. gDNA was isolated by phenol/chloroform/isoamylalcohol extraction and isopropanol precipitation.
PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.
OTHER: PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.

treatment_protocol: Cells were treated with 1 µg/ml doxycycline. Control cells were treated with ethanol. Mice were treated with doxycycline by feeding them with chow containing 625 mg/kg doxycycline (ssniff) ad libitum. Control mice received control chow.

value: tumor

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre

value: Control (standard chow)


title: Naïve-3


title: Fish4 zAcaa2-sg1

description:
Fish4
zAcaa2-sg1


title: Tra2b-PE-3


title: WAC19_HET_M


title: WAC20_WT_M


title: KPC_allograft_screen_preexperiment_Ctrl_50k

description: PCR amplified gDNA


title: Fish2 zAcaa2-sg1

description:
Fish2
zAcaa2-sg1


title: WAC18_WT_F


title: Fish1 zAcaa2-sg1

description:
Fish1
zAcaa2-sg1


title: Naïve-2


title: WAC17_WT_F


title: KPC_allograft_screen_preexperiment_Input_cells

description: PCR amplified gDNA

value: Control


title: KPC_allograft_screen_Dox_R5

description: PCR amplified gDNA

value: Doxycycline chow


title: Tra2b-PE-2


title: WAC21_HET_F


title: WAC16_WT_F