title: Syngeneic islet graft

city: Shenzhen

first: Lisha

last: Mou

state: Guangdong

address: Room 604, Building 1, Yinxingzhijie 1 Qi Guanlan, Longhua District

institute: Shenzhen Second People's Hospital

data_processing:
Sequences obtained from sequencing using the 10x Genomics single-cell RNA sequencing platform were demultiplexed and mapped to the mm10 transcriptome using the Cell Ranger package (10x Genomics). Cells were removed if they were expressing fewer than 200 unique genes, more than 4,500 unique genes, or greater than 15% mitochondrial reads. Genes not detected in at least 3 cells were removed from subsequent analysis.
To analyze the single-cell RNA-seq data, we performed Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) using the Seurat R Package (version 3.1.5) with the first 75 principal components, after performing principal component analysis (PCA) on the 2000 most variable genes. Identification of significant clusters was performed using the FindClusters() algorithm in the Seurat package with the resolution set as 0.6. Marker genes for each significant clusters were found using the Seurat function FindAllMarkers(). Cell types were determined using a combination of marker genes identified from the literature and the CellMarker web tool (http://biocc.hrbmu.edu.cn/CellMarker/).
All single-cell sequencing data statistical analysis was performed in R (version 4.0.5) using Seurat (3.1.5). Wilcoxon Rank Sum test was applied for comparisons in two groups. Statistical significance was accepted for p < 0.05.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files.

source_name: islet graft

extract_protocol:
After dissociation, the concentration of single-cell suspension was adjusted to 700–1,200 cells/μl. Cell viability was determined by trypan blue staining with TC20 automated cell counter (Bio-rad, Hercules, CA). The ratio of viable cells was required to be more than 85%. The input cells were then loaded onto the channel of Single Cell B Chip (v3 chemistry, PN-1000153) and loaded onto a Chromium Controller (10x Genomics, Pleasanton, CA) to generate single-cell GEMs (gel beads in emulsion).
Reverse transcription and library preparation was performed using the Chromium Single Cell 3’ Reagent Kits following the 10x Genomics protocol.
Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell on an Illumina NovaSeq 6000 by Novogene Bioinformatics Technology Co., Ltd (Tianjing, China).

tag: strain

value: pancreatic islet

tag: condition

value: C57bl/6 islets to C57bl/6 recipients


title: Allogeneic islet graft

status: Public on May 25 2022

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: Balb/c

tag: tissue

value: Balb/c islets to C57bl/6 recipients


title: MC3T3-E1 cells, FR1

city: Hangzhou

first: Yi

last: Zhang

state: Zhejiang

address: 166 North Qiutao Rd

department: Department of Endodontics

institute: Zhejiang University

description: 30ppm F- resistant MC3T3-E1 cells exposed to a gradient of 30 ppm F-

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: cell line

growth_protocol: The mouse osteoblast-like cell line MC3T3-E1 (ATCC: CRL-2594) was cultured in Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomyc at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 5μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).  Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq 4000 (2 × 150bp read length).

treatment_protocol: Wild-type MC3T3-E1 (WT MC3T3-E1) cells were continuously exposed to a gradient of 10 ppm F- to induced them survive in fluorinated medium. During cell adaptation, the cell proliferation was continuously monitored using Cell Counting Kit-8 (CCK-8) kit until a normal cell proliferation rate was confirmed. The above procedure was repeated for all other MC3T3-E1 clones to develop desired fluorine resistance. Finally, the 30ppm F- resistant MC3T3-E1 (FR MC3T3-E1) cells were obtained.

value: cell line

tag: cell line

tag: cell type

value: Osteoblasts

tag: phenotype

value: 30ppm F- resistant

tag: treatment

value: gradient of 30 ppm F-


title: H3K27ac_siPHF13_TGFb_rep2

city: Shenyang

first: Wanhua

last: Xie

address: Huanghe North Street 146

institute: Shenyang Medical college

library_source: genomic

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered ChIP-seq reads were aligned to the hg19 genome using bowtie2 (Version 2.4.1) with   default parameters. PCR duplicates in bam files were moved by using Picard tool.
MACS2 (Version 2.2.7.1 43) was used to call narrow peaks for H3K4me3 and H3K27ac with the parameters (-q 0.001) or broad peaks for H3K27me3 with the parameters (-q 0.1 --broad). The input sequencing data was set as a control.
The ChIP signal was normalized by using bamCoverage function in deeptools 3.5.0 with the parameters ( --normalizeUsing CPM,  --ignoreDuplicates,  --minMappingQuality 30,  --minFragmentLength 50)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files of the ChIP signal for each sample
Peak bed files of each sample include the significant enriched regions of the detected hitone modifications

molecule: genomic DNA

organism: Homo sapiens

source_name: Pancreas

growth_protocol: PANC-1 cells were cultured in  high-glucose DMEM/F12 (Invitrogen) supplemented with 10% FBS (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37 °C, 5% CO2.

extract_protocol:
106 cells were crosslinked in 1% formaldehyde for 10 minutes and quenched using 125mM of Glycine for 5 minutes. The chromosome was fragmented to the fragment range of 200-400 bp in the Bioruptor® Pico via sonicating 5 cycles. The fragmented histone-DNA complexes were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
The VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607)  was used with 5 ng of ChIP DNA of each sample for the construction of sequencing libraries.

treatment_protocol: siRNA transfections were performed using RNAiMAX (Invitrogen) according to the manufacturer’s instructions. The following day, cells were cultured in 10 ng/ml of TGFb (R&D systems) supplemented growth medium for 48 hours to induce epithelial-mesenchymal transition (EMT)

value: treated with TGFb for 48 hours

tag: chip antibody


title: 30

city: Rennes

first: Bastien

last: Sadoul

address: 65 rue de Saint Brieuc

country: France

institute: Institut Agro

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing and trimming were performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.2.9), was used to align the RNA-Seq reads to the Dicentrarchus labrax genome (NCBI, reference GCA_000689215.1) with a set of gene model annotations (Tine et al., 2014)
Final read alignments having more than 3 mismatches were discarded. Samtools (v1.5) was used to sort the alignment files. Then, the counting was performed with Featurecounts 1.6.2. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Genome_build: Dicentrarchus labrax seabass V1
Supplementary_files_format_and_content: tab-delimited text file include raw gene counts for every gene (ID|Symbol) and every sample

organism: Dicentrarchus labrax

source_name: head kidney

growth_protocol: Eggs were reared at 13±3 °C degrees in 9 different tanks until hatching. Temperature was then set at 15 degrees. From 121 days post fertilization (dpf) onwards fish were reared at 21°C. Individuals used for RNA-sequencing were sexed and sampled at 478 dpf.

extract_protocol:
All samples were mechanically disrupted (45 seconds at 30 rpm) in a 2 mL tube filled with 500 µL MR1 and 1 μL of TCEP from NucleoMag® RNA extraction kit (Macherey-Nagel) and 2 stainless steel beads. After a two minutes centrifugation at 13000 rpm, a sub-sample of 200 μL was transferred in a 96 deep-wells plate filled with 150 µL MR1. Automatic extraction was then performed using a KingFisher robot following manufacturer’s instructions for the NucleoMag® RNA kits.
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions ; Libraries were pooled in equimolar amounts, denatured with NaOH, and diluted to 20 pM before clustering on a cBot system (Illumina, San Diego, CA, USA). Sequencing was performed on an HiSeq 2500 (Illumina, San Diego, CA, USA) using the single-end 1*50 nt protocol on 3 lanes of a flow cell V4

treatment_protocol: Bold individuals were selected for their constant risk-taking behavior measured by a low latency to exit a sheltered side of a tank. Shy individuals on the contrary either never went out or showed an extremely high latency to exit.

value: head kidney

tag: Sex

value: M

tag: behavior

value: bold behavior


title: H3K27ac_siControl_TGFb_rep2

value: siControl


title: 29

value: F


title: ISPY2_348009

type: RNA

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

country: USA

institute: University of California, San Francisco

hyb_protocol: Hybridization was performed by Agendia Inc (Irvine, CA). This company is referenced by the platforms used: GPL20078 and GPL30494 (updated version of GPL16233).

scan_protocol: Scanning was performed by Agendia Inc (Irvine, CA).

data_processing:
For each array, gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to its 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out; and a fixed value of 9.5 was added to avoid negative values. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct raw files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding a normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes. The linear adjustment factors and updated probe annotation files per platform are provided, as is the ComBat-normalized data we used in our analysis (supplemental file "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt").
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt: Normalized, gene-level, batch-/platform- adjusted pre-treatment Agilent 44K expression data for patients from 10 arms of the neoadjuvant I-SPY 2 platform trial for early stage, aggressive breast cancer (n=988 samples for 987 patients). This is the dataset we used in our pan-arm analysis, and constitutes part of the I-SPY2-990 mRNA/RPPA Data Resource. To derive this matrix, probeset level expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were mean-collapsed by gene and combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct new files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding the resulting normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2_LinearFit_forCombiningExp_20078.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agendia32627_DPv1.14_SCFGplus [gene-collapsed using annotation GPL20078] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt, the normalized expression matrix in the I-SPY2-990 data resource.
ISPY2_LinearFit_forCombiningExp_GPL30493_wasGPL16233.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233)] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt.
ProbeAnnotation_ISPY2Edit_GPL30493_wasGPL16233.txt: This is the probeset annotation file for GPL30493, a minor update of GPL16233. For each probeset ID (row), the associated gene name, systematic name and DNA sequence is described (columns).

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Labeling was performed by Agendia Inc (Irvine, CA).

extract_protocol: Extraction was performed by Agendia Inc (Irvine, CA).

tag: patient id

value: Breast cancer biopsy (pre-treatment)

tag: hr

tag: mp

tag: pcr

tag: arm

value: Paclitaxel + ABT 888 + Carboplatin

tag: adjustment method

value: ComBat Adjust


title: KO-6h-rep#2

city: Guangzhou

first: Yan

last: Xu

address: No. 600 Tianhe Road

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
RNA-seq reads were mapped to the mouse mm10 genome with STAR v2.5.3a
The uniquely mapped reads with q score no less than 250 was kept
Gene counting was performed by featureCounts v2.0.1 with exon features documented in the Gencode mouse annotation gtf file
Differentially expressed genes between WT and KO at different time points were identified by edgeR package
Assembly: mm10
Supplementary files format and content: xlsx files containing ensembl gene accession number, gene name and gene counts for each transcript

source_name: Mettl3 cKO primary hepatocyte-6 hours after ActD treatment-#rep2

growth_protocol: C57BL/6J mice were housed under specific pathogen free conditions. Experiments were performed with animals under ethical conditions approved by the Institutional Animal Care and Use Committee of The Third Affiliated Hospital of Sun Yat-sen University.

extract_protocol:
Total RNA was extracted from the cultured cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform and 150 bp paired-end reads were generated.

treatment_protocol: Primary hepatocytes were isolated according to traditional two-step collagenase perfusion methods. After 16 hours culturing, cells were treated with 5 μM Actinomycin D for 0 hour, 2 hours, and 6 hours.

value: primary hepatocyte

tag: genotype

value: Mettl3-hepatic specific deletion


title: K562 cells expressing dCas9-KRAB [Ultima sequencing]

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

description: Ultima sequencing of 3' scRNA-seq library

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were conducted using Cell Ranger software v4.0.0 count function.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CML

extract_protocol: 10x Genomics 3' v3 user guide CG000184 Rev C

value: CML

tag: sequencing instrument

value: Ultima

tag: age

value: unperturbed


title: H3K27ac_siControl_TGFb_rep1


title: H3K27ac_siControl_rep2

value: untreated


title: KO-6h-rep#1

source_name: Mettl3 cKO primary hepatocyte-6 hours after ActD treatment-#rep1


title: WT-6h-rep#2

source_name: WT primary hepatocyte-6 hours after ActD treatment-#rep2

value: WT


title: H3K27ac_siControl_rep1


title: ISPY2_350331

tag: tissue

value: Paclitaxel + Trastuzumab


title: ISPY2_340186


title: ISPY2_345574


title: KO-2h-rep#2

source_name: Mettl3 cKO primary hepatocyte-2 hours after ActD treatment-#rep2


title: WT-6h-rep#1

source_name: WT primary hepatocyte-6 hours after ActD treatment-#rep1


title: H3K27ac_siPHF13_TGFb_rep1

tag: cell line

value: treated with TGFb for 48 hours


title: Caco-2, Rinse Aid, 1:40000, Rep5

city: Davos

first: ISMAIL

last: OGULUR

address: Herman-Burchard-Strasse 9

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parameters- Minimum length (R1): 20  Quality cutoff: 20)
Trimmed sequence reads were mapped to the reference genome GRCh38/hg38 by STAR aligner version 2.7.9a. (parameters- Gene model: gencode.v38.annotation.gtf   Length of the genomic sequence around annotated junctions: 100)
Read counts assesed by featureCounts (parameter- Minimum mapping quality per read: 10)
Differentially expressed genes were assessed by DESeq2 version 1.32.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts each sample

extract_protocol:
RNeasy Plus Micro Kit
PolyA, TruSeq RNA Kit

value: Rinse Aid, 1:40000


title: ISPY2_335091


title: ISPY2_349225

value: Paclitaxel


title: Caco-2, Rinse Aid, 1:40000, Rep4


title: H3K27me3_siPHF13_TGFb_rep1


title: ISPY2_327142

value: Paclitaxel + Neratinib


title: ISPY2_331192


title: WT-2h-rep#2

source_name: WT primary hepatocyte-2 hours after ActD treatment-#rep2

tag: cell type


title: Caco-2, Rinse Aid, 1:40000, Rep3


title: H3K27me3_siControl_TGFb_rep2

value: siControl


title: H3K27me3_siControl_TGFb_rep1


title: H3K27me3_siControl_rep2


title: KO-0h-rep#2

source_name: Mettl3 cKO primary hepatocyte-0 hour after ActD treatment-#rep2


title: ISPY2_327133


title: K562 cells expressing dCas9-KRAB [Illumina sequencing]

description: Illumina sequencing of 3' scRNA-seq library

value: Illumina NovaSeq 6000


title: WT-2h-rep#1

source_name: WT primary hepatocyte-2 hours after ActD treatment-#rep1


title: Caco-2, Rinse Aid, 1:40000, Rep1


title: H3K27me3_siPHF13_TGFb_rep2


title: KO-0h-rep#1

source_name: Mettl3 cKO primary hepatocyte-0 hour after ActD treatment-#rep1


title: ISPY2_318569

value: Breast cancer biopsy (pre-treatment)


title: H3K27me3_siControl_rep1


title: ISPY2_318438


title: KO-2h-rep#1

source_name: Mettl3 cKO primary hepatocyte-2 hours after ActD treatment-#rep1


title: Caco-2, Rinse Aid, 1:10000, Rep4

value: Rinse Aid, 1:10000


title: WT-0h-rep#2

source_name: WT primary hepatocyte-0 hour after ActD treatment-#rep2


title: ISPY2_316996

value: ComBat Adjust


title: Caco-2, Rinse Aid, 1:40000, Rep2


title: H3K4me3_siPHF13_TGFb_rep2


title: H3K4me3_siPHF13_TGFb_rep1


title: Caco-2, Rinse Aid, 1:10000, Rep3


title: WT-0h-rep#1

source_name: WT primary hepatocyte-0 hour after ActD treatment-#rep1

value: primary hepatocyte


title: ISPY2_307659


title: W4-Mettl3 cKO-rep#2

data_processing:
Sequence reads were aligned to the mouse genome version mm10 with HISAT2.1.0
Differentially expressed genes (DEGs) were calculated by DESeq2 under the following criteria: |log2FC| > 1 and P value < 0.05
Gene set enrichment analysis (GSEA) was conducted using the GSEA software (https://www.broadinstitute.org/gsea/)
Assembly: mm10
Supplementary files format and content: xlsx files containing ensembl gene accession number, gene name, and FPKM for each transcript

source_name: mouse liver tissue total RNA

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform and 150 bp paired-end reads were generated.

treatment_protocol: Mice were sacrificed at indicated age. Control and Mettl3 cKO liver tissues were collected and frozen in liquid nitrogen.

value: liver

value: Mettl3-hepatic specific deletion


title: H3K4me3_siControl_TGFb_rep2

source_name: Pancreas


title: ISPY2_306127

value: Paclitaxel + ABT 888 + Carboplatin


title: W4-Mettl3 cKO-rep#1


title: H3K4me3_siControl_TGFb_rep1


title: W4-Control-rep#2


title: Caco-2, Rinse Aid, 1:10000, Rep1


title: Caco-2, Rinse Aid, 1:10000, Rep5


title: ISPY2_303947


title: H3K4me3_siControl_rep2


title: Caco-2, Unexposed, Control, Rep4

value: Unexposed, Control


title: ISPY2_294176


title: ISPY2_299364


title: Caco-2, Unexposed, Control, Rep5


title: H3K4me3_siControl_rep1

value: untreated


title: ISPY2_298101

value: Paclitaxel + MK-2206 + Trastuzumab


title: siPHF13_TGFβ_rep2

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered reads were mapped to hg19 genome using STAR 2.7.0 with  parameters  --bamRemoveDuplicatesType UniqueIdentical
The reads on exon of each genes were counted using Htseq-count 0.12.4 with parameters -s no -t exon -i gene_id -m union
Normalization and differential analysis of gene counts were performed by the DESeq2 package in R
Genome_build: hg19
Supplementary_files_format_and_content: CSV files include DESeq2-normalied counts for every gene and every sample
CPM-normalized bigWig files for each sample were generated using bamCoverage functions in deeptools 3.5.0
Supplementary_files_format_and_content: Matrix table with DESeq2 analyzed results for each conditions

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using QIAzol reagent (Qiagen) and quantitated using a Bioan-alyzer 2100 (Agilent).  1 ug of total RNA was used to prepare seqencing library
VAHTS mRNA-seq V3 Library Prep Kit for Illumina  (Vazyme) was used to prepare the seqencing libraries.

treatment_protocol: siRNA transfections were performed using RNAiMAX (Invitrogen) according to the manufacturer’s instructions. The following day, cells were cultured in 10 ng/ml of TGFβ (R&D systems) supplemented growth medium for 48 hours to induce epithelial-mesenchymal transition (EMT)

value: treated with TGFβ for 48 hours


title: W2-Mettl3 cKO-rep#2


title: Caco-2, Unexposed, Control, Rep1


title: W4-Control-rep#1

value: WT


title: Caco-2, Unexposed, Control, Rep3


title: Caco-2, Unexposed, Control, Rep2


title: W2-Mettl3 cKO-rep#1


title: siPHF13_TGFβ_rep1


title: W2-Control-rep#2


title: W2-Control-rep#1


title: siControl_TGFβ_rep2


title: ISPY2_287300


title: siControl_TGFβ_rep1


title: ISPY2_291515


title: W1-Mettl3 cKO-rep#2


title: ISPY2_286984

value: Paclitaxel + MK-2206


title: siPHF13_rep1


title: W1-Control-rep#2


title: ISPY2_284593


title: W1-Mettl3 cKO-rep#1


title: siPHF13_rep2


title: ISPY2_282644


title: W1-Control-rep#1


title: P1-Mettl3 cKO-rep#2


title: ISPY2_284355


title: Caki-1 cells, ANGPTL8 knockout, rep1

city: Kitakyushu

first: Takuo

last: Matsukawa

address: 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, Fukuoka

country: Japan

institute: University of Occupational and Environmental Health

description: KO output.xlsx

data_processing:
WinSCP software
we check the quality of the sequence data by fastQC and trim the fastq file by Trimmomatic.
Trimmed sequence reads were mapped to GRCH38/hg38 using bowtie2 version 2.2.6 and Tophat2 version 2.1.0
Read count extraction and normalization were performed using Cufflinks version 2.2.1.
Assembly: GRCH38/hg38
Supplementary files format and content: Excel files include FPKM values for each Sample

growth_protocol: Caki-1 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). At least 7.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA Library.

value: clear cell renal cell carcinoma cell

value: ANGPTL8 knockout


title: Caki-1 cells, ANGPTL8 overexpressing, rep1

description: output.xlsx

value: ANGPTL8 overexpressing


title: Caki-1 cells, ANGPTL8 knockout, rep2

description: KO output.xlsx


title: Caki-1 cells, control, rep3

description: output.xlsx

value: control


title: Caki-1 cells, ANGPTL8 overexpressing, rep2

description: output.xlsx


title: Caki-1 cells, ANGPTL8 overexpressing, rep3

description: output.xlsx


title: Caki-1 cells, ANGPTL8 knockout, rep3

description: KO output.xlsx


title: ISPY2_273745

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel


title: P1-Control-rep#2


title: Caco-2, Rinse Aid, 1:10000, Rep2

value: Rinse Aid, 1:10000


title: siControl_rep1

value: siControl


title: Caki-1 cells, control, rep2

description: output.xlsx


title: ISPY2_277848

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: P1-Mettl3 cKO-rep#1

value: liver

value: Mettl3-hepatic specific deletion


title: Jak2v617f_day7_MEP_Ruxolitinib_2

city: Philadelphia

first: Robert

middle: L

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

data_processing:
FASTQ files were mapped with STAR to mm10
Reads were assigned to exons according to ensemble M13
Read counts were extracted and trascript level data was aggregated to gene level data in R
Assembly: mm10
Supplementary files format and content: Gene aggregates raw count data from STAR by featureCounts

source_name: MEP

growth_protocol: Jak2V617F was activated with Dre mRNA ex vivo and then transplanted into lethally irradiated recipients.  Mice were treated with either vehicle, ruxolitinib or tamoxifen to activate Cre and delete Jak2V617F.

extract_protocol:
RNA was isolated using the Direct-Zol kit from Zymo
Paired end RNA-seq libraries were constructed with the Takara HT-Seq kit.

treatment_protocol: After treatment, mice were euthanized and stem cells LSK, or progenitors MEPs, were sorted into TriZOL for RNA isolation.

value: MEP

tag: timepoint

value: Ruxolitinib

tag: batch

value: C


title: Jak2v617f_day7_LSK_Ruxolitinib_3

source_name: LSK

value: LSK

tag: treatment


title: Caki-1 cells, control, rep1

description: output.xlsx


title: Jak2v617f_day7_MEP_Ruxolitinib_3


title: Jak2v617f_day7_LSK_Ruxolitinib_2


title: siControl_rep2

value: untreated


title: ISPY2_262131

source_name: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + ABT 888 + Carboplatin


title: ISPY2_282082


title: rs3742076_G_2

first: Shaoxing

last: Guan

address: 132# Waihuan Dong Road,Guangzhou University

institute: sun yat-sen university

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
 And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
 The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
 All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: PC9 cells, rs3742076_G, gefitinib 100nM, 24h

growth_protocol: PC9 cells were maintained in RPM1640 supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: lung

value: lung cancer cells

value: gefitinib 100nM, 24h

value: FOXM1 rs3742076_G overexpression


title: ISPY2_259206

value: Breast cancer biopsy (pre-treatment)


title: rs3742076_G_1


title: rs3742076_A_3

source_name: PC9 cells, rs3742076_A, gefitinib 100nM, 24h

value: FOXM1 rs3742076_A overexpression


title: 4 weeks - IP

data_processing:
RNA-seq reads werealigned to the mouse genome version mm10 with HISAT2.1.0.
Differential m6A-modified peaks between RIP and input samples were identified using exomePeak
The longest isoform was retained if a gene has more than one isoform
Motif search was conducted with HOMER
Assembly: mm10
Supplementary files format and content: xlsx files containing ensembl gene accession number, gene name, and m6A peak analysis of indicated genes.

source_name: mouse liver tissue mRNA

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. mRNA was purified and fragmented for further experiments
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform and 150 bp paired-end reads were generated.

treatment_protocol: Mice were sacrificed at indicated age. Liver tissues were collected and frozen in liquid nitrogen.

value: WT


title: Jak2v617f_day7_MEP_TAM_3

value: TAM

value: A


title: 4 weeks - Input

value: liver


title: P1-Control-rep#1


title: Jak2v617f_day7_MEP_Ruxolitinib_1


title: Jak2v617f_day7_LSK_TAM_3


title: rs3742076_G_3


title: ISPY2_255535

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: 8 weeks - IP


title: Jak2v617f_day7_LSK_Ruxolitinib_1

value: Ruxolitinib


title: ISPY2_267306


title: 8 weeks - Input


title: 1 week - IP


title: rs3742076_A_2


title: Jak2v617f_day7_LSK_TAM_4


title: ISPY2_264678

value: Paclitaxel


title: rs3742076_A_1


title: 2 weeks - IP


title: Jak2v617f_day7_MEP_TAM_2

value: MEP


title: ISPY2_255078


title: ISPY2_246134

value: Paclitaxel + Trastuzumab


title: ISPY2_255388

value: Paclitaxel + MK-2206 + Trastuzumab


title: ISPY2_248255

value: Paclitaxel + Ganitumab


title: ISPY2_245655


title: RNA-seq of adjacent nontumoral renal tissue 8

city: Chongqing

first: xiaomao

last: Tian

address: Zhongshan 2nd Road, Yuzhong District, Chongqing 400014, P.R. China

institute: Children’s Hospital of Chongqing Medical University, Chongqing, P.R. China

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；mRNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: nontumoral renal tissue

extract_protocol:
Total RNA was extracted from 8 pairs of WT samples using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nontumoral renal tissue


title: RNA-seq of adjacent nontumoral renal tissue 7


title: Jak2v617f_day7_LSK_TAM_1

value: LSK


title: Jak2v617f_day7_MEP_TAM_1


title: RNA-seq of adjacent nontumoral renal tissue 6


title: RNA-seq of adjacent nontumoral renal tissue 5


title: ISPY2_243836


title: Jak2v617f_day3_LSK_TAM_3


title: day 1 - IP


title: ISPY2_239061


title: RNA-seq of adjacent nontumoral renal tissue 4


title: 2 weeks - Input


title: kdm5b_si_E7.5ExE_K4_1

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm9 and hg19 genome using bwa mem (0.7.12-r1039) with default paraments.
PCR duplicates were removed and only the reads with high quality (MAPQ>20) were retained for further analysis.
The signal trackings were normalized by input values using macs2 (2.1.2) bdgcmp with paraments -m logFE -p 1 and normalized with the size factors which were calculated using hg19 promoter counts.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig

source_name: extraembryonic ectoderm

extract_protocol:
According to previous studies, approximately 500-1000 cells were used per library and 5% human cells 293T was added as spike in control. Approximately 1 µg of histone H3K4me3 antibody was used for the immunoprecipitation reaction.
The sequence libraries were generated with a Kapa Hyper Prep Kit.

value: extraembryonic ectoderm

value: control

tag: developmental stage

tag: chip antibody

value: H3K4me3 (Cell Signaling Technology, 9727S, USA)


title: day 1 - Input

value: WT


title: Jak2v617f_day3_MEP_TAM_4

value: TAM


title: ISPY2_238790

tag: patient id

value: Breast cancer biopsy (pre-treatment)


title: kdm5b_si_E7.5ExE_input_1


title: Jak2v617f_day7_LSK_TAM_2

value: A


title: Jak2v617f_day3_MEP_TAM_3


title: RNA-seq of adjacent nontumoral renal tissue 3


title: RNA-seq of adjacent nontumoral renal tissue 2


title: Jak2v617f_day3_LSK_TAM_2


title: ISPY2_234723

tag: hr

value: Paclitaxel + AMG 386


title: 1 week - Input

value: liver


title: kdm5b_control_E7.5ExE_K4_1


title: ISPY2_234272

tag: mp

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: RNA-seq of adjacent nontumoral renal tissue 1


title: ISPY2_233962

tag: pcr


title: Jak2v617f_day3_MEP_TAM_2

value: MEP


title: RNA_kdm5bcontrol_E7.5_ExE_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 genome_tran using hisat2 (version 2.1.0) with default parameters. Only Reads with high quality (MAPQ>=60) were retained for further analysis.
The reads count for every gene was counted by featureCounts (Version 1.6.1), and the normalized abundance was calculated as log2(reads per million +1) using R edgeR package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: kdm5b_si_control_exp.txt: Tab-delimited text file with normalized abundance for every gene and every sample.
Supplementary_files_format_and_content: kdm5b_si_control_counts.txt: Tab-delimited text file with raw counts for every gene and every sample

extract_protocol:
According to previous methods, approximately 10-20 cells were used to construct each library. The prepared cells were transferred to lysis buffer by mouth pipetting. Reverse transcription was performed directly using oligo (dT) primers in lysates containing complete cytoplasm. Second-strand cDNA was synthesized depending on template switching with a TSO.
Fragment cDNA was prepared for sequence library construction using a Covaris sonicator. A Kapa Hyper Prep Kit was used to complete the sequence libraries.


title: RNA-seq of  wilms tumor tissue 7

source_name: wilms tumor tissue

value: wilms tumor tissue


title: Jak2v617f_day3_LSK_TAM_1


title: Jak2v617f_day3_MEP_TAM_1


title: RNA-seq of  wilms tumor tissue 8


title: ISPY2_229824

tag: arm

value: Paclitaxel + ABT 888 + Carboplatin


title: Jak2v617f_day0_LSK_Vehicle_4a

value: Vehicle


title: RNA-seq of  wilms tumor tissue 5


title: RNA_kdm5bsi_E7.5_ExE_2

value: Kdm5b siRNA


title: ISPY2_233832

tag: adjustment method


title: ISPY2_228340


title: ISPY2_229144

value: Paclitaxel


title: Jak2v617f_day0_MEP_Vehicle_3a

tag: genotype


title: ISPY2_227881


title: RNA_kdm5bsi_E7.5_ExE_1

value: extraembryonic ectoderm


title: RNA-seq of  wilms tumor tissue 3


title: kdm5b_control_E7.5ExE_input_1


title: RNA-seq of  wilms tumor tissue 4


title: ISPY2_227832


title: RNA-seq of  wilms tumor tissue 2


title: RNA-seq of  wilms tumor tissue 1


title: D14-CARCD19-RAJI-IL2

city: Houston

first: Katayoun

last: Rezvani

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Cellranger mkfastq v3.01 to generate FASTQ
Cellranger count v3.01 to generate count matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: [Cellranger files] comprising a MatrixMarket file (matrix.mtx) and two tab separated metadata files (barcodes.tsv, features.tsv)

source_name: NK cells + CD19+ cell line of raji

growth_protocol: CD19+ cell lines of Raji were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1% GlutaMAX™.  For NK cells, cord blood (CB) units were provided by the MD Anderson Cord Blood Bank. CB-derived NK cells (CB-NK) were isolated and expanded. In brief, lymphocytes were collected by density-gradient centrifugation using Ficoll-Histopaque solution. CD56+CD3- NK cells were then purified using an NK negative isolation kit, and co-cultured with irradiated (100 Gy) uAPCs at a 2:1 ratio in complete stem cell growth medium (SCGM), supplemented with 200 U/ml recombinant human IL-2 (Proleukin). On Day 4 post uAPC stimulation, fresh NK cells were purified again and transduced with retroviral vectors expressing CAR-constructs. Irradiated uAPC were added weekly to the NK cell culture to support NK cell expansion.

extract_protocol:
By applying single-cell RNA sequencing, we first compared the genexpression profiles of CAR-engineered NK cells in the presence or absence of supplemental IL-15 signaling in vitro. We subsequently validated our findings in vivo in a non-curative lymphoma model by systematically tracking the evolution of both the tumor and CAR-NK cells collected from liver, spleen, blood, and bone marrow from animals in each of our treatment groups, NT-NK, CAR19 NK and Car19/IL-15 NK cells. Mouse-derived samples were collected serailly at different time point after CAR-NK cell infusion. Cryopreserved tumor and NK cells isolated from mouse tissues were thawed and stained with antibodies against human CD45 (Clone HI30: Biolegend), CD56 (Clone HCD56: Biolegend) and CD20 (Clone 2H7: Biolegend). NK cells (identified as hCD45+CD56+) and tumor cells (identified as hCD45+CD20+) were sorted into separate tubes containing cell culture medium and kept on ice. NK cells and tumor cells were mixed in one tube at 1:1 ratio before generating single cell libraries.
Single-cell libraries were prepared using the 10X Genomics Chromium 3’ scRNAseq according to manufacturer’s protocol. Briefly, single cells were partitioned into Gel beads in Emulsion (GEM) in the 10X Chromium Controller instrument followed by cell lysis, barcoded reverse transcription of RNA, and amplification.  Subsequent to 5’ adapter ligation, samples were indexed for sequencing. On average, 5000 cells were loaded on each channel, resulting in recovery of an average of 1200 cells/sample. Libraries were sequenced on Illumina (NovaSeq6000, SP flow cell -100 cycle kit per pool), Paired end reads: read 1, 28 bp, Read 2, 91 bp.

treatment_protocol: NOD/SCID IL-2Rγnull (NSG) mice grafted with aggressive, NK-resistant tumor cells CD19+ Raji lymphoma were used to examine the anti-tumor activity of CAR-NK populations. Seven-week-old female NSG mice (Jackson Laboratories) were irradiated (300 cGy) on Day -1. On Day 0 firefly luciferase-GFP labeled Raji cells were injected intravenously (i.v.) at the dose level of 0.2×10e5 Raji cells. The mice were then serially treated with 1×10e7 CAR-NK cell i.v. After CAR-NK cell infusion, cells were collected from different organs (blood, bone marrow, liver, and spleen) of mice at different time points.

value: NK cells + CD19+ cell line of raji

value: blood+spleen+bm+liver

tag: strain

value: NSG

tag: condition

value: Co-cultured with Raji and engineered NK cells with CAR19 + IL2 in day14


title: D21-CARCD19-raji

tag: tissue

value: Co-cultured with Raji and engineered NK cells with CAR19 in day21


title: CB-NK-CARCD19

source_name: NK cells

value: NK cells

value: Engineered NK cells with CAR19


title: Jak2v617f_day0_LSK_Vehicle_3a

value: LSK

value: A


title: ISPY2_225836

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: Jak2v617f_day0_MEP_Vehicle_1a

value: MEP


title: circRNA-seq of adjacent nontumoral renal tissue 4

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
circRNA-seq reads were aligned to the hg38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
CIRI (circRNA identifier) software was used to predict circRNA. The prediction results were compared with circBase database to identify which circRNAs are known.Fold change was calculated by SRPBM (spliced reads per billion mapping). SRPBM = number of circular reads/total mapped reads (units in billion).
Differential expression analysis for circRNA was performed using R package（version 3.4.3）edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized SRPBM values and raw fragment counts for each Sample

source_name: adjacent nontumoral renal tissue

extract_protocol:
The total RNA samples of 4 pairs of WT samples were treated with the RiboZero   rRNA Removal Kit (Epicentre, WI, USA) for deleting rRNA, according to the   manufacturer's instructions.
Next, the rRNA depleted and RNase R digested RNA   samples were fragmented and synthesized cDNA with random primer. Purified the  PCR amplification products of cDNA, then the libraries were quality controlled and   sequenced by NovaSeq6000 (Illumina, San Diego, CA, USA).

value: adjacent nontumoral renal tissue


title: ISPY2_223526


title: D14-CARCD19IL15-RAJI

value: Co-cultured with Raji and engineered NK cells with CAR19 + IL-15 in day14


title: Jak2v617f_day0_LSK_Vehicle_1a

value: Vehicle


title: circRNA-seq of adjacent nontumoral renal tissue 3


title: circRNA-seq of adjacent nontumoral renal tissue 2


title: Jak2v617f_day0_LSK_Vehicle_2a


title: CB-NK-NT

value: Non-transduced NK cells


title: Jak2v617f_day0_MEP_Vehicle_2c

value: C


title: D7-CARCD19-raji

value: NK cells + CD19+ cell line of raji

value: blood+spleen+bm+liver

value: Co-cultured with Raji and engineered NK cells with CAR19 in day7


title: D21-CARCD19IL15-RAJI

value: NSG

value: Co-cultured with Raji and engineered NK cells with CAR19 + IL-15 in day21


title: Jak2v617f_day0_LSK_Vehicle_2c


title: ISPY2_211408


title: Jak2v617f_day0_MEP_Vehicle_3c


title: ISPY2_222135

value: Paclitaxel + AMG 386


title: circRNA-seq of adjacent nontumoral renal tissue 1


title: D7-CARCD19IL15-RAJI

value: Co-cultured with Raji and engineered NK cells with CAR19 + IL-15 in day7


title: Jak2v617f_day0_MEP_Vehicle_1c


title: ISPY2_208265

value: Paclitaxel + ABT 888 + Carboplatin


title: D28-CARCD19IL15-RAJI

value: Co-cultured with Raji and engineered NK cells with CAR19 + IL-15 in day28


title: D7-CARCD19-RAJI-IL2

value: Co-cultured with Raji and engineered NK cells with IL-2 in day7


title: circRNA-seq of  wilms tumor tissue 2

value: wilms tumor tissue


title: circRNA-seq of  wilms tumor tissue 3


title: ISPY2_220664

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: D7-CARCD19IL15

value: NK cells

value: Engineered NK cells with CAR19 + IL-15 in day 7


title: circRNA-seq of  wilms tumor tissue 1


title: WT_4w_GMP_3

description: BMT F2 3 GMP

source_name: GMP

growth_protocol: Mutations were activated with either Cre Dre or Flp recombinase. At either the indicated timepoint, or when symptomatic, mice were euthanized. LSK stem cells and GMP progenitors were isolated by flow cytometry and sorted into Trizol

extract_protocol:
RNA was isolated using the Direct-Zol kit from Zymo
Paired end RNA-seq libraries were constructed with the Takara HT-Seq kit. Single end libraries were generatined with the Takara Smart Seq V4 3' DE kit

treatment_protocol: Lineage negative HSPCs were isolated from mice treated with either vehicle, or tamoxifen for 7 days to delete the Flt3 oncogene.

value: GMP

value: WT


title: WT_4w_LSK_3

description: BMT F2 3 LSK

value: LSK


title: hypoxia 24h 3

first: Xianjun

last: Yu

address: 270 Dong An Road, Shanghai

department: Department of Pancreatic Surgery

institute: Fudan University Shanghai Cancer Center

data_processing:
Paired-end 150 bp high throughout sequencing was performed using a novaseq 6000 (Illumina)
Raw data was converted to fastq files using bcl2fastq v2.20.0.422 and quality checked using fastqc v 1.0.0.
RNA-seq reads were aligned to mm10 genome by the STAR  aligner V2.5.3a
Reads Per Kilobase of exon per Megabase  (RPKM) estimation of reference genes and transcripts using Cufflinks V2.0
Differential expression was calculated using DEseq2 (v1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file for processed data file

extract_protocol:
HMC-1 cells were cultured with or without hypoxia and were put into Trizol LS
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: hypoxia

tag: time


title: circRNA-seq of  wilms tumor tissue 4


title: CB-NK-CARCD19-IL15

tag: cell type

value: NSG

value: Engineered NK cells with CAR19 + IL-15


title: ISPY2_202539

extract_protocol: Extraction was performed by Agendia Inc (Irvine, CA).

value: Paclitaxel


title: WT_4w_GMP_2

description: BMT F2 2 GMP

tag: timepoint


title: D7-NT-raji

value: NK cells + CD19+ cell line of raji

value: blood+spleen+bm+liver

tag: treatment

value: NT-NK

value: Co-cultured with Raji and Non-transduced NK cells in day7


title: ISPY2_201873


title: RNA_kdm5bcontrol_E7.5_ExE_1

value: extraembryonic ectoderm

value: control

tag: developmental stage


title: RNA-seq of  wilms tumor tissue 6

value: wilms tumor tissue


title: ISPY2_198891

value: Breast cancer biopsy (pre-treatment)

value: ComBat Adjust


title: WT_4w_LSK_2

description: BMT F2 2 LSK


title: D21-NT-raji

value: Co-cultured with Raji and Non-transduced NK cells in day21


title: hypoxia 24h 2


title: ISPY2_202956

value: Paclitaxel + Neratinib


title: Jak2v617f_day0_LSK_Vehicle_1c

value: Vehicle

tag: batch

value: C


title: ISPY2_203254

tag: patient id

value: Paclitaxel + MK-2206


title: hypoxia 24h 1

value: hypoxia


title: WT_4w_GMP_1

description: BMT F2 1 GMP

value: GMP

value: WT


title: ISPY2_197942

tag: hr

value: Paclitaxel


title: D21-CARCD19-RAJI-IL2

value: NK cells + CD19+ cell line of raji

value: blood+spleen+bm+liver

value: NSG

value: Co-cultured with Raji and engineered NK cells with CAR19 + IL-2 in day21


title: CB-NK-IL15

value: NK cells

value: Engineered NK cells with IL-15


title: WT_4w_LSK_1

description: BMT F2 1 LSK

value: LSK


title: hypoxia 12h 3


title: ISPY2_192548

value: Breast cancer biopsy (pre-treatment)

tag: mp

value: Paclitaxel + ABT 888 + Carboplatin

value: ComBat Adjust


title: ISPY2_190224

tag: pcr


title: hypoxia 12h 2


title: Flt3_8w_GMP_3

description: BMTB4 14 GMP


title: D14-CARCD19IL15

value: Engineered NK cells with CAR19 + IL-15 in day14


title: Flt3_8w_LSK_3

description: BMTB4 14 LSK


title: control 2

value: control


title: hypoxia 12h 1


title: D14-NT-raji

value: NT-NK

value: Co-cultured with Raji and Non-transduced NK cells in day14


title: PT-WT-14-days_5

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

data_processing:
Illumina software RTA  was used for basecalling.
Reads of the samples were aligned to  the reference genome (Mouse_mm10) and the annotated transcripts using  STAR and RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts and FPKM values for each Sample

source_name: Primary tumor

growth_protocol: The 6DT1 mouse mammary tumor explant cell line was cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. 1x10^5 6DT1 cells were injected orthotopically into the fourth mammary fat pad of wildtype or CLIC4 knockout syngeneic FVB/N mice.

extract_protocol:
Frozen tissue was lysed in Qiagen buffer RLT using a Precellys (Bertin) tissue homogenizer. Total RNA was isolated using the RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using llumina TruSeq Stranded mRNA Library Prep.
The mRNA-Seq samples were sequenced on Illumina instrument using paired-end sequencing.

treatment_protocol: Lung tissue was isolated from wildtype and CLIC4 knockout mice at baseline or 14 days after orthografting. Primary tumor tissue was isolated at 14 days after orthografting. Tissue was snap-frozen in liquid nitrogen and stored at -80C until RNA extraction.

value: FVB/N

tag: host genotype

value: Wildtype

tag: orthograft time

value: 14 days

value: 6DT1-derived orthograft


title: Flt3_8w_GMP_2

description: BMTB4 12 GMP

value: GMP

tag: genotype


title: ISPY2_188511

data_processing:
For each array, gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to its 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out; and a fixed value of 9.5 was added to avoid negative values. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified. Expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct raw files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding a normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes. The linear adjustment factors and updated probe annotation files per platform are provided, as is the ComBat-normalized data we used in our analysis (supplemental file "ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt").
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt: Normalized, gene-level, batch-/platform- adjusted pre-treatment Agilent 44K expression data for patients from 10 arms of the neoadjuvant I-SPY 2 platform trial for early stage, aggressive breast cancer (n=988 samples for 987 patients). This is the dataset we used in our pan-arm analysis, and constitutes part of the I-SPY2-990 mRNA/RPPA Data Resource. To derive this matrix, probeset level expression data from the first ~900 I-SPY2 patients distributed over the two platforms GPL30494 (updated version of GPL16233; n=334) and GPL20078 (n=545) were mean-collapsed by gene and combined into a single gene-level dataset after batch-adjusting using ComBat [PMID:16632515]. Linear adjustment factors were derived from the ComBat transformation, per platform, which can be used to batch correct new files. The subsequent ~100 samples, assayed on GPL20078, were batch corrected using these factors and added to the original set, yielding the resulting normalized expression dataset comprising 988 samples (987 unique patients) x 19,134 (common) genes.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agendia32627_DPv1.14_SCFGplus [with annotation GPL20078 (n=654)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt: Normalized probeset level pre-treatment gene expression data from Agilent 44K expression arrays Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233; n=334)] from the I-SPY 2 platform trial for early stage, aggressive breast cancer. Each column represents a patient sample. Per column, green-channel (Cy3) normalized signal intensity (log2) data, as provided in the raw files on each patient, was extracted and aligned to its (within-array) 75th quantile by Agendia as per the manufacturer’s data processing recommendations. All values indicated for non-conformity are NA'd out; and a fixed value of 9.5 was added to avoid negative values.
ISPY2_LinearFit_forCombiningExp_20078.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agendia32627_DPv1.14_SCFGplus [gene-collapsed using annotation GPL20078] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL20078_ProbeLevel_n654.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt, the normalized expression matrix in the I-SPY2-990 data resource.
ISPY2_LinearFit_forCombiningExp_GPL30493_wasGPL16233.txt: This file contains linear adjustment factors (intercept and linear coefficient) derived from the ComBat transformation combining data (~900 samples) from GPL20078 and GPL30493 that can be used to batch-/platform- correct new Agilent 44K expression arrays of the type Agilent_human_DiscoverPrint_15746 [with annotation GPL30493 (update of GPL16233)] for inclusion in the larger normalized dataset. Application of this transformation to columns from ISPY2ResID_AgilentGeneExp_990_FrshFrzn_GPL30493.wasGPL16233_ProbeLevel_n334.txt, once mean-collapsed to gene level using GPL20078, results in values nearly identical to those in ISPY2ResID_AgilentGeneExp_990_FrshFrzn_meanCol_geneLevel_n988.txt.
ProbeAnnotation_ISPY2Edit_GPL30493_wasGPL16233.txt: This is the probeset annotation file for GPL30493, a minor update of GPL16233. For each probeset ID (row), the associated gene name, systematic name and DNA sequence is described (columns).

tag: arm

tag: adjustment method


title: ISPY2_183831

tag: tissue

value: Paclitaxel + MK-2206


title: PT-WT-14-days_6

tag: strain


title: PT-WT-14-days_4


title: Flt3_8w_LSK_2

description: BMTB4 12 LSK


title: ISPY2_181819

value: Paclitaxel


title: LNCaP_siDHX9_REP3

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

data_processing:
Raw pairend-ends reads fastq files were preprocessed to mask adapters with cutadapt v1.11.
Lower quality bases and adapters were removed with ERNE v.2.1.1.
Trimmed reads were mapped to hg38 using STAR v2.6.1d.
Statistics on strandness reads, genebody coverage, reads distribuition and insert size estimation were performed using RSeQC v.4.0.0.
The uniquely mapped reads from biological replicates were kept and counted with HTSeq v.0.11.1.
Differential gene expression on read counts matrix were performed using DESeq2 v.1.30.0.
Genome_build: hg38
Supplementary_files_format_and_content: .txt files with raw read counts

source_name: LNCaP prostate cancer cell line

growth_protocol: LNCaP cells were maintained in RPMI 1640 (Euroclone) supplemented with 10% fetal bovine serum (GIBCO), 4500 mg/L glucose (Sigma-Aldrich), 10 mM Hepes (Eurocolone), 1mM sodium pyruvate (Euroclone), 100 U/mL penicillin (Euroclone) and 100 μg/mL streptomycin (Euroclone).

extract_protocol: RNA was isolated and DNase digested using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s instruction.

treatment_protocol: Cells were transfected with siRNAs (Sigma-Aldrich), at final concentration of 50 nM, using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer's instructions. After 48 hours cells were lysed and total RNA was extracted.

tag: cell line

value: LNCaP

value: prostate cancer

value: siDHX9 for 48 hours


title: control 1

tag: time


title: Flt3_8w_GMP_1

description: BMTB4 11 GMP

tag: cell type

tag: timepoint


title: ISPY2_180027

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + AMG 386


title: PT-WT-14-days_3


title: LNCaP_siDHX9_REP2

tag: treatment


title: Flt3_8w_LSK_1

description: BMTB4 11 LSK

value: LSK


title: ISPY2_178815

value: Paclitaxel + Neratinib

value: ComBat Adjust


title: control 3

value: control


title: Flt3_6w_GMP_3

description: BMTB4 18 GMP


title: PT-WT-14-days_2


title: Flt3_6w_LSK_3

description: BMTB4 18 LSK


title: LNCaP_siSCR_REP3

value: siSCR for 48 hours


title: LNCaP_siSCR_REP2


title: ISPY2_188091


title: Flt3_6w_LSK_2

description: BMTB4 13 LSK


title: Flt3_6w_GMP_2

description: BMTB4 13 GMP


title: ISPY2_174903


title: LNCaP_siSCR_REP1


title: PT-WT-14-days_1

value: FVB/N


title: PT-KO-14-days_6


title: PT-KO-14-days_5


title: ISPY2_172283


title: ISPY2_178649


title: Flt3_6w_LSK_1

description: BMTB4 10 LSK


title: ISPY2_166412

value: Paclitaxel + Trastuzumab


title: PT-KO-14-days_2

value: 14 days


title: ISPY2_169536


title: PT-KO-14-days_4

value: 6DT1-derived orthograft


title: Flt3_4w_GMP_3

description: BMTB4 7 GMP

value: GMP


title: PT-KO-14-days_1


title: ISPY2_166782


title: Flt3_6w_GMP_1

description: BMTB4 10 GMP


title: PT-KO-14-days_3


title: Clone 596-11 NovaSeq Replicate 2 No Dox

first: Jonathan

last: Hernandez

address: Building 37

institute: NCI/NIH

description:
596-11-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

data_processing:
24 Total RNA-Seq samples were pooled and sequenced on NovaSeq 6000 and NextSeq 500 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing.
Basecalling was performed by RTA (version 3.4.4).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.20) allowing 1 mismatch.
Reads were filtered with a base call quality >91% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using CutAdapt (v1.18).
STAR (version 2.7.6a) is run in twopass basic mode to align trimmed reads to custom hg38+shRNA reference genome
Gene-level expression quantificiation  was performed using RSEM (version 1.3.3) and the hg38 (Gencode v35) + custom shRNA gene annotation.
Quantile-normalization and differential expression was performed using limma-voom (version 3.48.3).
Genome_build: hg38+shRNA (custom)
Supplementary_files_format_and_content: Tab-delimited text file contains limma-voom normalized counts output.

source_name: HT-29 colon adenocarcinoma

growth_protocol: 596 clones were grown in McCoy's 5A medium with 10% tetracycline-free FBS, 1% penicillin-streptomycin and 3µg/ml of puromycin.

extract_protocol:
Total RNA, treated with Dnase I (Qiagen; 79254), was extracted using RNeasy kit (Qiagen; 74106).
Stranded total RNA library was prepared according to the Illumina library prep protocol (Illumina; Document # 1000000040499 v00).
Stranded Total RNAseq

treatment_protocol: Doxycycline (1μg/ml) was treated for 24 hours to induce shRNA expression.

value: HT-29-derived clone 596-11 cell

value: Doxycycline untreated


title: ISPY2_160120

value: Paclitaxel + ABT 888 + Carboplatin


title: Clone 596-11 NovaSeq Replicate 1 Dox

description:
596-11-Dox-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: Doxycycline treated

value: ephrinB2 silencing


title: ISPY2_159352

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + MK-2206 + Trastuzumab


title: Clone 596-11 NovaSeq Replicate 2 Dox

description:
596-11-Dox-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv


title: LNCaP_siDHX9_REP1

value: LNCaP

value: prostate cancer

value: siDHX9 for 48 hours


title: Lung-WT-Control_4

source_name: Lung

value: Wildtype

value: Baseline

value: Control lung tissue


title: Clone 596-11 NovaSeq Replicate 1 No Dox

description:
596-11-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: control


title: Clone 596-7 NovaSeq Replicate 2 Dox

description:
596-7-Dox-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: HT-29-derived clone 596-7 cell


title: Flt3_4w_GMP_2

description: BMTB4 15 GMP


title: ISPY2_157463

value: ComBat Adjust


title: Lung-WT-Control_3

value: FVB/N


title: Clone 596-7 NovaSeq Replicate 1 Dox

description:
596-7-Dox-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv


title: Flt3_4w_LSK_2

description: BMTB4 15 LSK

value: LSK


title: Lung-WT-Control_2


title: Lung-WT-Control_1


title: Flt3_4w_LSK_3

description: BMTB4 7 LSK


title: ISPY2_154293

value: Paclitaxel + Neratinib


title: Lung-WT-14-days_6

value: 14 days

value: Pre-metastatic lung tissue


title: ISPY2_151481

value: Paclitaxel


title: Flt3_4w_LSK_1

description: BMTB4 1 LSK


title: Clone 596-6 NovaSeq Replicate 2 Dox

description:
596-6-Dox-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: HT-29-derived clone 596-6 cell

value: Doxycycline treated

value: ephrinB2 silencing


title: ISPY2_153880

value: Breast cancer biopsy (pre-treatment)

value: Paclitaxel + Trastuzumab


title: Clone 596-7 NovaSeq Replicate 2 No Dox

description:
596-7-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: Doxycycline untreated


title: ISPY2_155171

value: Paclitaxel + ABT 888 + Carboplatin


title: Lung-WT-14-days_5

value: Wildtype


title: Clone 596-7 NovaSeq Replicate 1 No Dox

description:
596-7-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: control


title: Clone 596-6 NovaSeq Replicate 1 Dox

description:
596-6-Dox-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv


title: Flt3_2w_GMP_2

description: BMTB4 6 GMP

value: GMP


title: Flt3_2w_GMP_3

description: BMTB4 8 GMP


title: Flt3_2w_LSK_2

description: BMTB4 6 LSK


title: Clone 596-6 NovaSeq Replicate 2 No Dox

description:
596-6-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv


title: Clone 596-6 NovaSeq Replicate 1 No Dox

description:
596-6-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv


title: Lung-WT-14-days_2


title: Flt3_4w_GMP_1

description: BMTB4 1 GMP


title: Clone 596-1 NovaSeq Replicate 2 Dox

description:
596-1-Dox-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: HT-29-derived clone 596-1 cell


title: ISPY2_141782

value: ComBat Adjust


title: Lung-WT-14-days_3

value: FVB/N


title: ISPY2_145513

value: Paclitaxel + MK-2206 + Trastuzumab


title: Flt3_2w_GMP_1

description: BMTB4 9 GMP


title: ISPY2_139771

value: Paclitaxel + Neratinib


title: Flt3_2w_LSK_1

description: BMTB4 9 LSK

value: LSK


title: Lung-WT-14-days_1

value: 14 days

value: Pre-metastatic lung tissue


title: Flt3_2w_LSK_3

description: BMTB4 8 LSK


title: Clone 596-1 NovaSeq Replicate 1 Dox

description:
596-1-Dox-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: Doxycycline treated


title: Jak2v617f_day0_MEP_Vehicle_2a

source_name: MEP

value: MEP

value: Vehicle

tag: batch

value: A


title: Npm1 Flt3__Lin- HSPCs_TAM_3

source_name: Lin- HSPCs

value: Lin- HSPCs

value: Npm1 Flt3

value: TAM


title: ISPY2_151230

source_name: Breast cancer biopsy (pre-treatment)

tag: patient id

value: Breast cancer biopsy (pre-treatment)


title: Lung-WT-14-days_4

value: Wildtype


title: ISPY2_134526

tag: hr


title: Lung-KO-Control_4

value: Baseline

value: Control lung tissue


title: Clone 596-1 NovaSeq Replicate 2 No Dox

description:
596-1-2_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: HT-29-derived clone 596-1 cell

value: Doxycycline untreated

value: control


title: ISPY2_129973

tag: mp

value: Paclitaxel + ABT 888 + Carboplatin

value: ComBat Adjust


title: Npm1 Flt3__Lin- HSPCs_Vehicle_3


title: Lung-KO-Control_3

value: FVB/N


title: Lung-KO-Control_2


title: Npm1 Flt3__Lin- HSPCs_Vehicle_2


title: ISPY2_129837

tag: pcr


title: ATAC-Seq Th17_72h_LNA4_replicate3_LANE2

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly with Bowtie2 (v. 2.3.3.1)
Reads with mapping quality value < 30 were filtered out using samtools (v. 1.9) and duplicate reads were removed using Picard tool's (v. 2.20.2) MarkDuplicates function.
Peaks were called using MACS2 (v. 2.2.6) with the following settings: -g hs -q 0.05
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files generated with MACS2

source_name: cord blood

growth_protocol: Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D).  CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304) (3750 ng/well in a six-well culture plate), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in the medium in a concentration of 1 μg/mL. X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2. For Th17 polarization of CD4+ cells, IL-6 (20 ng/mL; Roche, cat# 11138600 001), IL-1β (10 ng/mL, R&D Systems, cat# 201 LB) and TGFβ (10 ng/mL, R&D Systems, cat# 240) were used as the cytokine cocktail along with neutralizing antibodies against IFNγ (1 μg/mL, R&D Systems, cat# MAB-285) and IL4 (1 μg/mL, R&D Systems, cat# MAB204). Nonpolarizing control (Th0) cells were activated with anti-CD3 and anti-CD28 antibodies in the presence of the neutralizing antibodies without differentiating cytokines.

extract_protocol:
MIAT deficient and sufficient cells were differentiated under Th17 conditions for 72 h in three biological replicates. Nuclei were isolated as described earlier (Buenrostro et al., 2013, 2015) except that the cells were lysed by Digitonin (Promega, cat no. G9441) to avoid mitochondrial DNA contamination.
Nextera DNA library preparation kit with i7 and i5 indices (15028212) and AMPURE-XP beads (B46053, Beckman Coulter) were used to prepare and purify the libraries, following the manufacturer’s instructions.
18 samples pooled into one pool and sequenced on 2 lanes with 2x50 bp read length. Sequencing was performed at the Finnish Functional Genomics Centre using the NovaSeq 6000 S1 Next-Generation Sequencing platform.

treatment_protocol: For LNA transfections, 4 million cells mixed with 150 pmols of LNA, prepared in 100 μL volume of OptiMEM (Gibco by Life Technologies, cat # 31985-047), were used to transfect the cells using the Amaxa Nucleofector II system (Lonza). After transfection, cells were first rested at 37° C for 48 h in RPMI 1640 (Sigma-Aldrich) medium supplemented with 10% FCS, 50 U/mL penicillin, 50 μg/mL streptomycin, and 2 mM L-glutamine and then activated and cultured as described above. The following LNAs (provided by QIAGEN) were used:  LNA-NC (non-targeting control): 5´-AACACGTCTATACGC -3´;  LNA-1: 5'-ACTTTGGCATTCTAGG-3´;  LNA-4: 5'-AGGCTGGTAGGCTATG-3´.

value: In vitro differentiated Th17 cells

value: Nucleofected cells differentiated for 72 hour in Th17 media


title: Lung-KO-Control_1

tag: host genotype


title: Npm1 Flt3__Lin- HSPCs_Vehicle_1

value: Vehicle


title: Npm1 Flt3__Lin- HSPCs_TAM_2


title: ISPY2_127675

value: Paclitaxel + Neratinib


title: ISPY2_125385


title: Npm1 Flt3__Lin- HSPCs_TAM_1

value: Lin- HSPCs


title: Lung-KO-14-days_5

tag: orthograft time

value: 14 days

value: Pre-metastatic lung tissue


title: ISPY2_139137

value: Breast cancer biopsy (pre-treatment)


title: ATAC-Seq Th17_72h_LNA1_replicate3_LANE2


title: ISPY2_122795

value: Paclitaxel + Ganitumab


title: Lung-KO-14-days_6


title: Lung-KO-14-days_4


title: ISPY2_120001


title: Lung-KO-14-days_3


title: Dnmt3a Flt3__LSK_3

source_name: LSK

value: LSK

tag: genotype

value: Dnmt3a Flt3


title: ATAC-Seq Th17_72h_LNA1_replicate3_LANE1


title: Clone 596-1 NovaSeq Replicate 1 No Dox

description:
596-1-1_NovaSeq
RSEM.genes.limmavoom_normalized.Novaseq.tsv

value: HT-29-derived clone 596-1 cell


title: Lung-KO-14-days_2


title: ATAC-Seq Th17_72h_LNANT_replicate3_LANE1


title: ATAC-Seq Th17_72h_LNANT_replicate3_LANE2


title: Dnmt3a Flt3__GMP_3

value: GMP


title: ATAC-Seq Th17_24h_LNA4_replicate3_LANE2

value: Nucleofected cells differentiated for 24 hour in Th17 media


title: ISPY2_117424

tag: arm


title: ISPY2_112606

value: Paclitaxel + Trastuzumab

tag: adjustment method


title: Dnmt3a Flt3__GMP_2


title: Lung-KO-14-days_1

tag: tissue


title: ATAC-Seq Th17_24h_LNA4_replicate3_LANE1


title: ISPY2_111881

value: ComBat Adjust


title: ATAC-Seq Th17_24h_LNA1_replicate3_LANE2


title: Dnmt3a Flt3__LSK_2


title: Dnmt3a Flt3__GMP_1


title: ISPY2_111674

value: Paclitaxel + ABT 888 + Carboplatin


title: ISPY2_111038

value: Paclitaxel + AMG 386


title: ATAC-Seq Th17_24h_LNA1_replicate3_LANE1

value: In vitro differentiated Th17 cells


title: Npm1 Flt3__LSK_4

value: Npm1 Flt3


title: ISPY2_109980

value: Paclitaxel + Neratinib


title: ATAC-Seq Th17_24h_LNANT_replicate3_LANE2


title: Npm1 Flt3__GMP_4


title: ISPY2_108969


title: ATAC-Seq Th17_24h_LNANT_replicate3_LANE1


title: Npm1 Flt3__GMP_3


title: ISPY2_107700

value: Paclitaxel + MK-2206 + Trastuzumab


title: Npm1 Flt3__LSK_3


title: ATAC-Seq Th17_72h_LNA4_replicate2_LANE1

value: Nucleofected cells differentiated for 72 hour in Th17 media


title: ATAC-Seq Th17_72h_LNA1_replicate2_LANE2


title: ISPY2_108939


title: ATAC-Seq Th17_72h_LNA4_replicate2_LANE2


title: GST-APIP5

city: Beijing

first: Fan

last: Zhang

address: No. 2 Yuanmingyuan West Road, Haidian District

institute: Chinese Academy of Agricultural Sciences

data_processing:
Base-calling performed using Illumina bcf2fastq v2.20 software.
Adaptor sequences and low quality nucleotides (<Q20) were trimmed from raw sequences for each sample using Trimmomatic software (LEANDING:3 TRAILING:3 SLIDINGWINDOW:7:15 MINLEN:50).
The clean reads were mapped to the MSU Rice Genome Annotation Project (MSU RGAP; ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0) using bowtie2 with parameters--end-to-end --sensitive.
Peaks were called using MACS2 with q value <= 0.05.
Peaks were annotated using chipseeker with parameters overlap:all.
Assembly: MSU Rice Genome Annotation Project (MSU RGAP; ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0) using bowtie2 with parameters--end-to-end --sensitive.
Supplementary files format and content: peak files and peak annotation

organism: Oryza sativa

source_name: Rice leaves

growth_protocol: NPB seeds were germinated on half-strength Murashige and Skoog (MS) medium for 10 days and then transferred to soil. Seedlings were kept in a growth chamber at 26°C and 70% relative humidity with 12-h light/dark photoperiod.

extract_protocol:
Total DNA of Nipponbare and purified GST-APIP5 and GST were used for ChIP assays. DNA was prepared from 1-month-old rice leaves using CATB method. The total DNA was sheared into 100-500bp fragments using ultrasonic crusher. The recombinant proteins GST-APIP5 and GST were expressed in Escherichia coli, and were purified with Glutathione Sepharose 4B (GE Healthcare). GST-APIP5 or GST was incubated with an equal amount of DNA fragments for 2h, respectively. The incubation buffer includes: 50mM Tris (pH 7.0), 1mM EDTA, 100mM KCl, 5% Glycerol, 0.1% Triton X-100, 1mM DTT. After co-incubation, the beads were washed 5-10 times using incubation buffer. The precipitated DNA fragments were recovered eith CTAB and dissolved in sterile water for constructing Illumina sequencing library.
Libraries were prepared according to Illumina's instructions.

tag: cultivar

value: Nipponbare

tag: developmental stage

value: about 1-month-old seedlings

tag: chip anitbody


title: Npm1 Flt3__LSK_2

tag: cell type


title: Npm1 Flt3__GMP_2


title: ATAC-Seq Th17_72h_LNA1_replicate2_LANE1


title: Npm1 Flt3__LSK_1


title: GST

value: GST


title: ATAC-Seq Th17_72h_LNANT_replicate2_LANE1


title: Npm1 Flt3__GMP_1


title: reoxygenation 24h 2

data_processing:
Single-end 75 bp high throughout sequencing was performed using a NextSeq 500 (Illumina)
Raw data was converted to fastq files using bcl2fastq v2.20.0.422 and quality checked using fastqc v 1.0.0.
RNA-seq reads were aligned to mm10 genome by the STAR  aligner V2.5.3a
Reads Per Kilobase of exon per Megabase  (RPKM) estimation of reference genes and transcripts using Cufflinks V2.0
Differential expression was calculated using DEseq2 (v1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Text file for processed data file, and Fastq files for each sample

extract_protocol:
Mice ILC2 cells were FACS sorted based on the following surface expression:Lin-CD127+ST2+. Cells were cultured with or without hypoxia and were put into Trizol LS
RNA libraries were prepared for sequencing using standard Illumina protocols

value: reoxygenation

tag: time

value: 24 hr


title: ATAC-Seq Th17_72h_LNANT_replicate2_LANE2

tag: treatment


title: reoxygenation 24h 3


title: reoxygenation 24h 1


title: ATAC-Seq Th17_24h_LNA1_replicate2_LANE2


title: ATAC-Seq Th17_24h_LNANT_replicate2_LANE2


title: hypoxia 24h 2

value: hypoxia


title: ATAC-Seq Th17_24h_LNA1_replicate2_LANE1


title: ATAC-Seq Th17_72h_LNA4_replicate3_LANE1


title: ATAC-Seq Th17_72h_LNA4_replicate1_LANE2


title: hypoxia 8h 3

value: 8 hr


title: hypoxia 8h 2


title: ATAC-Seq Th17_24h_LNANT_replicate2_LANE1

value: Nucleofected cells differentiated for 24 hour in Th17 media


title: Dnmt3a Flt3__LSK_1

value: LSK

value: Dnmt3a Flt3


title: Air_Pollution_Labyrinth

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Demultiplexed fastq files were processed using cellranger count against the mm10 referece, to obtain single cell feature counts.
Cellranger count output files were aggregated using the cellranger aggr
Output from cellranger aggr has been used to create a Seurat object and a standard Seurat pipeline was used for downstream analysis.
Supplementary_files_format_and_content: Expression Matrix

source_name: Placental cell at Gestational D19

growth_protocol: C57BL/6J mouse were obtained from Jackson Laboratories housed under dark: light 12:12(h) conditions with free access to water and chow in the University of California Animal Facility

extract_protocol:
For scRNA-seq library prep, single suspension of each placental compartment was prepared separately by enzymatic digestion of the tissue followed by passing the cell suspension through 100μm cell strainer (MACS, Smart Steiner)
Single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit (P/N 1000075, 10x Genomics) following manufacturer’s instructions. scRNA sequencing libraries were sequenced by the NovaSeq-6000  (Illumina Inc.; San Diego, CA, USA).

treatment_protocol: Female mice were exposed to SRM1649b particles (resuspend in sterile PBS and sonicated to obtain a concentration of 15μg/µl) intranasally either starting from 2months prior to gestation followed by 18th day of gestation.

tag: strain

value: Placenta – labyrinth

value: Air pollution


title: Input DNA

value: Input DNA


title: Air_Pollution_Junction

value: Placenta – junction


title: ATAC-Seq Th17_72h_LNA1_replicate1_LANE2

value: In vitro differentiated Th17 cells


title: hypoxia 8h 1


title: ATAC-Seq Th17_24h_LNA4_replicate2_LANE1


title: ATAC-Seq Th17_24h_LNA4_replicate2_LANE2


title: control 3

value: control


title: control 2


title: ATAC-Seq Th17_72h_LNA1_replicate1_LANE1

value: Nucleofected cells differentiated for 72 hour in Th17 media


title: hypoxia 24h 3


title: ATAC-Seq Th17_72h_LNANT_replicate1_LANE2


title: control 1


title: ATAC-Seq Th17_72h_LNANT_replicate1_LANE1


title: hypoxia 24h 1


title: CONTROL_Labyrinth

value: Control


title: ATAC-Seq - treated - neural progenitor cells - rep3

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
ATACseq reads were trimmed to remove the adapter using trim_galore. Short reads were aligned to the mouse reference genome (mm10) using bwa mem aligner version 0.7.17. Reads mapping to mitochondrial DNA were removed before analysis. PCR duplicates are removed with picard (v2.18.12). To identify peaks from ATAC-seq reads, we used the macs2 package (v2.1.1.20160309) with ‘-f BEDPE’ parameter.  To visualize individual ATAC-seq data on Integrative Genomics Viewer (IGV), we converted bam output files into normalized bigwig format using the bamCoverage function in deepTools (v3.3.0) with options “--binSize 10 --normalizeUsing RPKM -p=2”
Chipseq reads were trimmed to remove the adapter using trim_galore. Short reads were aligned to the mouse reference genome (mm10) using bowtie2 aligner version 2.4.1. To identify peaks from Chipseq reads, we used the macs2 package (v2.1.1.20160309) with ‘-B --SPMR --qvalue .05 --gsize mm --nomodel --extsize 200’ parameter.  To visualize individual chipseq data on Integrative Genomics Viewer (IGV), we converted bam output files into normalized bigwig format using the bamCoverage function in deepTools (v3.3.0) with options “--binSize 10 --normalizeUsing RPKM -p=2”
Genome_build: mm10
Supplementary_files_format_and_content: peak files, bigwig

source_name: neural progenitor cells

growth_protocol: NSPCs derived from the telencephalon were generated from individual C57Bl/6 female mouse embryos on   embryonic day 14.5 (E14.5), dissociated into single cells, and grown as three-dimensional neurosphere   cultures. Neurospheres were passaged every 3-4 days, and all experimental treatments were given at the end of the third passage.

extract_protocol:
(1) For ATAC-seq, a detailed protocol is described by Corces et al., 2017. In brief, nuclei were resuspended in transposase reaction mix containing 1:20 dilution of Transposase (Illumina) in 1X TD buffer (Illumina) and incubated at 37oC for 30 minutes with mixing.  Fragmented product was purified using a Zymo DNA Clean and Concentrator-5 kit prior to PCR amplification, adapter sequence incorporation, and library preparation. (2) For ChIP-seq, a detailed protocol is described by Rollins and Rogatsky et al., 2019. In brief, lysates were clarified from sonicated nuclei and GR-DNA complexes were isolated with antibody. Purified DNA was eluted using the QIAquick PCR Purification Kit according to manufacturer’s directions. DNA was stored at -20 oC until next generation sequencing using an Illumina HiSeq 2500 system.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with an ethanol vehicle or dexamethasone (10-7M) for a total of 4 hours.

value: ES-derived neural progenitor cells

value: cerebral cortex

tag: age

value: embryonic day 14.5

value: dexamethasone (10-7M)

tag: chip antibody


title: CONTROL_Junction


title: ATAC-Seq Th17_72h_LNA4_replicate1_LANE1


title: CONTROL_Decidua

value: Placenta – decidua


title: ATAC-Seq Th17_24h_LNA4_replicate1_LANE2


title: ATAC-Seq Th17_24h_LNA4_replicate1_LANE1


title: ATAC-Seq Th17_24h_LNA1_replicate1_LANE2


title: Nanopore_S23 Parhyale embryo RNA-Seq

city: Woods Hole

first: Nipam

middle: H

last: Patel

state: MA

address: 7 Mbl Street

institute: Marine Biological Laboratory

description:
Par-haw_Nanopore_stringtie2.fasta
Par-haw_Nanopore_stringtie2.gtf

data_processing:
Reads were quality trimmed using trim_galore (FASTQC + cutadapt)
Trimmed reads were assembled into de novo transcriptomes using Trinity
A genome-guided transcriptome was also assembled after mapping reads to the genome using hisat2
A combined short- & long-read transcriptome was generated using StringTie2
FPKM quantification was performed using kallisto + RSEM via the Trinity pipeline
Differential expression analysis was performed using Trinity
Transcriptomes were merged with the previous genome annotation using Mikado
Mikado and MAKER annotations were functionally annotated using eggNOG
Mikado and MAKER annotations were compared to the Drosophila proteome using OrthoFinder
Assembly: phaw_5.0
Supplementary files format and content: DAS.mikado.loci.fasta and DAS.mikado.loci.fasta.gene_trans_map are the final Mikado merged transcriptome files
Supplementary files format and content: The files beginning with "Orthogroups" are the output from OrthoFinder. The output for Mikado does not have an additional suffix, whereas the output for MAKER has the suffix "_MAKER"
Supplementary files format and content: The files in the format "S##_vs_S##_RNASeq_Results.csv" are pairwise differential expression comparisions made using DESeq2
Supplementary files format and content: The files beginning with "Sall_peaktypes" are summarized gene models containing useful information (such as categories of nearby genes and peaks)
Supplementary files format and content: The files beginning with "Omni_vs_RNA_" are peak-gene pairs from differential expression and accessibility analysis between timepoints. CC pairs are concordant; DC pairs are discordant; all peaks are found in the "peak" file whereas inferred promoter peaks are found in the "pro" file
Supplementary files format and content: The "portcullis" files are the predicted splice junctions from the Mikado pipeline
Supplementary files format and content: The "FASTA_metadata.csv" file contains additional descriptions of the transcriptomes included in this dataset
Supplementary files format and content: The "Sun_annotations…" and "Blondel_annotations…" files contain the eggNOG-assigned gene annotations for the Mikado and MAKER annotations, respectively

organism: Parhyale hawaiensis

source_name: whole embryo

extract_protocol:
RNA was isolated using the Zymo Direct-Zol Miniprep Plus kit
Libraries were prepared using the TaKaRa SMART-Seq v4 Ultra Low-Input kit

value: whole embryo

value: Chicago F Isogenic


title: E5

city: Seoul

first: June-young

last: Lee

department: Dept. of Biology

country: South Korea

institute: KyungHee University

data_processing:
The base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38(mm10) whole genome using Salmon
Salmon quantification file was imported to Deseq2 and visualized.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-separated file with gene quantification file

extract_protocol:
mRNA of Lung tissue was isolated using Trizol reagent and Purelink RNA mini kit. Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used and sequencing libraries preapred by TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E.
mRNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

value: Lung tissue

tag: infection

value: Mycobacterium infection

value: Arginine treated


title: ATAC-Seq - treated - neural progenitor cells - rep1


title: Air_Pollution_Decidua

value: Air pollution


title: ATAC-Seq - untreated - neural progenitor cells - rep3

value: ethanol vehicle


title: C5

value: Untreated


title: E3


title: ATAC-Seq Th17_24h_LNA1_replicate1_LANE1

value: In vitro differentiated Th17 cells

value: Nucleofected cells differentiated for 24 hour in Th17 media


title: ATAC-Seq Th17_24h_LNANT_replicate1_LANE2


title: ATAC-Seq - untreated - neural progenitor cells - rep1


title: Nanopore_S19 Parhyale embryo RNA-Seq


title: Nanopore_S13 Parhyale embryo RNA-Seq


title: ATAC-Seq - untreated - neural progenitor cells - rep2


title: C3


title: ATAC-Seq - treated - neural progenitor cells - rep2


title: DTX3: iB cells Tcrd-GDL d8 3 atac

status: Public on May 24 2022

city: Heidelberg

first: Elisa

last: Donato

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

country: Germany

institute: Deutsches Krebsforschungszentrum  (DKFZ) - German Cancer Research Center

description: ATAC-seq

data_processing:
Adapter trimming was performed using TrimGalore version 0.4.3
Reads alignment was performed using bowtie 2 version 2.3.2
peak calling was performed using macs2 version 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing list of called peaks

source_name: spleen

extract_protocol:
ATAC-seq: NUCLEI ISOLATION KIT NUCLEI EZ PREP from Sigma (NUC101-1KT)
ATAC seq: Libraries were prepared according to Illumina's instructions accompanying the kit: DNA tagmentation using TDE1 Tagment DNA Enzyme, TD Tagment DNA Buffer (Illumina cat#15027865, 15027866).

treatment_protocol: In vivo: mice were treated i.p. with two injections of 15 ng DTx per gram body weight separated by 48 hours. Mice were analyzed eight days after the first injection

value: Tcrd-GDL

value: immature B cells (B220+CD93+)

value: DTx, eight days


title: DTX2: iB cells Tcrd-GDL d8 2 atac

description: ATAC-seq


title: DTX1: iB cells Tcrd-GDL d8 1 atac

description: ATAC-seq


title: CTRL2: iB cells Tcrd-GDL ctl 2 atac

description: ATAC-seq

value: untreated


title: CTRL3: iB cells Tcrd-GDL ctl 3 atac

description: ATAC-seq


title: Nanopore_S21 Parhyale embryo RNA-Seq