title: T13_2

first: Yuxin

last: Duan

state: Chongqing

address: No.1, Youyi Road, Yuanjiagang, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

description: Transcriptomics of HCC after iRFA 10 minutes

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
At the same time, Q20, Q30 and GC content the clean data were calculated
All the downstream analyses were based on the clean data with high quality.
Assembly: NA
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.

source_name: periablated hepatocellular carcinoma tissues

extract_protocol:
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® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hepatocellular carcinoma cells

value: incomplete radiofrequency ablation


title: T12_2

status: Public on Sep 05 2022

type: SRA

city: Chongqing

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: Mo_PBS_3

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: The whole-body were sampled from pool of five 5-7-day-old female mosquitoes

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30, GC-content, and sequence duplication levels of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
For RNA-seq data, the adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the Aedes aegypti genome sequence (NCBI: GCF_002204515.2_AaegL5.0). Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
For RNA-seq clean data, the mapped reads were assembled with the Bowtie2 software (version 2.2.5).
For RNA-seq clean data, after detecting transcriptome library was eligible, The library preparations were sequenced on a platform of MGISEQ-2000. The FPKM（Fragments Per Kilobase of transcript per Million fragments mapped）value representing the expression level of transcripts was calculated.
For RNA-seq clean data, differential expression analysis of the control and treated groups was performed using the DESeq2 (version 1.6.3). DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.001 found by DESeq2 were assigned as differentially expressed.
Genome_build: Aedes aegypti genome sequence (NCBI:GCF_002204515.2_AaegL5.0).
Supplementary_files_format_and_content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data

molecule: polyA RNA

organism: Aedes aegypti

source_name: Whole body

growth_protocol: Mosquitoes were maintained under standard insectary conditions of 27 ± 1°C, 12:12 h photoperiods, and 80 ± 5% humidity.

extract_protocol:
Total RNA from the pool of five female mosquitoes in the control and spinetoram-treated group with and without DENV-2 infection was extracted by using the TRIzol reagent according to the manufacturer’s protocol (Invitrogen, California, USA).
To construct the library for the MGISEQ-2000, total RNA was used for library construction using the MGIEasy RNA Directional Library Prep Kit (MGI). Next, paired-end sequencing was performed using the MGISEQ-2000 sequencing instrument, according to the manufacturer’s instructions, yielding 150-bp paired-end reads.

treatment_protocol: The third-instar larvae (L3, N = 100 per treatment) were separated into four 500 mL plastic pots with 200 mL of water and turtle food for survival rate analysis. The larvae were exposed to different concentrations of spinetoram (0, 2, 10, 20 and 50 μg/L) for 36 h, and were then transferred to dechlorinated water after the treatments. Two to three-day-old surviving Ae. aegypti female mosquitoes were infected with DENV-2 via intrathoracic injection. Mosquitoes were anesthetized on ice and injected with 100 nL of DENV-2 stock or PBS using a Nanoject II injector (Drummond Scientific, Broomall, PA, USA).

tag: strain

value: 5-7-day-old female adult

tag: culture environment

value: Feed on 10% sucrose water

value: without Spinetoram exposure and with PBS injection

tag: replicate

tag: Sex

value: female

tag: tissue

value: whole body


title: P2ry14KO-Eos-4

status: Public on Sep 06 2022

city: Research Triangle Park

first: Donald

middle: Nelson

last: Cook

state: NC

address: 111 T.W. Alexander Drive

department: IIDL

country: USA

institute: NIEHS

data_processing:
Raw reads were filtered to retain only those with average base quality score >20.
Reads were aligned to mm10 via STAR v2.5 (parameters: --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical).
Read counts per gene were determined by Subread featureCounts v1.5.0-p1 (parameters: -s0).
Coverage tracks were generated by STAR v2.5 (parameters: --outWigStrand Unstranded --outWigNorm None), normalized by DESeq2 size factors, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: normalized depth tracks in bigWig format; RNAseq counts per gene in tab-delimited text format

organism: Mus musculus

source_name: P2ry14-null_lung eosinophils

extract_protocol:
RNA was isolated using TRizol Plus reagent, followed by DNase treatment and additional cleanup step using PureLink RNA Mini kit (Thermo Fisher Scientific) according to the manufacturer's instructions.
Libraries were constructed via Illumina TruSeq RNA sample prep kit.

treatment_protocol: Mice were sensitized twice, week apart, by oropharyngeal instillation of 50 µg OVA and 20 μg protease from Aspergillus oryzae. Seven days after the second sensitization, mice were challenged by exposing them to an aerosol of 1% OVA and lung eosinophils were purified using FACS sorting 16 h later.

value: male

value: FACS-purified lung eosinophils

tag: treatment condition

value: OVA/Aspergillus asthma model, 16 hrs after OVA challenge


title: Mo_PBS_2


title: Spin_PBS_3

value: with Spinetoram exposure and PBS injection


title: AR1, biol rep 1

city: Beijing

first: Baoli

last: Lin

address: No.7 Beinong Road, Shigezhuang Street

institute: College of Landscape Architecture, Beijing Agricultural College

description: AR is a healthy red leaf sample from a bud mutation branches of Acer pictum subsp. mono.(15-20 days ahead of color change) we found.

data_processing:
AP Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using AP genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using AP genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using AP genomic benchwork
Assembly: without reference genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Acer pictum subsp. mono

source_name: leaf cells

growth_protocol: Both wild-type branch leaves and mutant branch leaves of Acer pictum subsp. mono grow in the wild under natural conditions.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Two leaves grown in the wild in their natural state were collected and stored in an ultra-low temperature refrigerator at -80 degrees Celsius without any treatment.

value: leaf cells

value: Day 0


title: T9_2


title: Spin_PBS_2


title: T11_2


title: T5_2


title: T6_2


title: T8_2


title: T7_2


title: T13_1

description: Transcriptomics of HCC before iRFA

source_name: hepatocellular carcinoma tissues

value: no treatment


title: T3_2


title: Spin_DENV_2

value: with Spinetorma exposure and DENV-2  injection


title: Spin_DENV_1


title: Mo_PBS_1


title: Mo_DENV_3

value: without Spinetorma exposure and DENV-2  injection


title: T11_1

description: Transcriptomics of HCC before iRFA


title: Mo_DENV_1


title: T4_2


title: T9_1

description: Transcriptomics of HCC before iRFA


title: Mo_DENV_2


title: T8_1

description: Transcriptomics of HCC before iRFA


title: ZPR1-AID + DMSO 3h rep3

city: Cambridge

first: Vladimir

last: Denic

state: MA

address: 52 Oxford St

institute: Harvard University

data_processing:
Raw reads from Illumina HiSeq were checked for read quality using FastQC (v. 0.11.5) and aligned to the reference genome S288c (v. R64-3-1) using the RNA-seq aligner STAR (v.2.7.0)
Genewise counts obtained from STAR were passed to the Bioconductor package DESeq2 (v. 1.34.0) to identify differentially expressed genes after ZPR1 depletion relative to the DMSO vehicle control (Benjamini-Hochberg FDR < 0.05).
Assembly: S288c (v. R64-3-1)
Supplementary files format and content: csv file with raw read counts per gene for all samples

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase and snap frozen before submission to GENEWIZ for processing.

extract_protocol:
RNA samples were extracted by the NGS facility at GENEWIZ according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ZPR1 was depleted by treating cells with 5-Ph-IAA for either 0.5h, 1.5h or 3 h.

tag: genotype

value: 3h DMSO

tag: time


title: ZPR1-AID + DMSO 3h rep2


title: T7_1

description: Transcriptomics of HCC before iRFA

value: hepatocellular carcinoma cells


title: ZPR1-AID + DMSO 3h rep1


title: Spin_DENV_3


title: ZPR1-AID + IAA 3h rep3

value: 3h 5-Ph-IAA


title: T6_1

description: Transcriptomics of HCC before iRFA


title: D90-PF1

city: San Francisco

first: Deepak

middle: A

last: Lamba

state: CA

address: 35 Medical Center Way, Rm1024

institute: University of California, San Francisco

data_processing:
Following QC (error rates <0.03%), alignments were parsed using STAR (v2.5) program79 and mapped to Homo sapiens genome assembly GRCh37 (hg19).
Differential expressions were determined through DESeq2 R package (v1.14.1 ).81 Genes with an adjusted p-value <0.05 (Benjamini and Hochberg’s approach) found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
Assembly: GRCH37(hg19)
Supplementary files format and content: CSV file of readcounts from various conditions

source_name: CE-iPSC line

growth_protocol: iPSC-derived retinal organoids were generated using our previously described protocol (Chirco et al Stem Cell Reports 2021)

extract_protocol:
RNA was harvested using TriReagent and Chloroform-Ethanol extraction.
Library preparation and Illumina-based transcriptome sequencing was carried out at Novogene

treatment_protocol: On treatment day, organoids were treated with 10μM PF03084014 (PF4014) dissolved in media. After 3 days, fresh non-PF media was given every 2-3 days until collection day.

tag: cell line

value: CE-iPSC line

value: retinal organoids

value: WT

tag: Stage


title: D90-PF2


title: T5_1

description: Transcriptomics of HCC before iRFA


title: T4_1

description: Transcriptomics of HCC before iRFA


title: ZPR1-AID + IAA 3h rep2


title: D90-C2

value: Vehicle


title: T12_1

description: Transcriptomics of HCC before iRFA


title: D60-PF3


title: D90-C1


title: T3_1

description: Transcriptomics of HCC before iRFA


title: ZPR1-AID + IAA 1.5h rep2

value: 1.5h 5-Ph-IAA


title: ZPR1-AID + IAA 1.5h rep3


title: ZPR1-AID + IAA 3h rep1


title: D60-PF1


title: D60-C2


title: ATAC_CMVpos1_CMVpos3_CMVneg3_CMVneg4

city: Berlin

first: Timo

last: Rückert

address: Charitéplatz 1

department: Innate Immunity

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: Each of the BAM files belong to one experiment where the same pool of cells was split over four 10x Genomics lanes. They all contain the scATAC reads for different cells which were aggregated in the deposited fragment file.

library_source: genomic

data_processing:
Fastqs were demultiplexed usiing cellranger-ATAC mkfastq (v1.2.0) and bcl2fastq (v2.20.0.422)
Sequencing reads were aligned to a modified GRCh38 reference using CellRanger-ATAC count (v1.2.0). Data was merged and single-cells were called using the default parameters.
Nucleotide-barcode labelled antibodies were pseudo-aligned and counted using bustools-kite. Hashtagged cells were demultiplexed using HTODemux in Seurat.
Mitochondrial genotyping was performed with mgatk, results imported into R with ReadMGATK and merged per experiment.
SNPs and indels were removed from aligned bam files with bamboozle to anonymize data.
Assembly: GRCh38 (hardmasked according to mitoblacklist by Caleb Lareau)
Supplementary files format and content: Processed fragment files from 10x cellranger-ATAC count. Antibody-derived tag (ADT) counts and hashtag-based cell identities for cells passing QC thresholds. mgatk results exported as mito assay from Signac.

molecule: genomic DNA

source_name: primary NK cells

growth_protocol: NK cells were enriched from freshly drawn blood by CD3 CD14 CD19 depletion. The enriched fraction was stained with fluorochrome-conjugated antibodies and Fc receptors blocked using Human TruStain FcX for 15 min at 4 °C. Dead cells were excluded using Fixable Viability Dye eFluor780. In a second step, cells were stained with nucleotide-barcode labelled antibodies for 30 min at 4 °C. As described in the ASAP-Seq and mitochondrial scATACseq protocols, cells were fixed with 1 % para-formaldehyde for 10 min. Fixation was quenched by adding Glycin to 0.125 M final concentration, and cells were washed twice with PBS/BSA. NK cells were sorted on a FACS Aria II (BD Biosciences) as viable, single cells being CD3- CD14- CD19- CD7+, separating NKG2C+ and NKG2C- cells.

extract_protocol:
ASAP-seq/mtscATAC-seq = fixation: 1% FA, lysis: 0.1% NP40 wash: No tween wash
Custom 10x Genomics scATAC-seq (mtscATAC-seq/ASAP-seq)

treatment_protocol: untreated

value: Peripheral Blood

tag: donor id


title: D60-C1


title: D45-PF3


title: POP_Y6_miRNA

city: chengdu

first: Xia

last: Yu

address: No.1617 Ri Yue Street, Chengdu, Sichuan

institute: Chengdu women and Children's hospital

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

source_name: anterior vaginal wall

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: anterior vaginal wall

tag: disease state

value: Pelvic organ prolapse (POP)


title: D45-PF2


title: ZPR1-AID + IAA 1.5h rep1


title: ZPR1-AID + IAA 30min rep3

value: 30 min 5-Ph-IAA


title: D45-PF1


title: ZPR1-AID + IAA 30min rep2


title: D45-C3


title: D45-C2


title: POP_Y5_miRNA


title: D60-PF2


title: ZPR1-AID + IAA 30min rep1


title: D60-C3


title: D45-C1


title: ZPR1-AID untreated rep3

value: untreated


title: POP_Y2_miRNA


title: POP_Y3_miRNA


title: Patients in chronic pahse of CML C_1003

city: Wenzhou

first: Zhanguo

last: Chen

state: Zhejiang

address: 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325000, P.R. China

department: Department of Clinical Laboratory

institute: The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University

description: Patients in chronic pahse of CML

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b).
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1).
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b).
Supplementary files format and content: The AA group, CC group and NN group were compared with each other, and the list of circRNA up-regulation and down-regulation of differences was presented in Excel file.

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from  samples using TRIzol® (Invitrogen, USA) reagent and purifiled using  Ribo-ZeroTM rRNA Removal Kit (Epicenter, Madison, WI, USA)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocols.

value: Peripheral blood

value: Peripheral blood mononuclear cells


title: ZPR1-AID untreated rep2


title: Healthy control N_1001

description: Healthy control


title: Healthy control N_1003

description: Healthy control


title: ZPR1-AID untreated rep1


title: POP_Y1_miRNA


title: Healthy control N_1002

description: Healthy control


title: Patients in accelerate phase of CML A_1003

description: Patients in accelerate phase of CML


title: Patients in chronic pahse of CML C_1002

description: Patients in chronic pahse of CML


title: POP_D6_miRNA


title: Patients in accelerate phase of CML A_1002

description: Patients in accelerate phase of CML


title: Patients in accelerate phase of CML A_1001

description: Patients in accelerate phase of CML


title: CKD627_2_Tomato_Nega

city: Tokyo

first: Makoto

last: Nakanishi

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: Institute of Medical Science, University of Tokyo

description: Sample 7

data_processing:
The sequencing data were aligned to a mouse reference genome (mm10) using Rsubread (v2.4.3)
Raw counts were obtained from read alignments through refGene for gene counts, and then further transferred into CPM by edgeR (v3.32.1)
After filtering out low-expression genes with CPM lower than 10, differential expression was analyzed with the linear model using limma (v3.46.0)
For gene set enrichment analysis (GSEA), the order ranked gene list by log2 fold change was inputted into pre-ranked GSEA function in clusterProfiler (v3.18.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files
Supplementary files format and content: include CPM for each Sample

source_name: Kidney

extract_protocol:
The total RNA was extracted using a single cell RNA purification kit (51800, NORGEN) according to the manufacturer’s protocols.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (Cat No. 7530).

value: Kidney

value: Kidney cell

value: Proximal tubular epithelial cell

value: p16-tdTomato mice

value: CKD induction


title: CKD627_1_Tomato_Posi

description: Sample 6


title: CKD627_2_Tomato_Posi

description: Sample 8


title: POP_D5_miRNA


title: POP_D3_miRNA


title: POP_D4_miRNA


title: POP_Y4_miRNA


title: POP_D2_miRNA


title: CKD627_1_Tomato_Nega

description: Sample 5


title: CKD523_3_Tomato_Posi

description: Sample 4


title: CKD523_2_Tomato_Posi

description: Sample 2


title: Control_Y6_miRNA

source_name: uterosacral ligaments

value: uterosacral ligaments

value: Control


title: CKD523_3_Tomato_Nega

description: Sample 3


title: POP_D1_miRNA


title: Control_Y4_miRNA


title: Control_Y5_miRNA


title: Patients in chronic pahse of CML C_1001

description: Patients in chronic pahse of CML


title: WT_18-Mock-infected

city: Rochester

first: Aram

middle: F.

last: Hezel

state: NY

address: 300 Elmwood Avenue

department: Wilmot Cancer Institute

institute: University of Rochester Medical Center

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.1.
Quality filtering and adapter removal were performed using FastP version 0.20.0
Processed/cleaned reads were then mapped to the mus musculus reference genome using STAR 2.7.0f
Gene-level read quantification was derived using the subread 1.6.4 package (featureCounts)
Differential expression analysis was performed using DESeq2 1.22.1
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MEFs were maintained in DMEM 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). 1.0 ug of total RNA was used for the construction of sequencing libraries.
mRNA sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit with 200ng total RNA following the manufacturer’s specifications

treatment_protocol:
MEFs from passage 3 were infected with Adenovirus (Ad5-CMV-Cre or Ad5-CMV-eGFP) with 1 μg/mL polybrene overnight.
The infected cells at passage 5 and 80% confluency were harvested for RNA-seq and ATAC-seq analyses

value: mouse embryonic cells

value: WT

value: Mock-infected

value: passage 5


title: CKD523_2_Tomato_Nega

description: Sample 1


title: WT_17-Ad-CMV-GFP

value: Ad-CMV-GFP


title: D250_HT_6

city: Leipzig

first: Jana

last: Schor

state: Saxony

address: Permoserstr. 15

department: Molecular Systems Biology

institute: Helmholtz Centre for Environmental Research

data_processing:
For demultiplexing we used bcl2fastq (release 2.20), which is provided by Illumina.  Sequencing adapters were trimmed using the cutadapt (release 1.5) software, and subsequent quality control was performed using the fastqc program (release 0.11.2) and the fastx-toolkit (release 0.013). Reads were aligned to the human genome (UCSC Human Dec. 2013 GRCh38/hg38 Assembly) using the hisat2 mapping tool (release 2.1.0) and subsequently sorted by name and genomic location using samtools (release 1.1).
New transcripts were generated with the stringtie tool (release 1.3.3, reference annotation: Gencode v26), and sample wise assemblies were merged applying stringtie-merge. Subsequently, the new transcripts were annotated with respect to their relative genomic position to known genes using cuffcompare (2.2.1). Transcripts that entirely fall within a reference intron, are intergenic, and those that overlap an exon of a known gene on the opposite strand were kept. The number of reads that overlap either a new transcript or a known gene from the reference annotation were counted using the htseq-count program (0.6.1).
Genome_build: UCSC Human Dec. 2013 GRCh38/hg38 Assembly
Supplementary_files_format_and_content: Tab-delimited text files include rlog values for each Sample.

extract_protocol:
Organoids were lysed in 300µl TRIzol by mortar-pestle homogenization, RNA was isolated using miRNeasy Kit (Qiagen) and Maxtract High Density tubes (Qiagen), residual DNA was removed using Ambion TURBO DNA-free Kit (Thermo Fisher) and RNA cleaned up by ethanol-precipitation.
The RNA integrity for each sample was controlled with the RNA 6000 Nano Assay and the Agilent 2100 Bioanalyzer (Agilent Technologies). 100ng total RNA was used for rRNA depletion. Ribosomal RNAs were removed from total RNA. A strand-specific library using the Ribo-Zero Gold H/M/R Magnetic Kit (Illumina, San Diego, CA, USA). A strand-specific library was prepared using the ScripSeqv2 Kit (Illumina), was checked by Agilent 2100 Bioanalyzer system with a High Sensitivity DNA Kit (Agilent). Library concentration was determined by Qubit 2.0 instrument using the Quant-iT dsDNA High Sensitivity kit (Thermo Fisher Scientific).  size selected in a range of 200-600 bp using preparative agarose gel in combination with MinElute Gel Extraction Kit (Qiagen).

value: retina organoid

tag: age

value: Development day 250

value: HBEGF-TNF


title: Control_Y3_miRNA


title: WT_16-Ad-CMV-Cre

value: Ad-CMV-Cre


title: D250_HT_5


title: WT_19-Ad-CMV-Cre


title: Control_Y1_miRNA


title: Control_Y2_miRNA


title: D250_HT_4


title: D250_HT_3


title: D250_HT_2


title: WT_3-Ad-CMV-Cre


title: WT_2-Ad-CMV-Cre


title: D250_HT_1


title: Control_D4_miRNA


title: D250_Ctrl_6


title: Control_D5_miRNA


title: D250_Ctrl_5


title: D250_Ctrl_4


title: Control_D3_miRNA


title: D250_Ctrl_3


title: KA_14-Ad-CMV-GFP

value: KA


title: D250_Ctrl_2


title: D200_HT_6

value: Development day 200


title: Control_D2_miRNA


title: Control_D6_miRNA


title: D200_HT_5


title: Control_D1_miRNA


title: D200_HT_4


title: KA_29-Ad-CMV-Cre


title: D200_HT_2


title: KA_30-Ad-CMV-Cre


title: D200_HT_3


title: POP_Y5

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: anterior vaginal wall

value: POP


title: WT_1-Ad-CMV-Cre


title: KA_28-Ad-CMV-Cre


title: POP_Y3


title: POP_Y4


title: D200_Ctrl_4


title: D200_Ctrl_5


title: D200_HT_1


title: D200_Ctrl_6


title: D200_Ctrl_3


title: D250_Ctrl_1


title: POP_Y2


title: D200_Ctrl_2


title: KA_12-Ad-CMV-Cre


title: KA_15-Mock-infected


title: KA_13-Ad-CMV-Cre


title: D200_Ctrl_1


title: D150_HT_6

value: Development day 150


title: D150_HT_5


title: K_23-Mock-infected

value: K


title: K_6-Mock-infected


title: D150_HT_4


title: POP_Y6


title: K_22-Ad-CMV-GFP


title: K_5-Ad-CMV-GFP


title: D150_HT_1


title: D150_Ctrl_6


title: POP_D5


title: K_21-Ad-CMV-Cre


title: POP_D4


title: D150_Ctrl_5


title: POP_D3


title: K_20-Ad-CMV-Cre


title: D150_Ctrl_3


title: D150_Ctrl_2


title: POP_D2


title: D150_Ctrl_1


title: POP_Y1


title: POP_D6


title: K_8-Ad-CMV-Cre


title: POP_D1


title: DMSO-treated_cmlc2/GFP-HRAS_3

city: Fribourg

first: Anna

last: Jazwinska

address: Chemin du Musée 10

country: Switzerland

institute: University of Fribourg

data_processing:
The reads were mapped to the reference genome Danio_rerio.GRCz11.94 using HiSat2 (v. 2.1.0). PCR duplicates were removed using UMI-Tools (v1.1.1). FeatureCounts (v. 1.6.0) was used to count the number of reads overlapping with each gene as specified in the genome annotation (Danio_rerio.GRCz11.94).
Genome_build: Ensembl GRCz11, build 94
Supplementary_files_format_and_content: txt file with raw counts of sequencing reads

organism: Danio rerio

source_name: Adult DMSO-treated cmlc2/GFP-HRAS heart

extract_protocol:
Total RNA was extracted using QIAzol Lysis Reagent (Qiagen) and purified using the RNeasy Micro Kit (Qiagen) with a DNase digestion.
Sequencing libraries were produced using a CORALL mRNA-Seq Library Prep Kit  in combination with UDI 12 nt Set A1

value: uninjured cardiac ventricle

value: 4 pulses 2.5 uM 4-OHT (overnight) + 0.05% DMSO over 16 days


title: Control_Y6

value: Control


title: Rap-treated_cmlc2/GFP-HRASe_3

source_name: Adult Rapamycin-treated cmlc2/GFP-HRAS heart

value: 4 pulses 2.5 uM 4-OHT (overnight) + 0.5 uM Rapamycin over 16 days


title: D150_HT_3


title: D150_Ctrl_4


title: K_4-Ad-CMV-Cre

value: mouse embryonic cells


title: Rap-treated_cmlc2/GFP-HRAS_2


title: DCKO 2

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

data_processing:
Transcripts were aligned to the indexed reference for mm10 (GRCm38.94) with default settings using TopHat2 v2.1.1 (Kim et al. 2013).
Reads were filtered using bamtools using the following settings: -isMapped true -isDuplicate false -mapQuality “>10” (Barnett et al. 2011).
Transcript reads were counted post-alignment using StringTie and the prepPE.py script for the ENSEMBL GRCm38.94 build (Pertea et al. 2015).
Low level genes were removed within each condition using median log2-transformed counts per gene per million mapped reads (cpm) of 1 and a union generated from those lists.
Differential expression testing was performed using edgeR v3.16.5 (Robinson and Smyth 2007; Robinson and Smyth 2008; Robinson et al. 2010; McCarthy et al. 2012; Zhou et al. 2014) and limma v3.30.13 (Ritchie et al. 2015) packages under a general linear model (GLM) framework in R v3.3.2.
Genome_build: mm10 (GRCm38.94)
Supplementary_files_format_and_content: DE_Results, TPM, counts

source_name: cranial neural tube_DCKO

growth_protocol: breeding and maintaining protocol: Mice were raised and maintained at the Baylor College of Medicine as per IACUC (Institutional Animal Care and Use Committee)  guidelines. Female mice were mated for timed dissection at embryonic day 10.5.

extract_protocol:
Cranial neural tubes were microdissected from E10.5 timed matings. RNA was isolated using the RNeasy Plus Mini Kit in accordance to the manufacturer’s instructions.
Barcoded Libraries were prepared using the Kapa stranded RNA-seq kit (KR0960) according to the manufacturer's instructions. Libraries were quantitated using the Agilent fragment analyser and pooled in equimolar amounts. The pooled libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

tag: genotype/variation

value: Lats1/2 double conditional knock out (Lats1 flox/flox; Lats2 flox/flox; E2f1 Tg(Wnt1-cre)2Sor/+, DCKO)

tag: developmental stage

value: cranial neural tube


title: D150_HT_2

value: retina organoid


title: Rap-treated_cmlc2/GFP-HRAS_1


title: DMSO-treated_cmlc2/GFP-HRAS_2


title: K_7-Ad-CMV-Cre

tag: cell type

value: passage 5


title: Control_Y5

tag: treatment


title: DCKO 1


title: Control_Y4


title: A_26-Mock-infected

value: A

value: Mock-infected


title: Rap-treated_cmlc2/RFP_3

source_name: Adult Rapamycin-treated cmlc2/RFP heart

tag: strain


title: A_25-Ad-CMV-GFP

value: Ad-CMV-GFP


title: Control_Y3


title: A_27-Ad-CMV-Cre

value: Ad-CMV-Cre


title: Control_Y2

value: anterior vaginal wall


title: Control_Y1


title: Rap-treated_cmlc2/RFP_2


title: A_24-Ad-CMV-Cre


title: A_11-Ad-CMV-Cre


title: Rap-treated_cmlc2/RFP_1


title: A_9-Ad-CMV-Cre


title: DMSO-treated_cmlc2/RFP_2

source_name: Adult DMSO-treated cmlc2/RFP heart


title: 7dpci_3

source_name: Adult 7 dpci heart

value: 7 dpci cardiac ventricle

value: no treatment


title: DMSO-treated_cmlc2/GFP-HRAS_1


title: DMSO-treated_cmlc2/RFP_1


title: 7dpci_2


title: Control_D3

value: uterosacral ligaments


title: Control_D1


title: 7dpci_1


title: Control_D5


title: Control 2

source_name: cranial neural tube_control

value: control (no E2f1 Tg(Wnt1-cre)2Sor/+)


title: Control_D2


title: Control 1


title: HEK293T, H3K9me3, WT

first: Shiqiang

last: Zhang

state: Beijing

address: Peking University

institute: Peking University

data_processing:
uniquely mapped reads were aligned using bowtie2 to GRCh38, and peaks were identified with MACS2 using the default parameters.
Assembly: GRCh38
Supplementary files format and content: peak file

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin, maintained at 37°C with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at RT, followed by quenching with 125mM glycine . Chromatin was fragmented by sonication to ensure the bulk is 200-500 bp.
ChIP-seq libraries were prepared by Berry Genomics (Beijing, China).

value: Human embryonic kidney

value: WT

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: DMSO-treated_cmlc2/RFP_3

value: uninjured cardiac ventricle

value: 4 pulses 2.5 uM 4-OHT (overnight) + 0.05% DMSO over 16 days


title: Uninjured_2

source_name: Adult uninjured heart


title: HEK293T, H3K9me3, WT_Input

value: No antibody


title: TKO_Dnmt3a2_E752K_RRBS_Rep1

first: Brian

last: Liau

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

description: RRBS sample

data_processing:
Sequencing reads were trimmed using Trim Galore (v0.6.7) (parameters: --illumina --rrbs --paired --length 21). Reads 1 and 2 were swapped for trimming because the xGen Methyl UDI-UMI adapters (Integrated DNA Technologies) used for library construction flip insert strandedness.
Trimmed reads were aligned to the prepared mm10 genome (UCSC) using Bismark (v0.23.1) (default bowtie2 alignment).
Samtools (v1.10) was used to sort and index bam files.
MethylDackel (v0.6.1) was used to extract CpG methylation, retaining only CpGs with at least 5x coverage (parameters: -d 5 --mergeContext --keepDupes).
Awk was used to calculate fractional methylation and remove extraneous columns and Bedtools2 intersect (v2.26.0) was used to filter for only common CpGs (at least 5x coverage across all samples). The resulting bedGraph files were converted to bigWig format using bedGraphToBigWig (UCSC).
bigWig files of fractional methylation (0.0–1.0) at each CpG site with at least 5x coverage across all samples, generated from bedGraph files of the format <chr> <start> <end> <fraction methylated>.
Assembly: mm10

source_name: KH2 mESC

growth_protocol: ESCs were cultured in a humidified 5% CO2 incubator at 37 °C. Media consisted of KnockOut DMEM (Gibco) supplemented with 15% fetal bovine serum (Gibco), 2 mM GlutaMAX (Gibco), 1x MEM non-essential amino acids (Gibco), 1000 U/mL ESGRO leukemia inhibitory factor (Millipore), 55 µM 2-mercaptoethanol (Gibco), and 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco). ESCs were cultured on a layer of mitomycin C-inactivated mouse embryonic fibroblast feeders (Lonza) plated on 0.2% gelatin-coated vessels. ESC medium was changed daily, and feeders were depleted prior to sample harvest.

extract_protocol:
Genomic DNA was purified from MEF-depleted ESCs using the QIAamp DNA Blood Mini kit.
80 ng of each sample was subjected to overnight digestion with 150 units of MspI (New England Biolabs) at 37 °C. The digest was purified by extraction with 25:24:1 phenol:chloroform:isoamyl alcohol (Thermo Fisher Scientific) and ethanol precipitation, followed by end-repair (End-It DNA End-Repair kit, Lucigen), A-tailing (Klenow fragment, New England Biolabs), and ligation to barcoded adapters (xGen Methyl UDI-UMI Adapters, Integrated DNA Technologies, 3 µL of 1.5 µM per ligation) using concentrated T4 ligase (New England Biolabs) at 16 °C overnight. Adapter-ligated DNA was purified by 1× SPRI, size-selected by gel extraction, bisulfite-converted (EZ DNA Methylation kit, Zymo; bisulfite conversion using the following thermocycler program: 55 cycles of 95 ˚C for 30 s, 50 ˚C for 15 min), and amplified using EpiMark hot start Taq DNA polymerase (New England Biolabs) and 17 cycles of PCR (KAPA library amplification primers).

treatment_protocol: Transfection with piggybac vector for ectopic Dnmt3a2 E752K expression and FACS sorting

value: mESC

value: Dnmt1/Dnmt3a/Dnmt3b triple-knockout + ectopic Dnmt3a2 E752K


title: Control_D4

value: Control


title: TKO_Dnmt3a2_E338K_RRBS_Rep2

description: RRBS sample

treatment_protocol: Transfection with piggybac vector for ectopic Dnmt3a2 E338K expression and FACS sorting

value: Dnmt1/Dnmt3a/Dnmt3b triple-knockout + ectopic Dnmt3a2 E338K


title: A_10-Ad-CMV-Cre

value: mouse embryonic cells

value: A

value: passage 5


title: Uninjured_1


title: TKO_Dnmt3a2_W326R_RRBS_Rep2

description: RRBS sample

treatment_protocol: Transfection with piggybac vector for ectopic Dnmt3a2 W326R expression and FACS sorting

value: Dnmt1/Dnmt3a/Dnmt3b triple-knockout + ectopic Dnmt3a2 W326R


title: HEK293T, H3K9me3, EV_Input

value: EV


title: HEK293T, H3K9me3, EV


title: TKO_Dnmt3a2_E338K_RRBS_Rep1

description: RRBS sample


title: short-term effects of MSCs administration, MICE14

city: Bialystok

first: Andrzej

last: Eljaszewicz

state: Podlaskie

address: Jana Kilinskiego 1

department: Centre for Regenerative Medicine

country: Poland

institute: Medical University of Bialystok

data_processing:
Sequencing quality was evaluated by FastQC version 0.11.5.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence (bbduk; minlength=30, qtrim=rl, trimq=15)
Reads were then mapped to the reference genome of Mus musculus (GRCm38) using STAR aligner version 2.5.3a with parameters --quantMode GeneCounts --runThreadN 4
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung

growth_protocol: Mesenchymal stem cells were isolated from adipose tissue obtained from the bariatric patients (n=5). Harvested adipose tissue was incubated with collagenase IV (Gibco) in standard cell culture conditions (37°C, 5% CO2) for 45 minutes followed by inactivation in 10% fetal bovine serum (FBS, PAN Biotech) in Dulbecco's Modified Eagle’s Medium (DMEM, PAN Biotech). Next adipose tissue was filtered through strainers (100µM pore size) and centrifuged 400g for 5 minutes. Cells were adhered to 175cm2 flasks and cultured in dedicated media Mesenchymal Stem Cells Basal Medium (ATCC) supplemented with Mesenchymal Stem Cell Growth Kit for Adipose, Umbilical, and Bone Marrow- derived MSCs (ATCC) up to 3rd passage and cryopreserved. Prior to MSCs administration to mice, cells were defrosted and cultured to approximately 90% confluency. A total of 500 000 of MSCs were resuspended in 20 microliters of 1X phosphate buffered saline and administrated to mice intranasally.

extract_protocol:
Lung lobes were stored in RNA later solution (Invitrogen) for 48 hours to stabilize RNA. Next, tissues were disrupted using TissueRuptor II (Qiagen) in RNeasy Lysis Buffer (Qiagen). Total RNA was isolated by using the RNeasy Mini Kit according to the manufacturer's protocol (Qiagen). Only the RNA with proper RNA integrity, namely RIN>8, was subjected to cDNA library establishment according to TruSeq Stranded Total RNA protocol (Illumina), followed by the quality confirmation (Agilent Technologies 2100 Bioanalyzer). The expected length of the final product was assumed at 260 base pairs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were intranasally administrated with 500 000 adipose tissue-derived mesenchymal stem cells in short- (2 days) and long-term (9 days) model. Control mice group was administrated with saline.

value: lung

value: female

value: wild type

value: MSC treated lungs after 2-days


title: TKO_Dnmt3a2_E752K_RRBS_Rep2

description: RRBS sample


title: TKO_Dnmt3a2_W326R_RRBS_Rep1

description: RRBS sample


title: Uninjured_3

value: no treatment


title: short-term effects of MSCs administration, MICE13


title: Control_D6

value: uterosacral ligaments


title: TKO_Dnmt3a2_R297W_RRBS_Rep2

description: RRBS sample

treatment_protocol: Transfection with piggybac vector for ectopic Dnmt3a2 R297W expression and FACS sorting

value: Dnmt1/Dnmt3a/Dnmt3b triple-knockout + ectopic Dnmt3a2 R297W


title: TKO_Dnmt3a2_WT_RRBS_Rep2

description: RRBS sample

treatment_protocol: Transfection with piggybac vector for ectopic Dnmt3a2 WT expression and FACS sorting

value: Dnmt1/Dnmt3a/Dnmt3b triple-knockout + ectopic Dnmt3a2 WT


title: HEK293T, MeDIP, K non-rep KO_Input

data_processing:
uniquely mapped reads were aligned using bowtie2 to GRCh38, and peaks were identified with MACS2 using the default parameters. The mean profiles of MeDIP peaks were generated by deepTools by unique sequence mapping using the default parameters.
Supplementary files format and content: peak file

extract_protocol:
Genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen). For each MeDIP experiment, 2 µg of DNA was fragmented into ~100-500 bp by sonication.
DNA fragments were subjected to end repair and adapter ligation using End Repair/dA-Tailing Module (NEB, E7442) and Ligation Module (NEB, E7445), respectively. Immunoprecipitation was performed with 2 µg of anti-5mC (Abcam, ab214727) in IP buffer (100 mM sodium phosphate, pH 7.0, 1.4 M NaCl and 0.5% Triton X-100). After overnight incubation at 4°C, 20 µl pre-washed protein A/G magnetic beads (Thermo Scientific) was added to the IP buffer, followed by an additional incubation at 4°C for 2 h. Beads were washed with IP buffer, and DNA was purified with phenol:chlorophorm:isoamyl alcohol after proteinase K digestion. The isolated DNA was amplified by PCR and size selected for deep sequencing

value: Human embryonic kidney

tag: medip antibody

value: No antibody


title: short-term effects of MSCs administration, MICE11

tag: Sex


title: HEK293T, MeDIP, K rep KO_Input


title: HEK293T, MeDIP, K rep KO


title: short-term effects of MSCs administration, MICE12

tag: tissue


title: HEK293T, MeDIP, K non-rep KO


title: long-term effects of MSCs administration, MICE10

value: MSC treated lungs after 9-days


title: TKO_Dnmt3a2_R297W_RRBS_Rep1

description: RRBS sample

value: mESC


title: HEK293T, H3K9me3, KD

value: KD

value: H3K9me3 (Abcam, ab8898)


title: TKO_Dnmt3a2_WT_RRBS_Rep1

description: RRBS sample


title: HEK293T, MeDIP, WT_Input


title: long-term effects of MSCs administration, MICE9


title: TKO_Parent_ChIP_Input

description: ChIP-seq input

data_processing:
Sequencing reads were aligned to the mm10 genome (UCSC) using bwa-backtrack (v0.7.17-r1188).
Samtools (v1.10) was used to convert sam files to bam files, which were then coordinate sorted and deduplicated using Picard (v2.26.9) SortSam and MarkDuplicate tools.
DeepTools (v3.5.1) bamCompare was used to create bigWig files for each histone modification ChIP normalized to input, using 200 bp genomic bins and 1 kb smoothing (parameters: --extendReads --operation log2 --skipZeroOverZero -bs 200 --smoothLength 1000 --scaleFactorsMethod SES).
bigWig files of normalized ChIP signal (log2 fold-change over input) averaged over 200 bp bins with 1 kb smoothing.
Assembly: mm10

extract_protocol:
MEF-depleted TKO ESCs were crosslinked with 1% formaldehyde (Sigma) for 10 min at room temperature with rotation and then quenched with 125 mM glycine. Cells were pelleted, washed twice with cold PBS, snap frozen on dry ice, and stored at −80 °C until use. To perform ChIP, cells were first resuspended in ChIP lysis buffer (50 mM Tris-HCl, pH 7.5, 1 mM EDTA, 1% sodium dodecyl sulfate (SDS), 0.25% sodium deoxycholate (NaDOC), 1× Halt protease inhibitor) and incubated on ice for 10 min. Then, ChIP dilution buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.01% SDS, 0.25% Triton X-100) was added and the lysate was sonicated using a Branson sonifier (0.7 s on, 1.3 s off, 5 min total on, 50% amplitude), followed by centrifugation to clarify lysates. The supernatant was further diluted with ChIP dilution buffer and a sample was reserved for ChIP input. The diluted lysate was aliquoted and incubated with the appropriate antibodies overnight at 4 °C with rotation. Protein G dynabeads were then added and the samples were incubated for 2.5 h at 4 °C with rotation. The beads were isolated and washed twice with ChIP wash buffer A (10 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% NaDOC, 1% Triton X-100), once with ChIP wash buffer B (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NaDOC, 0.5% Triton X-100), and once with ChIP wash buffer C (10 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM EDTA). DNA was eluted by incubation (65 °C, 1 h, 1000 rpm shaking) with ChIP elution buffer (10 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.1% SDS). Each sample was then treated with RNase and Proteinase K and purified by 2× SPRI.
2.5 ng each sample was subjected to end-repair (End-It DNA End-Repair kit, Lucigen), A-tailing (Klenow fragment, New England Biolabs), ligation to barcoded adapters (KAPA), and PCR library amplification (KAPA library amplification primers; NEB Ultra 2× master mix), followed by double-sided SPRI size selection.

value: Dnmt1/Dnmt3a/Dnmt3b triple-knockout

value: none (input)


title: long-term effects of MSCs administration, MICE8


title: HEK293T, MeDIP, WT


title: TKO_Parent_H3K36me2_ChIP

description: ChIP-seq sample

value: anti-H3K36me2 (Cell Signaling Technology, Cat#2901; RRID:AB_1030983; Lot#5)


title: short-term effects of MSCs administration, MICE15

value: lung


title: HEK293T, MeDIP, KD_Input


title: long-term effects of MSCs administration, MICE7

value: female


title: TKO_Parent_H3K27me3_ChIP

description: ChIP-seq sample

value: anti-H3K27me3 (Cell Signaling Technology, Cat#9733; RRID:AB_2616029; Lot#19)


title: long-term effects of MSCs administration, MICE6

value: wild type


title: HEK293T, MeDIP, KD


title: HEK293T, MeDIP, EV_Input


title: TKO_Parent_H3K4me3_ChIP

description: ChIP-seq sample


title: vehicle - NaCl, MICE5

value: untreated lungs


title: wtn1s

city: St Louis

first: Mary

middle: C

last: Dinauer

state: Missouri

address: 660 South Euclid Ave

department: Pathology & Immunology

institute: Washington University In St Louis

description: WT lung naïve mature neutrophils

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mouse Ensemble R76
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: mouse lung neutrophils

extract_protocol:
Total RNA isolation was performed using RNeasy Plus Micro Kit (Qiagen) according to the manufacture’s protocol.
RNA-seq libraries were prepared using the Clontech SMARTer Kit

treatment_protocol: Cells were sorted into RPMI1640 + 20% heat-inactivated FBS.

value: 12 weeks

tag: gender

value: Male

value: WT

tag: mouse strain

tag: mouse treatment

value: No treatment

tag: group

value: CD101pos Neutrophils


title: vehicle - NaCl, MICE3

tag: genotype


title: vehicle - NaCl, MICE4


title: wtn3s

description: WT lung naïve mature neutrophils


title: vehicle - NaCl, MICE2


title: cn1s

description: CGD lung naïve mature neutrophils

value: CGD/CYBB KO


title: HEK293T, Even

data_processing:
Uniquely mapped reads were aligned using bowtie2 to GRCh38, and peaks were identified with MACS2 using the default parameters. For ChIRP peaks, only those simultaneously obtained by both odd probes and even probes were considered as true signals.
Assembly: GRCh38
Supplementary files format and content: peak file
Library strategy: ChIRP-Seq

extract_protocol:
Cells were crosslinked with 3% formaldehyde for 30 min at room temperature, then quenched with glycine. Chromatin was fragmented by sonication to ensure the bulk is below 500 bp.
ChIRP-seq libraries were prepared by Berry Genomics (Beijing, China).

tag: cell line

value: Human embryonic kidney

tag: probes

value: Even


title: cn2s

description: CGD lung naïve mature neutrophils

tag: age


title: HEK293T, Odd

value: Odd


title: HEK293T, Input

value: No probes


title: cn3s

description: CGD lung naïve mature neutrophils


title: wt241b

description: WT lung mature neutrophils

value: 13 weeks

value: Female

value: 24h zymosan challenge in vivo


title: wt241a

description: WT lung immature neutrophils

value: CD101neg Neutrophils


title: stage E18 embryo 1 section 1 sector 3

first: Cui

last: Guizhong

address: 188 KaiYuan Road, Huangpu District

department: Center of Cell Lineage and Atlas

institute: Guangzhou Laboratory

data_processing:
Sequencing quality of raw sequencing data was evaluated by fastp
The genome sequence Macaca_fascicularis_5.0 for Crab-eating macaque (Macaca fascicularis)) were obtained from the Ensemble (https://asia.ensembl.org/index.html). Reads were mapped to the Macaca_fascicularis_5.0 genome assemblies by HISAT2 using default settings.
All mapped reads were processed by StringTie to quantify gene expression levels (measured by TPM , Transcripts Per Kilobase per Million mapped reads) using default parameters.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each samples

organism: Macaca fascicularis

source_name: Crab-eating macaque embryonic cells

growth_protocol: Embryos of gastrulating  Crab-eating macaque embryos  were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using Vayzme TD503 DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

value: embryo


title: stage E18 embryo 1 section 2 sector 2


title: IHF_Epi_2

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

department: Medicine

institute: The University of Chicago

data_processing:
RNA-seq reads were pseudoaligned using Kallisto v.0.44.0
The Kallisto index was made with default parameters and the GENCODE (Release 39 (GRCh38.p13) and was run in quant mode with default parameters
Assembly: hg38
Supplementary files format and content: tsv

source_name: Aorta

growth_protocol: primary human aortic endothelial cells (HAECs, passage 5 to 7) were grown in EGM-2 supplemented with SingleQuots from Lonza

extract_protocol:
Total RNA was isolated from HAECs using, GenElute™ Mammalian Total RNA Miniprep Kit
Oligo-dT mRNA directional

treatment_protocol: HAECs were exposed to alternating cycles of 5% O2 for 2 minutes followed by 20% O2 for 5 minutes on a cyclic perfusion  system with a flow rate of 5 ml/min, in the presence of absence of 10microMolar Epinephrine.

value: Aorta

value: Primary HAEC

value: Endothelial

value: wt

value: Intermittent hypoxia + Epinephrine


title: IHF_Epi_1


title: stage E18 embryo 1 section 1 sector 2


title: IHF_Epi_3


title: stage E18 embryo 1 section 2 sector 1


title: wt242a

description: WT lung immature neutrophils

value: WT


title: HEK293T, MeDIP, EV


title: IHF_3

value: Intermittent hypoxia


title: wt242b

description: WT lung mature neutrophils

value: CD101pos Neutrophils


title: IHF_2


title: stage E18 embryo 1 section 3 sector 1


title: IHF_1


title: stage E18 embryo 1 section 2 sector 3


title: wtn2s

description: WT lung naïve mature neutrophils

value: 12 weeks

value: Male

value: No treatment


title: vehicle - NaCl, MICE1

value: lung

value: female

value: wild type

value: untreated lungs


title: wt243a

description: WT lung immature neutrophils

value: 13 weeks

value: Female

value: 24h zymosan challenge in vivo

value: CD101neg Neutrophils


title: wt243b

description: WT lung mature neutrophils


title: NormF_Epi_2

value: Aorta

value: Primary HAEC

value: Endothelial

value: Normoxia + Epinephrine


title: c241a

description: CGD lung immature neutrophils

value: CGD/CYBB KO


title: NormF_Epi_3

value: wt


title: stage E18 embryo 1 section 3 sector 2

value: embryo


title: stage E18 embryo 1 section 3 sector 3


title: stage E18 embryo 1 section 3 sector 4


title: c241b

description: CGD lung mature nuetrophils

value: CD101pos Neutrophils


title: NormF_2

value: Normoxia


title: c242b

description: CGD lung mature nuetrophils


title: c243a

description: CGD lung immature neutrophils


title: stage E18 embryo 1 section 4 sector 1


title: stage E18 embryo 1 section 3 sector 5


title: stage E18 embryo 1 section 4 sector 3


title: NormF_1


title: NormF_Epi_1


title: stage E18 embryo 1 section 4 sector 2


title: stage E18 embryo 2 section 2 sector 4


title: stage E18 embryo 1 section 4 sector 4


title: stage E18 embryo 1 section 1 sector 1


title: Orthotopic_Tumor_TMPC_rep3

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

data_processing:
Bulk RNA sequenced reads were mapped to mm10 whole genome using STAR (v 2.6.0)
Counts of bulk RNA-seq were normalized by DESeq2
mm10
csv files with gene counts, normalized expression values, and statistical significance values

growth_protocol: Two months after orthotopic (TMP, TMPC) and subcutaneous (TM, TMP, and TMPC) transplantation, the mice were sacrificed to obtain their tumor tissue, and about 1cm3 tissue was taken for database construction.

extract_protocol:
RNA was extracted with standard workflow
RNA libraries were prepared using standard Illumina protocols. Transcriptome sequencing was performed by an Illumina NovaSeq 6000 sequencing platform with 150 bp paired-end sequencing.
Bulk RNA-seq

tag: library strategy

value: RNA-seq

tag: replicates


title: scRNAseq_Subcutaneous_Tumor

data_processing:
Seurat V3 workflow
mm10
rds and tar.gz files with gene counts for scRNA-seq

growth_protocol: As for single-cell RNA sequencing sample collections, orthotopic and subcutaneous tumor tissues were removed from recipient mice and cut up with sterile scissors.

extract_protocol:
Then tissues were dissociated into 15 mL conical tubes by pipetting and resuspension in TrypLETM (Gibco, #12604-028) for 1 hour at 37 ºC. During this period, the tip of the gun was used to blow it every 5 minutes until all were single cells under the microscope and centrifuged at 600 g for 10 minutes. Cells were resuspended with 4% BSA solution on ice.
Single-cell RNA library construction follwed by V3 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform
10X single-cell RNA-Seq

value: scRNA-seq


title: Orthotopic_Tumor_TMPC_rep2


title: stage E18 embryo 2 section 2 sector 3

city: Guangzhou

tag: developmental stage


title: scRNAseq_Orthotopic_Tumor


title: stage E18 embryo 2 section 2 sector 2


title: Orthotopic_Tumor_TMPC_rep1


title: stage E18 embryo 2 section 2 sector 1


title: Subcutaneous_Tumor_TMPC_rep3

description: 1_Subcutaneous_TM_TMP_TMPC_all_results.csv


title: stage E18 embryo 2 section 1 sector 5


title: stage E18 embryo 2 section 1 sector 4


title: stage E18 embryo 2 section 1 sector 3


title: Subcutaneous_Tumor_TMPC_rep1


title: NormF_3

tag: cell type

tag: treatment


title: c242a

description: CGD lung immature neutrophils


title: Subcutaneous_Tumor_TMP_rep3


title: Subcutaneous_Tumor_TMP_rep1


title: c243b

description: CGD lung mature nuetrophils


title: Subcutaneous_Tumor_TM_rep3


title: Subcutaneous_Tumor_TMP_rep2


title: stage E18 embryo 2 section 6 sector 8


title: Subcutaneous_Tumor_TM_rep2


title: stage E18 embryo 2 section 6 sector 6


title: stage E18 embryo 2 section 6 sector 7


title: stage E18 embryo 2 section 6 sector 5


title: Subcutaneous_Tumor_TM_rep1


title: stage E18 embryo 2 section 6 sector 4


title: stage E18 embryo 2 section 6 sector 3


title: stage E18 embryo 2 section 6 sector 2


title: Blood, BCG 2

city: Silver Spring

first: Sherry

last: Kurtz

address: 10903 New Hampshire Ave, Bldg 52/72 Rm 5328

institute: US Food and Drug Administration

data_processing:
analyses were performed using the CLC Workbench software package version 20.0.4 (Qiagen)
Reads were aligned to the Mus musculus genome Ensembl GRC.m38 (release 86) with default settings
Aligned reads were analyzed to determine DEGs, testing for differential expression due to vaccination using the “Differential Expression for RNASeq 2.4” function by comparing the two groups (naïve and BCG-vaccinated) based on a log2 fold change
Assembly: Ensembl GRC.m38 (release 86)
Supplementary files format and content: FPKMs

source_name: whole blood

extract_protocol:
Blood mRNA was isolated using the Mouse Blood Ribopure RNA kit (Invitrogen).  Samples were treated with DNAse and Globinclear to remove genomic DNA and globin transcripts.  Quality of mRNA was asssessed by Ribolyzer
Amplification and labeling of RNA samples were performed by the CBER/FDA Sequencing Core Facility using Illumina TotalPrep RNA Amplification (Applied Biosystems) and using an input of 1 mg of total RNA per sample.

treatment_protocol: Groups of 5 C57BL/6 mice were vaccinated with BCG, or sham-vaccinated with PBS.  14 days after vaccination, whole blood was collected in RNALater, and total mRNA was isolated.  RNA was pooled among mice within a group.  Triplicate experiments were performed. and those samples subjected to RNASeq analyses

tag: strain

value: whole blood

value: BCG-vaccination


title: Blood, BCG 1


title: Blood, Naïve 3

value: sham-PBS vaccination


title: stage E18 embryo 2 section 1 sector 2


title: Blood, Naïve 2


title: Subcutaneous_Tumor_TMPC_rep2


title: Blood, Naïve 1


title: MMNK1-shARID1A-set3

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.1.
Quality filtering and adapter removal were performed using FastP version 0.20.0
cleaned reads were then mapped to the mus musculus reference genome using STAR 2.7.0f
Gene-level read quantification was derived using the subread 1.6.4 package (featureCounts)
Differential expression analysis was performed using DESeq2 1.22.1
assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MMNK1 were maintained in DMEM 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). 1.0 ug of total RNA was used for the construction of sequencing libraries.
mRNA sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit with 200ng total RNA following the manufacturer’s specifications

treatment_protocol:
MMNK1 were infected with sh-Scramble or sh-Arid1a expression lentivisues followed by 48 hours recovery and  antibiotic selection
The infected cells at passage 5 and 80% confluency were harvested for RNA-seq analyses

value: immortalized human cholangiocyte cell line

tag: time


title: stage E18 embryo 2 section 5 sector 7


title: stage E18 embryo 2 section 5 sector 6


title: ATAC_CMVpos2_CMVpos4

data_processing:
Fastqs were demultiplexed usiing cellranger-ATAC mkfastq (v1.2.0) and bcl2fastq (v2.20.0.422)
Sequencing reads were aligned to a modified GRCh38 reference using CellRanger-ATAC count (v1.2.0). Data was merged and single-cells were called using the default parameters.
Nucleotide-barcode labelled antibodies were pseudo-aligned and counted using bustools-kite. Hashtagged cells were demultiplexed using HTODemux in Seurat.
Mitochondrial genotyping was performed with mgatk, results imported into R with ReadMGATK and merged per experiment.
SNPs and indels were removed from aligned bam files with bamboozle to anonymize data.
Genome_build: GRCh38 (hardmasked according to mitoblacklist by Caleb Lareau)
Supplementary_files_format_and_content: Processed fragment files from 10x cellranger-ATAC count. Antibody-derived tag (ADT) counts and hashtag-based cell identities for cells passing QC thresholds. mgatk results exported as mito assay from Signac.

source_name: primary NK cells

extract_protocol:
ASAP-seq/mtscATAC-seq = fixation: 1% FA, lysis: 0.1% NP40 wash: No tween wash
Custom 10x Genomics scATAC-seq (mtscATAC-seq/ASAP-seq)

value: Peripheral Blood

tag: donor id


title: Blood, BCG 3

tag: tissue


title: MMNK1-shScr-set3

value: sh-Scramble


title: scATAC after in vitro stimulation

data_processing:
Fastqs were demultiplexed usiing cellranger-ATAC mkfastq (v1.2.0) and bcl2fastq (v2.20.0.422)
Sequencing reads were aligned to a modified GRCh38 reference using CellRanger-ATAC count (v1.2.0). Data was merged and single-cells were called using the default parameters.
Nucleotide-barcode labelled antibodies were pseudo-aligned and counted using bustools-kite. Hashtagged cells were demultiplexed using HTODemux in Seurat.
SNPs and indels were removed from aligned bam files with bamboozle to anonymize data.
Genome_build: GRCh38 (hardmasked according to mitoblacklist by Caleb Lareau)
Supplementary_files_format_and_content: Processed fragment files from 10x cellranger-ATAC count. Antibody-derived tag (ADT) counts and hashtag-based cell identities for cells passing QC thresholds. Cell barcodes of cells included in final analysis.

growth_protocol: NK cells were isolated from freshly drawn blood by magnetic depletion of CD3+, followed by enrichment of CD56+ cells.

treatment_protocol: Purified NK cells were co-cultured for 12 h with peptide-pulsed RMA-S/HLA-E cells in RPMI 1640 with 10 % FCS, supplemented with 10 ng/mL IL 15 (Miltenyi Biotec), the respective peptides at 300 µM, in the presence or absence of 10 ng/mL IL-12 and 100 ng/mL IL-18. Cells were stained with fluorochrome-labelled antibodies and either analyzed by flow cytometry or additionally stained with nucleotide-barcode labelled antibodies, including hashtag antibodies marking experimental conditions and donors, before sorting for viable CD7+ NKG2C+ cells. Sorted cells were pooled at equal numbers per condition.

tag: cmv-serostatus

value: Negative


title: stage E18 embryo 2 section 5 sector 5


title: CMVpos1_CMVpos5_v3_Lib1

data_processing:
Fastqs were demultiplexed usiing cellranger-ATAC mkfastq (v3.0.2) and bcl2fastq (v2.20.0.422)
scRNA reads were mapped to the hg19 reference genome with cellranger count
Nucleotide-barcode labelled antibodies were quantified with CITE-Seq count or pseudo-aligned and counted using bustools-kite. Hashtagged cells were demultiplexed using HTODemux in Seurat.
SNPs and indels were removed from aligned bam files with bamboozle to anonymize data.
Genome_build: hg19
Supplementary_files_format_and_content: Processed gene-per-cell count tables files from 10x cellranger count. Antibody-derived tag (ADT) counts and hashtag-based cell identities for cells passing QC thresholds.

growth_protocol: NK cells were enriched from freshly drawn blood by CD3 CD14 CD19 depletion. The enriched fraction was stained with fluorochrome-conjugated antibodies and Fc receptors blocked using Human TruStain FcX for 15 min at 4 °C. Dead cells were excluded using Fixable Viability Dye eFluor780. In a second step, cells were stained with nucleotide-barcode labelled antibodies for 30 min at 4 °C. NKG2C+ and NKG2C- cells were separately labelled with different nucleotide-labelled hashtag antibodies (Biolegend). NKG2C+/- populations were pooled at a 1:1 ratio and the cell concentration adjusted to 1000 cells/µl for further processing.

extract_protocol: 10x Genomics 3' scRNA-seq (v2/v3) with feature barcoding (TotalSeqA)

value: Positive


title: CMVpos1_CMVpos5_v3_Lib2


title: MMNK1-shARID1A-set2


title: stage E18 embryo 2 section 5 sector 4


title: MMNK1-shScr-set2


title: exon 7 of LRRFIP2 variant 3-deleted MKN1 cell line #1 [MKN1_ko_1]

city: Seoul

first: Jihee

last: Lee

address: 92 Myeongdal-ro, Seocho-gu

country: South Korea

institute: GILO Institute

data_processing:
After sequencing, low quality reads were filtered out according to the following criteria by using cutadapt v.2.8 58: The adapter sequences and the ends of the reads less than Phred quality score 20, and simultaneously the reads shorter than 50 bp.
The whole filtering process was performed using scripts developed in-house.
Filtered reads were mapped to the GRCh38 genome related to the species using STAR v.2.7.1a alignment software.
Gene expression levels were measured with RSEM v1.3.160 using the ensemble database and quantified as the ratio of reads mapped to a gene to the gene length in kilobases and expressed as the fragments per kilobase of transcript per million fragments mapped (FPKM).
Genome_build: Filtered reads were mapped to the GRCh38 genome related to the species
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: gastric adenosquamous carcinoma

growth_protocol: The cells were maintained under standard conditions (RPMI-1640 containing 25 mM HEPES, 10% fetal bovine serum, 100 unit/mL streptomycin, and 100 units/mL penicillin at 37°C, 5% CO2).

extract_protocol:
The cDNA libraries were prepared from Total RNA for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina). Total RNA from each cell for RNA sequencing was isolated using TRIzol reagent following the manufacturer’s instructions. The mRNA molecules were purified and fragmented from 1ug of Total RNA using oligo (dT) magnetic beads.
After sequential process, cDNA libraries were amplified with PCR (Polymerase Chain Reaction) and were subsequently examined for quality using an Agilent 2100 bioanalyzer (Agilent). They were quantified with the KAPA library quantification kit (Kapa Biosystems) according to the manufacturer’s protocol.

value: Human gastric adenosquamous carcinoma

tag: genotype/variation

value: exon 7 of LRRFIP2 variant 3 KO by CRISPR/Cas9


title: stage E18 embryo 2 section 5 sector 3


title: exon 7 of LRRFIP2 variant 3-deleted MKN1 cell line #2 [MKN1_ko_2]


title: MMNK1-shARID1A-set1


title: Wild type MKN1 cell line [MKN1_ctrl]

value: Control


title: stage E18 embryo 2 section 5 sector 1


title: stage E18 embryo 2 section 1 sector 1


title: stage E18 embryo 2 section 6 sector 1


title: MMNK1-shScr-set1


title: stage E18 embryo 2 section 4 sector 5


title: stage E18 embryo 2 section 5 sector 2


title: CMVneg1

first: Timo

last: Rückert

address: Charitéplatz 1


title: CMVneg2


title: CMVpos4


title: stage E18 embryo 2 section 4 sector 4


title: CMVpos3


title: stage E18 embryo 2 section 4 sector 2


title: stage E18 embryo 2 section 4 sector 1


title: CMVpos2


title: ATAC_CMVpos3_CMVpos4


title: stage E18 embryo 2 section 4 sector 3


title: ATAC_CMVpos1_CMVpos3_CMVpos4_CMVneg1


title: stage E18 embryo 2 section 3 sector 1


title: stage E18 embryo 2 section 3 sector 2


title: ATAC_CMVpos2


title: stage E18 embryo 2 section 3 sector 3


title: stage E18 embryo 2 section 3 sector 4


title: siPHF14 MDA-MB-231, biological rep2

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using the subjunc function from the Rsubread package, and reads were mapped to the hg19 human reference genome using TH1= 2 and unique=TRUE parameters. The downstream analysis was performed on .bam files with duplicates removed using the samtools (v0.1.19) rmdup command. The FeatureCounts() function from the Rsubread package was used to assign reads to the UCSC hg19 KnownGenes (miRNAs were discarded from the analysis) using GTF.featureType = “exon”, GTF.attrType = “gene_id” and strandSpecific = 2 parameters with the duplicate-removed .bam files. Then, differential gene expression analysis and statistics were performed using the DESeq2 Bioconductor. Differentially expressed genes with adjusted p value < 0.05 and Log2FC > 0.5 (upregulated genes) or Log2FC < - 0.5 (downregulated genes) were selected for further analysis.
Genome_build: hg19 human reference genome
Supplementary_files_format_and_content: Raw counts per UCSC knownGenes for every gene and every sample

source_name: MDA-MB-231 triple-negative breast cancer cell

growth_protocol: Human MDA-MB-231 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen)
Poly(A) RNA was isolated, then the libraries were prepared with the TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the NextSeq 500 HIGH Output y 1x75 pb length parameters

treatment_protocol: Two independent cultures (replicates) were treated with each one of the following siRNA: siControl, siPHF14 or siHMG20A

value: Cells transfected  with siPHF14 RNA

tag: tissue origin

value: Breast cancer


title: siHMG20A MDA-MB-231, biological rep1

value: Cells transfected  with siHMG20A RNA


title: stage E20 embryo 1 section 5 sector 3

value: embryo


title: siHMG20A MDA-MB-231, biological rep2


title: stage E18 embryo 2 section 2 sector 5


title: siPHF14 MDA-MB-231, biological rep1


title: WT_19, Ad-CMV-Cre

data_processing:
ATAC-seq Raw reads were processed using Trimmomatic
Quality reads (FastQC) were aligned to mm9 using Bowtie2
Alignment quality was evaluated by BamQC and low-quality alignments were filtered using samtools based on MAPQ < 10
Significant regions were identified using MACS2 based on quality filtered PE alignments
Peaks called from each biological sample (replicate) were concatenated and merged if inter-interval distance is less than 300 bair pair.
Within-peak read counts were analyzed for differential accessibility via DESeq2
assembly: mm9
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
The infected cells at passage 5 and 80% confluency were harvested for RNA-seq and ATAC-seq analyses
Libraries were prepared utilizing methods outlined previously.(Myers et al., 2020)

treatment_protocol: mL polybrene overnight.

value: Mouse embryonic fibroblast


title: stage E20 embryo 1 section 4 sector 5


title: WT_16, Ad-CMV-Cre


title: stage E20 embryo 1 section 4 sector 4


title: siControl MDA-MB-231, biological rep2

value: Cells transfected  with siControl RNA


title: stage E20 embryo 1 section 5 sector 2


title: siControl MDA-MB-231, biological rep1

value: Cells transfected with siControl RNA


title: WT_1, Ad-CMV-Cre


title: stage E20 embryo 1 section 4 sector 6


title: KA_29, Ad-CMV-Cre


title: stage E20 embryo 1 section 4 sector 3


title: KA_28, Ad-CMV-Cre


title: stage E20 embryo 1 section 4 sector 2


title: GBM_plasma_1

city: Houston

first: Deqiang

last: Sun

state: TX

address: 2121 W Holcombe Blvd

department: Search Results Web results  Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology

institute: Texas A&M University

data_processing:
For the WGBS analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using LiBis.
MCALL module in MOABS software was used to calculate DNA methylation ratio and coverage for each CpG site.
The output bedGraph files from MCALL include single base resolution DNA methylation ratios, which were transformed to a bigwig file format.
The bigwig files were uploaded to the UCSC genome browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: BW

source_name: Glioblastoma patient blood

extract_protocol:
Total DNA containing cell-free DNA (cfDNA) was isolated from 200–400 µL CSF using a QIAamp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s instructions. For tumor tissue, DNA was isolated using an AllPrep DNA/RNA Mini Kit according to the manufacturer’s protocol. The isolated DNA concentration was measured using a Qubit 4 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific).
WGBS analysis was used to access the genome-wide DNA methylation profile. The cfDNA WGBS libraries were generated using a Pico Methyl-Seq Library Prep Kit (Zymo Research). Briefly, ctDNA was mixed with 0.1% unmethylated λ-bacteriophage DNA (w/w) (NEB), followed by sodium bisulfite conversion. The bisulfite-converted DNA was then annealed with random primers for initial amplification, followed by adaptor ligation and final amplification with Illumina TruSeq indices. Constructed libraries were run on a 2% agarose gel to assess size distribution, and the library concentration was measured using a Qubit 4 Fluorometer with a Qubit dsDNA High Sensitivity Assay Kit. Normalized libraries were pooled at an equimolar ratio and sequenced on a NextSeq 500 or a NovaSeq 6000 (Illumina).

tag: diagnosis

value: Glioblastoma

value: Blood


title: GBM_plasma_2


title: stage E18 embryo 2 section 3 sector 5


title: ATAC_CMVneg2

city: Berlin

institute: Deutsches Rheuma-Forschungszentrum


title: stage E20 embryo 1 section 5 sector 1


title: GBM_Tissue_2

source_name: Glioblastoma

value: Tumor


title: KA_12, Ad-CMV-Cre


title: GBM_Tissue_1


title: K_20, Ad-CMV-Cre


title: prGAL1-mAID-ZPR1_Depleted

city: Cambridge

first: Vladimir

last: Denic

address: 52 Oxford St

institute: Harvard University

library_source: other

data_processing:
Raw reads from Illumina NextSeq were checked for read quality using FastQC (v. 0.11.5)
Four random nucleotides generated during library prep were trimmed using seqtk (parameter trimfq -b 4) and 3' adapters were trimmed using cutadapt
Reads were aligned to ncRNA (rRNA, tRNA, snRNA, snoRNA, ncRNA) derived from S288C reference genome (R64-1-1) using the RNA-seq aligner STAR (v2.7.0) and unmapped reads kept
Reads were aligned to S288C reference genome (R64-1-1) using the RNA-seq aligner STAR (v2.7.0)
bigWig files were generated using bamCoverage tool of deepTools suite (binWidth = 1, normalized counts per million)
Assembly: S288c (v. R64-1-1)
Supplementary files format and content: bigWig files generated using bamCoverage tool of deepTools suite (normalized counts per million,  binWidth = 1)
Library strategy: Ribo-seq

molecule: other

growth_protocol: Cells were grown to an OD of 0.15

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, a preadenylated linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

tag: genotype

value: BY4741 MATa his3d1 leu2d0 ura3d0 met15d0 HO::ADH1p-OsTIR1-URA3 SkHIS3-GAL1p-mAID-ZPR1

value: 0.5 mM IAA


title: stage E20 embryo 1 section 3 sector 3


title: K_7, Ad-CMV-Cre

first: Aram

last: Hezel

address: 300 Elmwood Avenue

tag: cell line


title: stage E20 embryo 1 section 3 sector 2


title: ZPR1_WT

value: BY4741 MATa his3d1 leu2d0 ura3d0 met15d0 HO::ADH1p-OsTIR1-URA3


title: K_4, Ad-CMV-Cre


title: A_27, Ad-CMV-Cre


title: stage E20 embryo 1 section 2 sector 6


title: A_11, Ad-CMV-Cre


title: A_10, Ad-CMV-Cre


title: stage E20 embryo 1 section 3 sector 1


title: stage E20 embryo 1 section 2 sector 7


title: stage E20 embryo 1 section 2 sector 3


title: stage E20 embryo 1 section 2 sector 5


title: stage E20 embryo 1 section 4 sector 1


title: AM.WSN.PP1.III

city: Saint Paul

first: Yuying

last: Liang

state: MN

address: 1988 Fitch Avenue, Room 295 AS/VM

institute: University of Minnesota

data_processing:
All the raw RNA-Seq reads were processed with adapter trimming and low-quality base removal by Trimmomatic ( -phred33, seed mismatches = 2, palindrome clip threshold = 30, simple clip threshold = 10, LEADING: 10, TRAILING:10, SLIDINGWINDOW:4:20, MINLEN:36) and checked for quality using FASTQC.
All trimmed reads with a minimum read length of 36bp and average quality per base higher than 30 were mapped into the combined genome (mouse+IAV) by STAR v2.5.3a.  (parameters: --sjdbOverhang 49 --outFilterType BySJout  --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterIntronMotifs None )
The number of reads mapped to gene features (read count) of all the genes,  including host and viral genes, were quantified by featureCounts
Assembly: GRCm38.95 for TrkA KI mouse, and NCBI Taxon ID 382835 for IAV WSN
Supplementary files format and content: tab-delimited text file include read count values for all genes in all samples
Supplementary files format and content: Comma-separated values (csv) files contain differential expression test results

source_name: alveolar macrophages

growth_protocol: Primary alveolar epithelial cells (AEC) and alveolar macrophages (AM) cells were isolated from TrkA KI mice. The enriched AEC suspensions were collected and cultured in DMEM/F12 Medium (Lonza, 12001-600) supplemented with 10% FBS on tissue culture-treated dishes. Enriched AMs were grown in DMEM/F12 Medium (Lonza, 12001-600) supplemented with 10% FBS,

extract_protocol:
Total RNA extraction was conducted by University of Minnesota Genomic Center (UMGC)
The cDNA libraries of the mRNAs of all 18 samples were created using TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA).

treatment_protocol: Primary AECs and AMs seeded on 6-well plates were subjected to three treatments: mock infection, A/WSN infection (MOI=10), and A/WSN infection (MOI=10) in the presence of 1NMPP1 (10 µm), each in triplicates.

value: alveolar macrophages

value: TrkA KI

value: A/WSN (MOI=10) + 1NMPP1 (10 µM), 10 hpi


title: stage E20 embryo 1 section 2 sector 4


title: AM.WSN.PP1.I


title: AM.WSN.PP1.II


title: chemoresistant patient 11

type: RNA

city: Beijing

first: Min

last: Yin

address: Dongcheng

institute: Peking Union Medical College Hospital

description: The nCounter PanCancer Pathways panel includes 770 genes from 35 canonical pathways and selected reference genes.

hyb_protocol: Hybridizations were carried out by combining 5µl of each RNA sample with 8µl nCounter Reporter probes in hybridization buffer and 2µl nCounter Capture probes (total reaction volume of 15µl), and allowed to incubate overnight at 65°C for 16–30 hours. Excess probes were removed using a two-step magnetic bead-based purification on the nCounter Prep Station (nanoString Technologies).

scan_protocol: Amount of specific target molecules were quantified on the nCounter Digital Analyzer by counting the individual fluorescent barcodes and assessing the target molecules. For each assay, a high-density scan encompassing 280 fields of view was performed. The data was collected using the nCounter Digital Analyzer, after taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera.

data_processing: mRNA data analysis, including measurement of fold change, was performed using the nSolver™ software analysis (freely available from nanoString Technologies). The mRNA profiling data was normalized using housekeeping genes.

source_name: ovarian clear cell carcinoma

growth_protocol: formalin-fixed, paraffin-embedded (FFPE) tissues

extract_protocol: Total RNA was extracted using the Qiagen RNeasy FFPE Kit according to the manufacturer’s protocol.

tag: disease state

value: ovarian clear cell carcinoma

tag: histology

value: OCCC

tag: phenotype

value: chemoresistant


title: chemoresistant patient 8

description: The nCounter PanCancer Pathways panel includes 770 genes from 32 canonical pathways and selected reference genes.

tag: age


title: chemoresistant patient 7

description: The nCounter PanCancer Pathways panel includes 770 genes from 31 canonical pathways and selected reference genes.


title: stage E20 embryo 1 section 2 sector 1

tag: developmental stage


title: chemoresistant patient 10

description: The nCounter PanCancer Pathways panel includes 770 genes from 34 canonical pathways and selected reference genes.


title: chemoresistant patient 12

description: The nCounter PanCancer Pathways panel includes 770 genes from 36 canonical pathways and selected reference genes.


title: stage E20 embryo 1 section 2 sector 2


title: stage E20 embryo 1 section 7 sector 4


title: chemoresistant patient 9

description: The nCounter PanCancer Pathways panel includes 770 genes from 33 canonical pathways and selected reference genes.


title: stage E20 embryo 1 section 7 sector 3


title: stage E20 embryo 1 section 7 sector 2


title: AM.mock.III

tag: cell type

value: PBS


title: AM.WSN.II

tag: treatment

value: A/WSN (MOI=10), 10 hpi


title: AM.WSN.I


title: chemoresistant patient 6

description: The nCounter PanCancer Pathways panel includes 770 genes from 30 canonical pathways and selected reference genes.


title: chemoresistant patient 5

description: The nCounter PanCancer Pathways panel includes 770 genes from 29 canonical pathways and selected reference genes.


title: chemoresistant patient 4

description: The nCounter PanCancer Pathways panel includes 770 genes from 28 canonical pathways and selected reference genes.


title: AM.mock.II


title: chemoresistant patient 2

description: The nCounter PanCancer Pathways panel includes 770 genes from 26 canonical pathways and selected reference genes.


title: chemoresistant patient 3

description: The nCounter PanCancer Pathways panel includes 770 genes from 27 canonical pathways and selected reference genes.


title: AM.WSN.III


title: AM.mock.I


title: stage E20 embryo 1 section 1 sector 9

value: embryo


title: AEC.WSN.PP1.III

source_name: alveolar epithelial cells

value: alveolar epithelial cells


title: stage E20 embryo 1 section 1 sector 8


title: chemoresistant patient 1

description: The nCounter PanCancer Pathways panel includes 770 genes from 25 canonical pathways and selected reference genes.


title: chemosensitive patient 12

description: The nCounter PanCancer Pathways panel includes 770 genes from 24 canonical pathways and selected reference genes.

value: chemosensitive


title: input-hdac4_rep2

city: Tianjin

first: Xuan

last: Zhao

state: Tianjin

address: No. 38 Tongyan Road, Haihe Education Park, Tianjin

department: State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by TrimGalore, then sequence reads were mapped to mm10 genome using Bowtie2.
Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal

source_name: embryonic stem cells (ESCs) E14

growth_protocol: Mouse embryonic stem cells (ESCs) E14 were cultured under 5 % CO2 at 37 ℃ on well plate coated with 0.2 % gelatin (Sigma), in DMEM (Hyclone) that supplemented with15 % FBS（Hyclone）,10 ng/ml mLIF (GeneScript)，1 % Penicillin-Streptomycin (Solarbio)，1 % L-glutamine (Gibco), 1 % nonessential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Cells were lysed with buffer and sonicated. After preclearing chromatin extract, anti-Hdac4 and anti-Hdac5 antibodies were used to immunoprecipiate in mESCs respectively. Proteins on chromatin associated with Hdac4/5 were digested and chromatin was decrosslinked at 65 ℃ overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Hdac4/5-assocated chromatin DNA was used in ChIP-seq library preparation.  Libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.

treatment_protocol: WT E14 ESCs were cultured in 10 cm dish until the cells grew to about 90 %, Then, Cells were cross-linked with formaldehyde and stored at -80 ℃.

value: embryonic stem cells (ESCs) E14

tag: strain

tag: antibody

value: input

value: untreated


title: IP-hdac5_rep2

value: hdac5, Cell Signaling Technology, D1J7V


title: stage E20 embryo 1 section 1 sector 7

data_processing:
Sequencing quality of raw sequencing data was evaluated by fastp
The genome sequence Macaca_fascicularis_5.0 for Crab-eating macaque (Macaca fascicularis)) were obtained from the Ensemble (https://asia.ensembl.org/index.html). Reads were mapped to the Macaca_fascicularis_5.0 genome assemblies by HISAT2 using default settings.
All mapped reads were processed by StringTie to quantify gene expression levels (measured by TPM , Transcripts Per Kilobase per Million mapped reads) using default parameters.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each samples


title: AEC.WSN.PP1.I


title: IP-hdac4_rep2

value: hdac4, Cell Signaling Technology, D8T3Q


title: AEC.WSN.PP1.II


title: input-hdac5_rep2


title: stage E20 embryo 1 section 1 sector 6


title: chemosensitive patient 11

description: The nCounter PanCancer Pathways panel includes 770 genes from 23 canonical pathways and selected reference genes.


title: stage E20 embryo 1 section 7 sector 1


title: AEC.WSN.III


title: chemosensitive patient 10

description: The nCounter PanCancer Pathways panel includes 770 genes from 22 canonical pathways and selected reference genes.


title: IP-hdac5_rep1


title: input-hdac4_rep1


title: AEC.WSN.I


title: AEC.WSN.II


title: input-hdac5_rep1


title: IP-hdac4_rep1


title: stage E20 embryo 1 section 1 sector 3


title: chemosensitive patient 7

description: The nCounter PanCancer Pathways panel includes 770 genes from 19 canonical pathways and selected reference genes.


title: chemosensitive patient 8

description: The nCounter PanCancer Pathways panel includes 770 genes from 20 canonical pathways and selected reference genes.


title: AEC.mock.III


title: chemosensitive patient 6

description: The nCounter PanCancer Pathways panel includes 770 genes from 18 canonical pathways and selected reference genes.


title: NIH3T3, Input

first: Shiqiang

last: Zhang

address: Peking University

data_processing: Reads were mapped using STAR-2.6.0c to GRCm38, and mapped reads were quantified and normalized by featureCount and FPKM, respectively.

growth_protocol: NIH3T3 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin, maintained at 37°C with 5% CO2.

extract_protocol:
cells were crosslinked with ultraviolet (UV) at 254 nm (400 mJ/cm2), followed by lysis in lysis buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, freshly added protease inhibitor) and digestion with RNAase I (Ambion). Immunoprecipitation was performed using anti-HP1 alpha antibody (Abcam, ab109028) and M-280 sheep anti-rabbit IgG beads (Invitrogen). After 3’ RNA adapter ligation, samples were run on protein gels and transferred to membranes (PVDF membrane for western blotting, nitrocellulose membrane for library preparation). A region 75 kDa above the HP1 alpha band on nitrocellulose membrane was cut and treated with proteinase K to isolate RNA. RNA was converted to cDNA followed by 3’ DNA adapter ligation. Then the sample was PCR amplified and fragment size selected by agarose gel electrophoresis and gel extraction.
eCLIP-seq libraries were prepared through 3’ RNA adapter ligation, western blotting, HP1 alpha band isolation, RNA convertion to cDNA, 3’ DNA adapter ligation, and PCR amplification.

value: Fibroblast

tag: eclip antibody

value: No antibody


title: AEC.mock.II

value: TrkA KI


title: stage E20 embryo 1 section 1 sector 1

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using Vayzme TD503 DNA sample preparation kit

tag: tissue


title: stage E20 embryo 1 section 1 sector 5


title: stage E20 embryo 1 section 6 sector 4


title: chemosensitive patient 5

description: The nCounter PanCancer Pathways panel includes 770 genes from 17 canonical pathways and selected reference genes.


title: Pim3_Control_2

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by TrimGalore, then sequence reads were mapped to GRCm38 genome using STAR.
Raw count were generated by featureCounts.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include raw count values for each Sample.

source_name: E14 Embryonic stem cells

growth_protocol: Mouse E14 ESCs were cultured on 12-well tissue culture plate (353043, FALCON, NY, USA) coated with 0.2 % gelatin (G1890, Sigma), in Dulbecco’s modified Eagle’s medium (DMEM, SH30243.01m, Hyclone) supplemented with 15 % fetal bovine serum (FBS, SH30070.03, Hyclone),1 % nonessential amino acids (Gibco), 1 % L-glutamine (Gibco),1 % Penicillin–Streptomycin (P1400, Solarbio), 10 ng/ml mouse LIF (Z03077, GeneScript) and 0.1 mM β-mercaptoethanol (M3148-250, Sigma) in an incubator with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted with RNAiso Plus (Takara) and was subjected to DNase Ｉ(Thermo Scientific) for 15 min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: We used  CRISPR/Cas9 to knockout Pim3 in embryonic stem cells. Wild-type (WT) ESC and Pim3 knockout cell lines were cultured under serum conditions.

value: E14 Embryonic stem cells

value: wild type


title: stage E20 embryo 1 section 1 sector 4


title: chemosensitive patient 9

description: The nCounter PanCancer Pathways panel includes 770 genes from 21 canonical pathways and selected reference genes.

value: ovarian clear cell carcinoma

value: OCCC


title: stage E20 embryo 1 section 6 sector 3


title: chemosensitive patient 4

description: The nCounter PanCancer Pathways panel includes 770 genes from 16 canonical pathways and selected reference genes.


title: p63KO5W

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave

institute: University of Pennsylvania School of Veterinary Medicine

description: After tamoxifen induction at puberty (4 weeks), mice were harvested after 5 weeks (long term)

data_processing:
reads was counted against transcipts described in gencode M21 using salmon
reads were summarized to the gene level using txImport
Genome_build: GRCm38, gencode m21 gene models
Supplementary_files_format_and_content: raw counts per gene

source_name: Mammary epithelial cells

growth_protocol: Mammary gland at 5 weeks and 35 weeks wre used

extract_protocol:
Mammary gland from iK14-Cre; DNp63 f/f mice were digested with collagenase/hyaluronidase using method obtained from Shackleton et al, 2006. Single cells were sorted for epithelial cell enriched populations. Epithelial cell enriched population was obtained by sorting out and removing stromal cells with CD45, CD31 and ter119 antibodies. 100, 000 cells were used.
Library construction protocol was made using standard protol from Illumina

treatment_protocol: Tamoxifen (1.5mg/ml) was given to induce the deletion of DNp63

value: Mammary epithelial cells

value: Dnp63 cKO

tag: timepoint


title: Pim3_Control_1


title: chemosensitive patient 3

description: The nCounter PanCancer Pathways panel includes 770 genes from 15 canonical pathways and selected reference genes.


title: stage E20 embryo 1 section 1 sector 2

value: embryo


title: stage E20 embryo 1 section 6 sector 1


title: NIH3T3, HP1

value: HP1 alpha


title: chemosensitive patient 2

description: The nCounter PanCancer Pathways panel includes 770 genes from 14 canonical pathways and selected reference genes.

value: chemosensitive


title: stage E20 embryo 1 section 6 sector 2


title: p63WT5W

value: WT


title: Pim3_KO_2


title: chemosensitive patient 1

description: The nCounter PanCancer Pathways panel includes 770 genes from 13 canonical pathways and selected reference genes.


title: Pim3_KO_1


title: p63KO10D

description: After tamoxifen induction at puberty (4 weeks), mice were harvested after 10 days


title: AEC.mock.I

value: alveolar epithelial cells

value: PBS


title: p63WT10D