title: C01.MCF7.Y117L.factor2.1

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Pre-processing of the raw data files were done using Fastqc, and alinged to the reference genome using STAR aligner followed by read counting using featureCounts.
Assembly: Mm10
Supplementary files format and content: Count Data

source_name: MCF7 cells, induced to express ULF mutant vimentin

growth_protocol: MCF7 cells obtained from the American Type Culture Collection (#ATCC HTB-22) were cultured in MEM (11095-080, Thermo Fisher Scientific, USA) supplemented with fetal bovine serum (Cytiva Hyclone, Fisher Scientific, USA), 50U/ml of Penicillin and 0.05mg/ml of Streptomycin (P4333, Sigma-Aldrich, St.Louis, USA), MEM non-essential amino acids (25-025-CI, Corning, USA), sodium pyruvate (25-000-CI) and 0.01 mg/ml bovine insulin (I6634, Sigma-Aldrich, St.Louis, USA). The cells were maintained at 37°C with 5 % CO2.

extract_protocol:
RNA from cell lines was isolated using RNAeasy Plus mini kit (Qiagen, Germany) and mRNA was isolated from 80 ng of purified total RNA using oligo-dT beads (New England Biolabs, Inc)
NEBNext Ultra™ RNA kit (New England Biolabs, USA) was used for full-length cDNA synthesis and library preparation. Libraries were pooled, denatured and diluted, resulting in a 2.0 pM DNA solution. PhiX control was spiked at 1%. Libraries were sequenced on an Illumina NextSeq 500 instrument (Illumina Inc) using NextSeq 500 High Output reagent kit (Illumina Inc) (1x75 cycles)

treatment_protocol: Cells expressing WT vimentin or ULF mutant vimentin were induced with 5X cumate inducer

value: Epithelial cell

value: ULF mutant vimentin expressing cells

value: Induced with cumate


title: Healthy CON_11 (Male)

status: Public on Sep 30 2022

type: SRA

city: Seongnam-si

first: Minsoo

last: Kwon

address: 335 Pangyo-ro

department: Pharmacology

country: South Korea

institute: CHA University

library_source: transcriptomic

data_processing:
Trimming with Average Q20 using BBDuk
Mapping using Bowtie2 to reference genome
Calculation read count using Bedtools
TMM + CPM normalization using EdgeR
Assembly: Human hg19 UCSC
Supplementary files format and content: Normalized counts.csv

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
RNA quality was assessed with an Agilent 2100 bioanalyzer using an RNA 6000 Nano Chip (Agilent Technolo- gies, Amstelveen, Netherlands).
The library construction was performed using a QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria

tag: tissue

value: Peripheral blood

tag: disease state

value: healthy

tag: cell type

value: PBMC-derived microglia-like cell

tag: Sex

value: Male


title: Healthy CON_7 (Female)

value: Female


title: H01.MCF7.Induced.factor2.3

country: USA

source_name: MCF7 cells, induced to express WT vimentin

tag: cell line

tag: genotype

value: WT vimentin expressing cells

tag: treatment


title: yMH104 (control) - Input DNA_rep1

city: Beijing

first: Ran

last: Wei

address: Haidian District, Beijing Summer Palace Road No. 5

country: China

institute: Peking University

description: Baker yeast S. cerevisiae

library_source: genomic

data_processing:
ChIP-seq raw reads were cleaned by using Cutadapt (version 2.6) to trim the sequencing adapters.
Clean reads were aligned to the reference genome using Bowtie2 (version 2.3.5).
PCR duplicates were removed using Picard (version 1.118).
MACS2 (version 2.2.5) was used to call significant peaks.
The final mapped bam files were converted to the Bigwig format using bamCoverage for visualization in IGV.
Genome_build: We merged the sacCer3 genome and the dChr DNA sequence to obtain our reference genome, and the reference genome was indexed for mapping.
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage for each sample.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Baker yeast S. cerevisiae strains yMH104 cell

growth_protocol: We cultured yMH007 (containing dChr) and yMH104 (control) in tubes containing 4 ml SC-Ura liquid medium in a shaker incubator at 30 ℃. After overnight incubation, we diluted the liquid culture to 50 ml fresh SC-Ura liquid medium until the optical density at 600 nm (OD600) equaled 0.2. After culturing at 30 ℃ until the OD600 reached 1.0-1.2, we harvested the appropriate yeast cells.

extract_protocol:
Forty milliliters of the yeast culture was added to a 50 ml Falcon tube with 1.11 ml of 37% formaldehyde (1% final concentration). The lid was tightened to prevent leakage and the tube was placed in a silent mixer at room temperature for 25 min. Afterward, 2.74 ml of 2 M glycine was added and mixed at room temperature for 10 min to stop crosslink reactions. The mixture was washed thrice with 20 ml cold phosphate-buffered saline (PBS) and resuspended with 3 ml PBS containing protease inhibitor.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: condition

value: control, contains empty plasmid

tag: chip antibody


title: Kidney_WT_CRTC2_PTH30_rep2

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
Data was processed from NovaSeq 6000 with bcl2fastq
ChIP-seq raw files were mapped using bowtie2 with standard parameters ( -x input file) with sam file output.
Sam files were converted with samtools into sorted and indexed bam files
HOMER was used to process the bam files, find peaks, and create the bigWig files.
bigWig files were averaged using the wiggletools mean function: wiggletools mean file1.bigWig file2.bigWig, file3.bigWig | wigToBigWig stdin chrom.sizes *_averaged.bigWig
Assembly: mm9
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: kidney tissue

growth_protocol: C57BL/6 mice aged 8-9 wk (The Jackson Laboratory, Bar Harbor, ME) were housed in high density ventilated caging in the Animal Research Facility of University of Wisconsin-Madison under 12-hour light/dark cycles at 72°F and 45% humidity. All mice used in this study were maintained on a standard rodent chow diet (5008, Lab Diet, St. Louis, MO). All experiments and tissue collections were performed in the procedure rooms in the Research Animal Facility of University of Wisconsin-Madison. All animal studies were reviewed and approved by the Research Animal Care and Use Committee of University of Wisconsin-Madison under protocol A005478.

extract_protocol:
The kidneys were isolated, rinsed with cold 1× phosphate-buffered saline, and subjected to a cross-linking reaction for 10 min with 1.5% formaldehyde. After the fixative was neutralized for 5 min with glycine (0.125 m final concentration), the kidney tissue was homogenized briefly in phosphate-buffered saline using a loose fitting Dounce pestle, and the cells were collected via 70-μm nylon cell strainers (BD Falcon). Cells were then subjected to ChIP analysis as described previously (Yamamoto H, 2003, Journal Biol Chem).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA kit (NEB, #E7645S) with the NEBNext Multiplex Oligos for Illumina (NEB, #E6440S) according to the manufacturer’s protocols. Libraries were submitted to the University of Wisconsin – Madison Biotechnology Center’s DNA Sequencing Facility (Research Resource Identifier – RRID:SCR_017759). Libraries were sequenced on a NovaSeq 6000. Paired end, 250 bp sequencing with a target of 20+ million reads was performed.

treatment_protocol: Animals were subjected to intraperitoneal injection of 10 mg/kg body weight (bw) 1,25(OH)2D3 (in propylene glycol), 230 mg/kg bw PTH (1–84) (in phosphate buffered saline (PBS)), 50 mg/kg bw FGF23 (in PBS + 0.1% BSA), 30 mg/kg YKL-05-099 (PBS + 25mM HCl), 40 mg/kg SK-124 (15% HPBCD (hydroxypropyl β-cyclodextrin)), or vehicle (EtOH, PBS, or HPBCD). Animals were sacrificed and tissues collected at 30 min (PTH) or 60 min (all other treatments) and subjected to ChIP followed by ChIP-seq.

value: wild type C57BL6

value: 230 ng/g bw PTH (30 min)

tag: antibody

value: CRTC2 (Bethyl Labs, A300-737A, lot# 1)


title: Kidney_WT_CRTC2_PTH_rep2

value: 230 ng/g bw PTH (1 h)


title: Kidney_WT_CRTC2_PTH30_rep1


title: D02.MCF7.Y117L.factor2.4


title: Kidney_WT_CRTC2_FGF23YKL_rep3

value: 50 ng/g bw FGF23 + 30 ng/g bw YKL-05-099


title: F01.MCF7.Y117L.factor2.2


title: Kidney_WT_CRTC2_PTH15_rep3

value: 230 ng/g bw PTH (15 min)


title: Kidney_WT_CRTC2_PTH_rep1


title: yMH104 (control) - Input DNA_rep2

description: Baker yeast S. cerevisiae


title: A02.MCF7.Y117L.factor2.3


title: Kidney_WT_CRTC2_PTH_rep3


title: yMH007 (containing dChr) - Input DNA_rep2

description: Baker yeast S. cerevisiae

source_name: Baker yeast S. cerevisiae strains yMH007 cell

value: contains dChr


title: Kidney_WT_CRTC2_PTH15_rep1


title: Kidney_WT_CRTC2_SK124_rep3

value: 40 ng/g bw SK-124


title: Healthy CON_10 (Female)


title: Kidney_WT_CRTC2_FGF23PTH30_rep1

value: 50 ng/g bw FGF23 + 230 ng/g bw PTH (30 min)


title: G01.MCF7.Uninduced.factor2.3

source_name: MCF7 cells, uninduced

value: Epithelial cell

value: WT

value: Uninduced


title: C02.MCF7.Induced.factor2.4

value: Induced with cumate


title: Kidney_WT_CRTC2_SK124_rep2


title: Kidney_WT_CRTC2_125YKL_rep2


title: Kidney_WT_CRTC2_FGF23_rep1

value: 50 ng/g bw FGF23


title: E01.MCF7.Induced.factor2.2


title: yMH007 (containing dChr) - Input DNA_rep1

description: Baker yeast S. cerevisiae


title: Kidney_WT_CRTC2_125PTH30_rep2


title: Kidney_WT_CRTC2_125YKL_rep1


title: ScADR6c_S43

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

data_processing:
Partek Flow: Trim bases - Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Partek Flow: Alignment (STAR 2.7.3a) - Default settings from Partek Flow
Partek Flow: Quantify to annotation model (Partek E/M) - Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Partek Flow: Filter features - Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts
Partek Flow: Normalize counts - Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
Partek Flow: ANOVA for DEGs - Factors: Treatment + Sex + Treatment*Sex. Shrinkage of error term variance: Limma-trend

source_name: human engineered cartilage

growth_protocol: Human bone marrow aspirates were collected from the iliac crest of three male (ages 57-64) and three female (ages 59 -64) donors, the mononucleated cells (MNCs) of the aspirates were obtained after centrifugation. The isolated MNC were then expanded in the medium and The adherent hBMSC were then detached using 0.05% w/v trypsin-EDTA and expanded until passage 2 (P2) as previously described. To form bioengineered cartilage-like tissue, hBMSCs were seeded on type I collagen and prrcultured for 3 weeks

extract_protocol:
RNA was extracted using LunaNano PureSPIN columns with a DNAse digestion step. RNA concentrations were measured using a NanoDrop One. Equal masses of RNA from 4 replicate tissues from each donor in each condition were then pooled together to reduce inter-replicate variability (12 pools in total). These samples were then shipped to the UBC Biomedical Research Center for RNA sequencing.
Illumina NextSeq 500: PolyA selection, 20million paired reads

value: F

tag: donor

tag: mechanical condition

value: LabControl


title: yMH007 (containing dChr) - H3K4me3-ChIP-seq_rep2

description: Baker yeast S. cerevisiae


title: yMH007 (containing dChr) - H3K4me3-ChIP-seq_rep1

description: Baker yeast S. cerevisiae


title: Kidney_WT_CRTC2_FGF23YKL_rep2


title: Kidney_WT_CRTC2_125PTH30_rep3


title: Kidney_WT_CRTC2_FGF23PTH30_rep3


title: yMH104 (control) - H3K4me3-ChIP-seq_rep2

description: Baker yeast S. cerevisiae

value: control, contains empty plasmid


title: ScADR6c_S42

value: ParabolicFlight


title: Kidney_WT_CRTC2_125PTH30_rep1

value: wild type C57BL6


title: Kidney_WT_CRTC2_FGF23_rep3

value: CRTC2 (Bethyl Labs, A300-737A, lot# 1)


title: Kidney_WT_CRTC2_125_rep2


title: Kidney_WT_CRTC2_125_rep3


title: Kidney_WT_CRTC2_FGF23_rep2


title: yMH104 (control) - RNA-seq rep3

description:
Baker yeast S. cerevisiae
control_3

data_processing:
RNA-seq raw reads were cleaned by using Cutadapt (version 2.6) to trim the sequencing adapters. Clean reads were then mapped to the yeast reference genome (we merged the sacCer3 genome and the dChr DNA sequence to obtain our reference genome, and the reference genome was indexed for mapping) using hisat2 (version 2.0.5).
Stringtie (version 2.0) was used to quantify the gene expression levels.
The differentially expressed genes were called using DESeq2 (R package, version 1.26.0) in R (version 3.6.0).
Genome_build: We merged the sacCer3 genome and the dChr DNA sequence to obtain our reference genome, and the reference genome was indexed for mapping.
Supplementary_files_format_and_content: expr.TPM.txt: Matrix table with TPM values for every gene and every sample

growth_protocol: We cultured yMH007 (containing dChr) and yMH104 (control) in tubes containing 4 ml SC-Ura liquid medium in a shaker incubator at 30 ℃. After overnight incubation, we diluted the liquid culture to 50 ml fresh SC-Ura liquid medium until the optical density at 600 nm (OD600) equaled 0.2. After culturing at 30 ℃ until the OD600 reached 1.0-1.2, we harvested the appropriate yeast cells to perform RNA extraction.

extract_protocol:
Total RNA from yeast was purified according to the instructions for the Qiagen RNeasy Mini Kit (Catalog no. 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: control


title: B02.MCF7.Uninduced.factor2.4


title: ScADR5c_S41


title: yMH104 (control) - H3K4me3-ChIP-seq_rep1

description: Baker yeast S. cerevisiae


title: Kidney_WT_CRTC2_FGF23YKL_rep1

value: 50 ng/g bw FGF23 + 30 ng/g bw YKL-05-099


title: ScADR5b_S40


title: Kidney_WT_CRTC2_125_rep1


title: D01.MCF7.Uninduced.factor2.2


title: Kidney_WT_CRTC2_125YKL_rep3


title: yMH007 (containing dChr) - RNA-seq rep2

description:
Baker yeast S. cerevisiae
HM240_2


title: Kidney_WT_CBP_Veh_rep3

value: vehicle (EtOH, PBS)

value: CBP (Cell Signaling, D6C5, 7389, lot# 7)


title: ScADR6a_S46

value: GroundControl


title: yMH007 (containing dChr) - RNA-seq rep1

description:
Baker yeast S. cerevisiae
HM240_1

value: contains dChr


title: yMH104 (control) - RNA-seq rep2

description:
Baker yeast S. cerevisiae
control_2


title: yMH104 (control) - RNA-seq rep1

description:
Baker yeast S. cerevisiae
control_1


title: Kidney_WT_CBP_YKL_rep1


title: Kidney_WT_CBP_YKL_rep2


title: Kidney_WT_CBP_PTH30_rep3

value: 230 ng/g bw PTH (30 min)


title: Kidney_WT_CBP_YKL_rep3


title: ScADR4a_S36


title: ScADR5a_S39


title: K14CreERT2 IRE1 F/F_rep 2

city: University Park

first: Fiona

middle: E

last: Chalmers

state: Pennsylvania

address: 306C Life Sciences Building

institute: Penn State University

data_processing:
Demultiplexed reads were obtained in the form of FastQ files. The total number of reads per sample ranged from 7.5 million to 9.7 million. Obtained reads were checked for quality using FastQC (Andrews, 2010).
Adapter contamination, polyA read through, and low-quality tails were removed using BBDuk (https://sourceforge.net/projects/bbmap/).
The STAR aligner (Dobin et al., 2013) was used to align the filtered reads to the mouse reference genome
The quality of the alignment was checked using Qualimap (Okonechnikov, Conesa and García-Alcalde, 2016).
Finally, aligned BAM files were quantified using featureCounts (Liao, Smyth and Shi, 2014).
Obtained count files were imported to R for normalization and differential gene expression analysis and visualizations. DESeq2 was used to normalize the raw counts data from featureCounts. An arbitrary cut-off of 1 log2FoldChange was used to determine the significantly up- and down-regulated genes versus the Ire1αf/f control. Statistical significance was determined by q-value < 0.05.  Gene annotation was performed by BiomaRt (version: 2.38.0). Significant gene ontology terms were determined by p-adj < 0.05 and q < 0.05 and was performed and visualized using clusterProfiler  (version:  3.10.1).
Assembly: m38; NCBI:GCA_000001635.8
Supplementary files format and content: FC_NormalizedCounts_withGeneNames_Genotypes.csv  Contains normalized counts for all genes.
Supplementary files format and content: FC_DE_Genes_Results.csv  Contains list of differentially expressed genes (log2FC >1 or<1) in K14CreERT2 IRE1 F/F compared to IRE1 F/F

source_name: Tongue epithelium

extract_protocol:
The mouth of a euthanized mouse was rinsed in 1mL cold PBS containing ProtectRNA (Sigma) and the tongue was excised from the mouse. The mucosa was separated from the submucosa using an adapted version of a previously described method (Dando et al., 2015; Venkatesan, Boggs and Liu, 2016). Briefly, the tongue was injected under the epithelium with 1 mL of an ice-cold solution of 1 mg/mL neutral protease (Worthington), 1 mg/mL collagenase 1 (Worthington) and ProtectRNA (Sigma) in RNase-free PBS. The inflated tongue was immersed in the enzyme solution and incubated at 37°C for 10 mins. The tongue was cut in half lengthways, the mucosa was peeled from each half, rinsed in PBS and then placed in RNAlater (Ambion). The tissue was homogenized with a 1.5 mL tube pestle, followed by treatment with QiaShredder (Qiagen). RNA was extracted from the tissue using an RNeasy Mini Plus kit (Qiagen).
Library preparation was performed using QuantSeq 3’ mRNA-Seq kit

treatment_protocol: Tamoxifen (chemical inducer of conditional Cre recombination) was administered to all mice by IP injection daily for four consequetive days. On the fifth day, the mice were harvested.

value: Tongue epithelium

value: Keratinocyte

value: K14CreERT2 IRE1 F/F

value: Tamoxifen


title: Kidney_WT_CBP_SK124_rep3

value: 40 ng/g bw SK-124


title: ScADR4b_S37

value: F


title: Kidney_WT_CBP_Veh_rep2


title: K14CreERT2 IRE1 F/F_rep 1


title: yMH007 (containing dChr) - RNA-seq rep3

description:
Baker yeast S. cerevisiae
HM240_3


title: Kidney_WT_CBP_Veh_rep1


title: Kidney_WT_CBP_SK124_rep2


title: Kidney_WT_CBP_FGF23YKL_rep3


title: ScADR4c_S38

value: LabControl


title: WT-W3.5 replicate 3

city: Shanghai

first: Jin

last: Shi

address: 800 Dongchuan Rd

department: Life Science and technology Department

institute: Shanghai Jiaotong University

data_processing:
The quality of raw sequencing reads for all samples was examined using FastQC
Clean reads were mapped to the barley reference genome (GCA_004114815.1) using HISAT2 aligner (version 2.0.0) with default parameters except that ‘--dta’ was set.
FPKM was normalized using HTSeq (version 0.11.2).
Assembly: GCA_004114815.1
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Hordeum vulgare

source_name: inflorescence

growth_protocol: normal growth condition

extract_protocol:
Total RNA was extracted from 15–20 spikes for each of three biological replicates using TRIzol (Invitrogen) and purified using a RNeasy Micro Kit (Qiagen) following the manufacturer’s instructions.
Library preparation was performed using 1μg of high-integrity total RNA (RNA integrity number > 8) using the TruSeq RNA Library Preparation Kit v.2 (Illumina, RS-122-2101 and RS-122-2001), following the manufacturer’s instructions.

tag: cultivar

value: Golden Promise

value: inflorescence

value: wild type

tag: developmental stage

value: W3.5 stage


title: ScADR3b_S35

value: M

value: ParabolicFlight


title: Kidney_WT_CBP_SK124_rep1

value: wild type C57BL6

value: CBP (Cell Signaling, D6C5, 7389, lot# 7)


title: Kidney_WT_CBP_PTH30_rep2


title: IRE1F/F_rep 2


title: ScADR3c_S45


title: WT-W2.0 replicate 3

value: W2.0 stage


title: Kidney_WT_CBP_PTH30_rep1

value: 230 ng/g bw PTH (30 min)


title: Kidney_WT_CBP_FGF23YKL_rep1

value: 50 ng/g bw FGF23 + 30 ng/g bw YKL-05-099


title: WT-W3.5 replicate 2


title: WT-W3.5 replicate 1


title: K14CreERT2 IRE1 F/F_rep 3

value: Tongue epithelium

value: Keratinocyte


title: IRE1F/F_rep 3

value: Tamoxifen


title: HiC of Dmrt1 -/- P7 Sertoli Cells rep 2b

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
HiC_Dmrt1_null_null_rep_2b
AB_Compartments_Dmrt1_null_null_p7_Sertoli.bigWig
HiC_interactions_Dmrt1_null_null_p7_Sertoli.bedpe

data_processing:
For each of the experiments, reads were trimmed using Trim Galore (v0.6.0) and cutadapt (v1.18) and assessed for quality with FastQC (v0.11.8). STAR (v2.7.2a), BWA mem (v0.7.12) and HiC-Pro (v3.1.0) were used to map transcriptomic (RNA-seq), genomic (ChIP-seq),and 3D (Hi-C) trimmed reads to the GRCm38 (mm10) genome respectively
The GENCODE M25 gene annotation set was used to estimate strand-specific gene expression data in the RNA-seq data with the Bioconductor package RSubread (v1.28.1) and to assign the locations of nearby genes in the ChIP-seq datasets. For paired-end ChIP-seq experiments, duplicated reads were removed with Picard MarkDuplicates (v2.17.10) and low quality reads (MAPQ < 55) or reads that mapped to the mitochondrial genome were removed with SAMtools (v1.0).
Assembly: GRCm38/mm10
Supplementary files format and content: Tables of expression counts and bigWig Coverage files and called HiC compartments and interactions.

source_name: Sertoli Cells

extract_protocol: Hi-C were performed for each cell type on  about 1 million primary granulosa cells using the Arima Hi-C Kit (#A510008).  Cells were fixed in 2% methanol-free formaldehyde in PBS at RT for ten min. with occasional mixing then quenched by addition of glycine to 0.125M with occasional mixing for 5 min.. Cells were placed on ice for 15 min. prior to washing with 1X PBS and stored at -80o C.  Hi-C was performed according to Arima Genomics (Document part # A160134 v00).  Sequencing libraries were prepared using the KAPA Hyper Prep Kit and xGen Duplex Seq adapters (Integrated DNA Techologies) according to Arima Genomics (Document part # A160139 v00).

value: Sertoli Cells

value: Mixed 129Sv and C57Bl/6J

tag: age

value: Dmrt1 -/-


title: Kidney_WT_CBP_FGF23YKL_rep2


title: ScADR2b_S33


title: ScADR2c_S44

value: LabControl


title: Kidney_WT_CBP_FGF23PTH30_rep3

value: 50 ng/g bw FGF23 + 230 ng/g bw PTH (30 min)


title: IRE1F/F_rep 1


title: WT-W2.0 replicate 2

value: Golden Promise

value: inflorescence

value: wild type


title: WT-W2.0 replicate 1


title: mutant-W3.5 replicate 3

value: mutant

value: W3.5 stage


title: ScADR3a_S34

value: M

value: GroundControl


title: ScADR2a_S32


title: HiC of Dmrt1 -/- P7 Sertoli Cells rep 1b

description:
HiC_Dmrt1_null_null_rep_1b
AB_Compartments_Dmrt1_null_null_p7_Sertoli.bigWig
HiC_interactions_Dmrt1_null_null_p7_Sertoli.bedpe


title: Kidney_WT_CBP_FGF23_rep3

value: wild type C57BL6

value: 50 ng/g bw FGF23

value: CBP (Cell Signaling, D6C5, 7389, lot# 7)


title: ScADR1c_S31


title: mutant-W3.5 replicate 1


title: FOXL2 ChIP-seq of Dmrt1 +/- P28 XY Gonad rep 1

source_name: gonad

extract_protocol: Cells were fixed with 1% methanol-free formaldehyde in PBS (Thermo scientific #28906) for five minutes at RT with rotation.  Fixation was stopped by addition of glycine to 0.125M and rotation at RT for 10 min.  After pelleting, cells were washed in PBS and stored at -80o C until use.  Sertoli cell ChIP was performed with about 2.5 million cells and granulosa cell ChIP with about 1 million cells.  Nuclei were prepared from the fixed cells and chromatin was sheared to an average size of 300-400 bp in a Covaris S220 according to the manufacturer’s recommendations.  After shearing, the lysate was diluted 1:3 with complete DOC RIPA (37) and the sample was centrifuged at 21,000g for ten minutes at 4o C to pellet any insoluble material.  The supernatant was transferred to a fresh siliconized tube and the ChIP was initiated with the addition of ~1 ug of the relevant antibody and rotated at 4o C overnight.  Samples were then spun at 21,000g for 10 min. to pellet insoluble material and supernatant was mixed with 20 ul Protein A Dynabeads (Invitrogen, 10002D) previously blocked with BSA and yeast tRNA to inhibit non-specific binding.  After incubation at 4o C for 60 min. with rotation to allow association of protein A with the antibody, beads were applied to a magnet and washed sequentially as described previously (37).  After elution and cross link reversal, sequencing libraries were prepared using the Hyper Prep Kit (KAPA Biosystems, KK8502). Whole gonad ChIP-seq was performed essentially the same as for primary cells ChIP-seq except gonads from 2-3 animals were pooled and fixed in 1% paraformaldehyde (Electron Microscopy Sciences #15710) for 10 min. (ESR2 and FOXL2) or fixed in 2 mM disuccinimidyl glutarate (DSG, ThermoFisher Scientific #20593) at RT for 45 min. followed by 1% paraformaldehyde fixation at RT for 15 minutes (SOX9).  After quenching the fix with 0.125M glycine, chromatin was sheared to an average size of 300-500 bp using a tip sonicator.

value: gonad

value: Dmrt1 +/-


title: FOXL2 ChIP-seq of Dmrt1 -/- P28 XY Gonad rep 1


title: Kidney_WT_CBP_FGF23_rep2


title: ScADR1b_S30

value: ParabolicFlight


title: ScADR1a_S29


title: Kidney_WT_CBP_FGF23_rep1


title: ESR2 ChIP-seq of Dmrt1 R111G/+ P28 XY Gonad rep 1

value: Mixed 129Sv and C57Bl/6J

value: Dmrt1 R111G/+


title: Kidney_WT_CBP_FGF23PTH30_rep2


title: Kidney_WT_CBP_125YKL_rep3


title: LRH1 ChIP-seq of Dmrt1 +/- P28 XY Gonad rep 1


title: mutant-W2.0 replicate 1

value: W2.0 stage


title: HIGH_4

city: London

first: Holly

middle: T

last: Philpott

state: Ontario

address: 1551 Richmond St

institute: Western University

description: synovial tissue, cyclic tensile strain, 30 mins, high-frequency

data_processing:
FASTA files concatenated to form final FASTq files
Sequences were aligned and sorted by coordinates to NCBI hg38 version 98 using STAR aligned (version 0.7.0).
Quanification of genes was performed using featureCounts (v1.6.3)
DESeq2 was used to normalize feature counts and to find differentially expressed genes
Assembly: NCBI human genome build 38 version 98
Supplementary files format and content: tab-delimited text files include nromalized counts (DESeq2) for each sample and differential gene expression values for LOW vs CONTROL or HIGH vs CONTROL

source_name: tissue

growth_protocol: Tissue samples were maintained in a temperature controlled fluid chamber at 37 degrees Celsius, in DMEM,  for the duration of the tensile strain protocol (30 minutes) and then incubated in fresh DMEM for 6 hours before RNA was isolated

extract_protocol:
RNA was isolated using the Direct-zol RNA Microprep RNA purification Kit (Zymo Research). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina)  following manufacturer's protocols.

treatment_protocol: Cyclic tensile strain  - 3 experimental conditions (static control, low-frequency (0.3 Hz), and high-frequency (1.0 Hz). Tensile stain was carried out in uniaxial direction for 30 minutes

value: tissue

value: synovial tissue

value: high-frequency strain

tag: time

value: 30 minutes


title: ESR2 ChIP-seq of Dmrt1 -/- P28 XY Gonad rep 1

tag: tissue

value: Dmrt1 -/-


title: Kidney_WT_CBP_125YKL_rep2


title: Kidney_WT_CBP_FGF23PTH30_rep1

value: 50 ng/g bw FGF23 + 230 ng/g bw PTH (30 min)


title: mutant-W3.5 replicate 2

value: Golden Promise

value: inflorescence

value: mutant

value: W3.5 stage


title: mutant-W2.0 replicate 3


title: HIGH_3


title: HIGH_6


title: LRH1 ChIP-seq of Dmrt1 R111G/+ P28 XY Gonad rep 1


title: HIGH_5


title: E12-5 primitive bladder [E12_5_4]

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

country: Germany

institute: Georg-Speyer-Haus

data_processing:
50 million unique mapped paired-end reads were obtained from each RNA-seq experiment. The reads were aligned using STAR aligner with default settings.
Read count was calculated with GenomicFeatures Bioconductor package.
Calculation and normalization of “transcripts per kilobase million (TPM)” accounting for reads per kilobase (RPK) was performed using in house R script.
Genome_build: mm10
Supplementary_files_format_and_content: Data represented TPM values to ENSMBLIDs for each time point and replicate

source_name: primitive bladder

growth_protocol: Mice were time mated and the embryos removed from the mother at the desiganted time points.

extract_protocol:
Qiazol combined with RNAeasy Mini plus kit
TruSeq RNA Library Prep Kit v2

treatment_protocol: wild type CD-1 / SWISS strain mice

value: SWISS

value: primitive bladder


title: HIGH_2


title: Kidney_WT_CBP_125YKL_rep1

value: wild type C57BL6

value: CBP (Cell Signaling, D6C5, 7389, lot# 7)


title: E15-5 bladder [E15_5_4]

source_name: bladder

value: bladder


title: mutant-W2.0 replicate 2


title: E12-5 primitive bladder [E12_5_3]


title: LRH1 ChIP-seq of Dmrt1 -/- P28 XY Gonad rep 1

value: gonad

value: Mixed 129Sv and C57Bl/6J


title: E15-5 bladder [E15_5_2]


title: ESR2 ChIP-seq of Dmrt1 +/- P28 XY Gonad rep 1

value: Dmrt1 +/-


title: Kidney_WT_CBP_125PTH30_rep3


title: E15-5 bladder [E15_5_3]


title: LRH1 ChIP-seq of Adult Ovary rep 1

value: Adult

value: Wild Type


title: Kidney_WT_CBP_125PTH30_rep1


title: DMRT1 ChIP-seq of Dmrt1 R111G/+ P3 Gonad rep 2

description:
testis_p3_R111G_WT_N14_Dmrt1ChIP_Index8
DMRT1_ChIP_Dmrt1_R111G_wt_p28_XY_gonad.bigWig

value: Dmrt1 R111G/+


title: E12-5 primitive bladder [E12_5_1]


title: LOW_6

description: synovial tissue, cyclic tensile strain, 30 mins, low-frequency

value: tissue

value: synovial tissue

value: low-frequency strain

value: 30 minutes


title: Kidney_WT_CBP_125_rep3


title: Kidney_WT_CBP_125_rep2


title: Kidney_WT_CBP_125PTH30_rep2


title: E10-5 URG [E10_5_4]

source_name: Urogenital ridge

value: Urogenital ridge


title: LOW_5


title: Kidney_WT_BRD4_YKL_rep3

value: BRD4 (Bethyl Labs, A700-004, lot# 3)


title: DMRT1 ChIP-seq of Dmrt1 R111G/- P3 Gonad rep 2

description:
testis_p3_R111G_null_N11_Dmrt1ChIP_Index5
DMRT1_ChIP_Dmrt1_R111G_null_p28_XY_gonad.bigWig

value: Dmrt1 R111G/-


title: HIGH_1

value: high-frequency strain


title: Kidney_WT_CBP_125_rep1

value: wild type C57BL6


title: E10-5 URG [E10_5_3]

value: SWISS


title: DMRT1 ChIP-seq of Dmrt1 R111G/+ P3 Gonad rep 1

description:
testis_p3_R111G_WT_N10_Dmrt1ChIP_Index4
DMRT1_ChIP_Dmrt1_R111G_wt_p28_XY_gonad.bigWig


title: LOW_2


title: Kidney_WT_BRD4_YKL_rep2


title: DMRT1 ChIP-seq of Dmrt1 +/- P3 Gonad rep 1

description:
testis_p3_WT_null_N9_Dmrt1ChIP_Index3
DMRT1_ChIP_Dmrt1_WT_null_p28_XY_gonad.bigWig


title: CONTROL_6

description: synovial tissue, static control, 30 mins

value: static control


title: Kidney_WT_BRD4_YKL_rep1


title: Kidney_WT_BRD4_Veh_rep3

value: vehicle (EtOH, PBS)


title: DMRT1 ChIP-seq of Dmrt1 +/- P3 Gonad rep 2

description:
testis_p3_WT_null_N12_Dmrt1ChIP_Index6
DMRT1_ChIP_Dmrt1_WT_null_p28_XY_gonad.bigWig

value: gonad

value: Mixed 129Sv and C57Bl/6J


title: DMRT1 ChIP-seq of Dmrt1 -/- P3 Gonad rep 2

description:
testis_p3_null_null_N13_Dmrt1ChIP_Index7
DMRT1_ChIP_Dmrt1_null_null_p28_XY_gonad.bigWig

value: Dmrt1 -/-


title: LOW_3


title: Kidney_WT_BRD4_Veh_rep2


title: embryo  control 3

city: Verona

first: Nicola

last: Vitulo

state: Verona

address: Ca' Vignal 1, Strada Le Grazie 15

department: Department Biotechnology

country: Italy

institute: University of Verona

description: AFN

data_processing:
Adapters were trimmed using cutadapt software and reads shorter than 16bp were removed
Reads were aligned on the reference mouse genome (GTCm38/mm10 version) downloaded from Ensembl (http://www.ensembl.org/) using a two-step procedure.
Reads were aligned using STAR program. All reads that did not align were realigned with bowtie using a local alignment strategy
Gene expression was quantified using the Ensembl gene annotation, version 75, with htseq-count program
Count matrix was normalized considering the GC content biases and the different coverage depth using full quantile normalization implemented EDASeq R package
Genome_build: GTCm38/mm10 version
Supplementary_files_format_and_content: Normalized gene count matrix

source_name: embryo

extract_protocol:
Embryos were collected from females in synchronized pregnancies at 14.5 days post conception. Fetal livers were smashed by gentle pipetting in ice-cold PBS 1 x plus 2% FBS and cell suspension was filtered through a 70um cell strainer. Cells were counted and stained with Fc Block antibody followed by staining with FITC-conjugated anti-TER119 antibody. After wash and resuspension in an appropriate PBS volume, erythroid cells were sorted through BD FACS ARIA. Dead cells and debris were excluded by gating on forward scatter and side scatter morphologic parameters. RNA was prepared using QIAGEN RNeasy kit (#74106). Total RNA samples were processed according to DynabeadsTM mRNA DIRECTTM Purification Kit (Ambion) to isolate mRNA.
The template library was prepared using the Ion Total RNA-Seq Kit v2 (Life Technologies). Quantity and size distribution of the library were analyzed using the Agilent Bioanalyzer 2100 DNA HS chip. Emulsion PCR using 10microl of 100pM library was performed using a OneTouch 2 instrument (Life Technologies) with an Ion PI Template OT2 200 kit following the manufacturer’s instructions. The enrichment of template library was achieved using the Ion OneTouch ES enrichment system (Life Technologies). Ion Proton sequencer and IPv2 chip were prepared according to the manufacturer’s recommendations.

treatment_protocol: untreated

value: fetal liver

tag: cells

value: purified TER119+ erythroid cells

value: prenatal 14.5 days post conception

value: control Csnk2b+/+ Vav+/Cre


title: DMRT1 ChIP-seq of Dmrt1 -/- P3 Gonad rep 1

description:
testis_p3_null_null_N7_Dmrt1ChIP_Index1
DMRT1_ChIP_Dmrt1_null_null_p28_XY_gonad.bigWig


title: E10-5 URG [E10_5_1]


title: CONTROL_4

value: tissue

tag: cell type

value: synovial tissue


title: LOW_1

value: low-frequency strain

value: 30 minutes


title: embryo  KO 2

description: AFQ

value: KO Csnk2bfl/fl Vav+/Cre


title: LOW_4


title: embryo  KO 1

description: AFP


title: embryo  control 1

description: AFL


title: CONTROL_5


title: CONTROL_3


title: CONTROL_2


title: DMRT1 ChIP-seq of Dmrt1 R111G/- P3 Gonad rep 1

description:
testis_p3_R111G_null_N8_Dmrt1ChIP_Index2
DMRT1_ChIP_Dmrt1_R111G_null_p28_XY_gonad.bigWig

value: Dmrt1 R111G/-


title: Kidney_WT_BRD4_Veh_rep1

value: wild type C57BL6

value: BRD4 (Bethyl Labs, A700-004, lot# 3)


title: CONTROL_1

value: static control


title: RNA-seq of Dmrt1 R111G/+ P3 Gonad rep 1

description:
Dmrt1 R111G/+ p3 Gonad rep 1
Gene_Expression_Count_Table.csv.gz

molecule: polyA RNA

extract_protocol: Cells or tissues were harvested into 1 ml Trizol reagent and stored at -80o C.  Total RNA was prepared according to Trizol reagent manufacturer’s protocols and further cleaned up using RNAeasy kit protocols and reagents (Qiagen).  RNA was quantified via Qubit RNA assay, and 500 ng total RNA per sample were used in stranded mRNA-seq library preparation (KAPA Biosystems, KK8481) for Illumina sequencing.

value: Dmrt1 R111G/+


title: RNA-seq of Dmrt1 R111G/- P3 Gonad rep 3

description:
Dmrt1 R111G/- p3 Gonad rep 3
Gene_Expression_Count_Table.csv.gz

value: gonad


title: RNA-seq of Dmrt1 R111G/- P3 Gonad rep 2

description:
Dmrt1 R111G/- p3 Gonad rep 2
Gene_Expression_Count_Table.csv.gz

value: Mixed 129Sv and C57Bl/6J


title: RNA-seq of Dmrt1 R111G/+ P3 Gonad rep 3

description:
Dmrt1 R111G/+ p3 Gonad rep 3
Gene_Expression_Count_Table.csv.gz


title: RNA-seq TE Middle Pregnancy sample4 [M4_TE]

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
Bases calling was performed with bcl2fastq software (version 2.17).
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
Assembly: hg19
Supplementary files format and content: Matrix table with gene expression level for every gene

source_name: blastocyst

extract_protocol:
Biopsy was performed on the heated stage of an IX-73 microscope (Olympus, Japan), equipped with micromanipulation (Narishige Group, Japan) and an infrared diode laser (Saturn 5TM Laser system; CooperSurgical, Inc., Japan), in dishes prepared with droplets of HEPES-buffered calcium/magnesium-free medium (Sage In-Vitro Fertilization, Inc., USA) and biopsy medium (1062; Origio, Denmark). A diode laser was used to assist the opening of a 10–20 μm hole in the zona pellucida by 2–4 laser shots. ICM biopsy was performed using a glass pipette (PIN20-20FT; PRIME TECH LTD., Japan) either by laser-assisted removal of a small area of the TE layer on the opposite side of the ICM or by directly introducing the biopsy pipette into the blastocoel cavity and aspiration of the ICM cells on the TE layer. TE biopsies were performed by aspirating cells from the TE layer removed during ICM biopsy or newly collected cells from the TE layer after ICM removal using a pipette. In the biopsies used in this study, 10–20 cells were collected for both ICM and TE. Biopsy samples were transferred to a PCR tube (FG-021F; NIPPON Genetics Co., Ltd, Japan) containing 0.5 µL of phosphate-buffered saline (PBS) and frozen. The frozen samples were stored at -80 °C until RNA-seq.
RNA-seq libraries of all biopsy samples were generated using a SMART-Seq HT Kit according to the manufacturer’s instructions (TAKARA, 634436, Japan). Library construction was performed using a Nextera XT DNA Library Prep Kit (Illumina, FC-131-1024, USA) with 200 pg of cDNA. The libraries were sequenced on a NextSeq 500 with single-end 75-bp reads (Illumina).

tag: expectation of pregnancy

value: Middle

value: Trophectoderm

value: wild type

value: blastocyst


title: RNA-seq ICM Middle Pregnancy sample4 [M4_ICM]

value: Inner cell mass


title: Kidney_WT_BRD4_PTH30_rep3

value: 230 ng/g bw PTH (30 min)


title: RNA-seq of Dmrt1 R111G/- P3 Gonad rep 1

description:
Dmrt1 R111G/- p3 Gonad rep 1
Gene_Expression_Count_Table.csv.gz


title: RNA-seq of Dmrt1 -/- P3 Gonad rep 3

description:
Dmrt1 -/- p3 Gonad rep 3
Gene_Expression_Count_Table.csv.gz

value: Dmrt1 -/-


title: RNA-seq of Dmrt1 R111G/+ P3 Gonad rep 2

description:
Dmrt1 R111G/+ p3 Gonad rep 2
Gene_Expression_Count_Table.csv.gz


title: Kidney_WT_BRD4_FGF23_rep3

value: 50 ng/g bw FGF23


title: embryo  control 2

description: AFM

value: fetal liver

value: purified TER119+ erythroid cells

value: prenatal 14.5 days post conception

value: control Csnk2b+/+ Vav+/Cre


title: Kidney_WT_BRD4_SK124_rep2

value: wild type C57BL6

value: 40 ng/g bw SK-124

value: BRD4 (Bethyl Labs, A700-004, lot# 3)


title: RNA-seq of Dmrt1 -/- P3 Gonad rep 2

description:
Dmrt1 -/- p3 Gonad rep 2
Gene_Expression_Count_Table.csv.gz

value: gonad


title: Tissue-nanopipette-020719-NV1 [rna-24]

city: Santa Cruz

first: John

last: Stanley

state: CA

address: 1156 High St

institute: UCSC

library_source: transcriptomic single cell

data_processing:
Shell Script with python.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic-0.36.
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR aligner.
Read count extraction was performed using HTSeq-count and gene annotation conversion done with Python and GencodeV37 gene-type annotations.
Assembly: hg38
Supplementary files format and content: *.tab: Tab-delimited text files include read counts for each Sample.

source_name: breast cancer tissue section

extract_protocol:
NVIGEN nanoparticle mRNA isolation protocol.
cDNA libraries for RNA-seq were prepared using NVIGEN sc-RNA-Seq library protocol.

value: breast cancer tissue section


title: Tissue-nanopipette-directRT [rna-12]


title: Tissue-nanopipette-directRT [rna-13]


title: RNA-seq of Dmrt1 -/- P3 Gonad rep 1

description:
Dmrt1 -/- p3 Gonad rep 1
Gene_Expression_Count_Table.csv.gz

value: Mixed 129Sv and C57Bl/6J


title: Tissue-nanopipette-directRT [rna-14]


title: Kidney_WT_BRD4_SK124_rep3


title: Kidney_WT_BRD4_FGF23_rep2


title: Tissue-nanopipette-directRT [rna-16]


title: Tissue-nanopipette-directRT [rna-15]


title: Kidney_WT_BRD4_PTH30_rep1


title: RNA-seq TE Middle Pregnancy sample1 [M1_TE]

value: Middle

value: Trophectoderm


title: Kidney_WT_BRD4_PTH30_rep2


title: Kidney_WT_BRD4_125_rep3


title: RNA-seq ICM Middle Pregnancy sample3 [M3_ICM]

value: wild type

value: blastocyst


title: Kidney_WT_BRD4_SK124_rep1


title: Kidney_WT_BRD4_125_rep2


title: Tissue-nanopipette-020719-NV1 [rna-21]


title: RNA-seq TE Middle Pregnancy sample3 [M3_TE]


title: Tissue-nanopipette-directRT [rna-11]


title: RNA-seq ICM Middle Pregnancy sample2 [M2_ICM]

value: Inner cell mass


title: Cell-nanopipette-020719-NV1 [rna-42]

tag: cell line

value: breast cancer


title: RNA-seq of Dmrt1 +/- P3 Gonad rep 3

description:
Dmrt1 +/- p3 Gonad rep 3
Gene_Expression_Count_Table.csv.gz

tag: genotype

value: Dmrt1 +/-


title: RNA-seq TE Low Pregnancy sample3 [L3_TE]

value: Low


title: RNA-seq ICM Low Pregnancy sample4 [L4_ICM]


title: Kidney_SIKTKOD2_pCREB_Veh_rep3

tag: treatment

value: vehicle (EtOH, PBS)


title: RNA-seq ICM Middle Pregnancy sample1 [M1_ICM]


title: RNA-seq TE Middle Pregnancy sample2 [M2_TE]


title: Tissue-nanopipette-020719-NV1 [rna-23]


title: Kidney_WT_BRD4_FGF23_rep1

value: 50 ng/g bw FGF23


title: RNA-seq TE Low Pregnancy sample4 [L4_TE]


title: RNA-seq of Dmrt1 +/- P3 Gonad rep 2

description:
Dmrt1 +/- p3 Gonad rep 2
Gene_Expression_Count_Table.csv.gz

tag: strain


title: Tissue-nanopipette-020719-NV1 [rna-22]


title: RNA-seq of Dmrt1 +/- P3 Gonad rep 1

description:
Dmrt1 +/- p3 Gonad rep 1
Gene_Expression_Count_Table.csv.gz


title: Kidney_SIKTKOD2_Input_rep1


title: Tissue-nanopipette-050320-NV1 [rna-31]


title: Kidney_SIKTKOD2_pCREB_Veh_rep2


title: RNA-seq of Dmrt1 -/- P7 Sertoli Cells rep 2

description:
Dmrt1 -/- p7 Sertoli rep 2
Gene_Expression_Count_Table.csv.gz

value: Sertoli Cells

value: Dmrt1 f/f; CAG-Stopflox-tdTomato; Dhh-Cre


title: RNA-seq ICM Low Pregnancy sample3 [L3_ICM]


title: RNA-seq of Dmrt1 -/- P7 Sertoli Cells rep 1

description:
Dmrt1 -/- p7 Sertoli rep 1
Gene_Expression_Count_Table.csv.gz


title: RNA-seq of Dmrt1 +/+ P7 Sertoli Cells rep 1

description:
Dmrt1 +/+ p7 Sertoli rep 1
Gene_Expression_Count_Table.csv.gz

value: Dmrt1 f/+; CAG-Stopflox-tdTomato; Dhh-Cre


title: RNA-seq of Dmrt1 -/- P7 Sertoli Cells rep 3

description:
Dmrt1 -/- p7 Sertoli rep 3
Gene_Expression_Count_Table.csv.gz


title: Tissue-nanopipette-050320-NV1 [rna-34]


title: RNA-seq of Dmrt1 +/+ P7 Sertoli Cells rep 2

description:
Dmrt1 +/+ p7 Sertoli rep 2
Gene_Expression_Count_Table.csv.gz


title: RNA-seq ICM Low Pregnancy sample1 [L1_ICM]


title: Cell-nanopipette-020719-NV1 [RNA-41]


title: Tissue-nanopipette-020719-NV17 [rna-28]


title: RNA-seq of Dmrt1 +/+ P7 Sertoli Cells rep 3

description:
Dmrt1 +/+ p7 Sertoli rep 3
Gene_Expression_Count_Table.csv.gz


title: RNA-seq ICM Low Pregnancy sample2 [L2_ICM]


title: Tissue-nanopipette-050320-NV1 [rna-33]


title: Kidney_SIKTKOD2_CRTC2_Veh_rep3

value: CRTC2 (Bethyl Labs, A300-737A, lot# 1)


title: Tissue-nanopipette-050320-NV1 [rna-32]


title: RNA-seq TE High Pregnancy sample5 [H5_TE]

value: High


title: RNA-seq TE Low Pregnancy sample2 [L2_TE]


title: RNA-seq TE Low Pregnancy sample1 [L1_TE]


title: Kidney_SIKTKOD2_pCREB_Veh_rep1


title: RNA-seq of Dmrt1 R111G/+ P28 Gonad rep 3

description:
Dmrt1 R111G/+ p28 Gonad rep 3
Gene_Expression_Count_Table.csv.gz

value: gonad

value: Dmrt1 R111G/+


title: RNA-seq of Dmrt1 R111G/+ P28 Gonad rep 2

description:
Dmrt1 R111G/+ p28 Gonad rep 2
Gene_Expression_Count_Table.csv.gz

value: Mixed 129Sv and C57Bl/6J


title: Tissue-nanopipette-020719-NV17 [rna-26]

value: breast cancer tissue section


title: Kidney_SIKTKOD2_CRTC2_Veh_rep2


title: Tissue-nanopipette-020719-NV17 [rna-27]


title: Kidney_SIKTKOD2_CRTC2_Veh_rep1


title: RNA-seq TE High Pregnancy sample4 [H4_TE]

value: Trophectoderm

value: wild type


title: Kidney_SIKTKOD2_CBP_Veh_rep2

value: CBP (Cell Signaling, D6C5, 7389, lot# 7)


title: RNA-seq ICM High Pregnancy sample5 [H5_ICM]

value: Inner cell mass

value: blastocyst


title: Kidney_SIKTKOD2_CBP_Veh_rep3


title: RNA-seq of Dmrt1 -/- P28 Gonad rep 2

description:
Dmrt1 -/- p28 Gonad rep 2
Gene_Expression_Count_Table.csv.gz

value: Dmrt1 -/-


title: RNA-seq of Dmrt1 -/- P28 Gonad rep 1

description:
Dmrt1 -/- p28 Gonad rep 1
Gene_Expression_Count_Table.csv.gz


title: Kidney_SIKTKOD2_CBP_Veh_rep1

value: vehicle (EtOH, PBS)


title: RNA-seq of Dmrt1 R111G/+ P28 Gonad rep 1

description:
Dmrt1 R111G/+ p28 Gonad rep 1
Gene_Expression_Count_Table.csv.gz


title: Tissue-nanopipette-050320-NV17 [rna-36]


title: RNA-seq of Dmrt1 -/- P28 Gonad rep 3

description:
Dmrt1 -/- p28 Gonad rep 3
Gene_Expression_Count_Table.csv.gz


title: Tissue-nanopipette-050320-NV17 [rna-35]


title: RNA-seq TE High Pregnancy sample2 [H2_TE]


title: RNA-seq of Dmrt1 +/- P28 Gonad rep 2

description:
Dmrt1 +/- p28 Gonad rep 2
Gene_Expression_Count_Table.csv.gz

value: Dmrt1 +/-


title: Tissue-nanopipette-020719-NV17 [rna-25]


title: RNA-seq ICM High Pregnancy sample4 [H4_ICM]


title: Kidney_SIKCTRLD2_Input_rep1


title: Kidney_SIKCTRLD2_CRTC2_Veh_rep3


title: RNA-seq of Dmrt1 +/- P28 Gonad rep 3

description:
Dmrt1 +/- p28 Gonad rep 3
Gene_Expression_Count_Table.csv.gz


title: Tissue-nanopipette-050320-NV17 [rna-38]


title: Ctrl-Tissue-NV13 [rna-44]


title: Tissue-nanopipette-050320-NV17 [rna-37]


title: Kidney_SIKCTRLD2_pCREB_Veh_rep3


title: Kidney_SIKCTRLD2_CRTC2_Veh_rep2


title: RNA-seq ICM High Pregnancy sample1 [H1_ICM]


title: Kidney_SIKCTRLD2_pCREB_Veh_rep2


title: RNA-seq TE High Pregnancy sample3 [H3_TE]


title: RNA-seq of Dmrt1 +/+ P28 Gonad rep 1

description:
Dmrt1 +/+ p28 Gonad rep 1
Gene_Expression_Count_Table.csv.gz

value: Dmrt1 +/+


title: RNA-seq ICM High Pregnancy sample2 [H2_ICM]


title: Kidney_SIKCTRLD2_pCREB_Veh_rep1


title: Ctrl-Tissue-3day-NV13 [rna-46]


title: Ctrl-Tissue-directRT [rna-18]


title: RNA-seq ICM High Pregnancy sample3 [H3_ICM]


title: RNA-seq TE High Pregnancy sample1 [H1_TE]


title: Ctrl-MCF7-3day-NV13 [rna-45]

value: breast cancer


title: HL60-V-D-1

city: Guangzhou

first: Bing

last: Long

address: No. 600 Tianhe Road

department: Department of Hematology

institute: The Third Affiliated Hospital, Sun Yat-sen University

description: HL60 treated with VC and DZNep

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

source_name: human acute promyelocytic leukemia cell line

growth_protocol: The human leukemia cell lines HL60 were grown in RPMI 1640 medium (GIBCO) with 10% FBS.

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

treatment_protocol: HL60 cells were treated by PBS, Vc or/and DZNep for 72 hours.

value: VC and DZNep treatment


title: RNA-seq of Dmrt1 +/- P28 Gonad rep 1

description:
Dmrt1 +/- p28 Gonad rep 1
Gene_Expression_Count_Table.csv.gz


title: Kidney_SIKCTRLD2_CRTC2_Veh_rep1

value: CRTC2 (Bethyl Labs, A300-737A, lot# 1)


title: delta0.7 24h rep1

city: Edinburgh

first: Sally

last: Lowell

state: Denmark

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

data_processing:
[Trimming]  Cutadapt (version cutadapt- 1.9.dev2). Trimmed for quality at the 3' end using a quality threshold of 30. Reads after trimming were required to have a minumum lenght of 35.
[Alignment]  STAR (version 2.5.2b); specifying paired-end reads and the option --outSAMtype BAM unsorted. .
[Read counting]  featureCounts (version 1.5.1). Strandness was set to 'reverse' and a minumum alignment quality of 10 was specified.
FPKM values were generated using rpkm () function of edgeR (version 3.16.5)
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: csv file includes fpkm values for each gene in all samples.

source_name: Embryonic stem cells

growth_protocol: Both E14Tg2a and delta 0.7 cells were cultured in serum-free N2B27 medium containing 2i and LIF prior to the differentiation initiation.

extract_protocol:
RNA extraction was performed with Qiagen Rnesy Plus Mini Kit according to the manufacturer's instructions.
1µg total RNA was used for the purification of mRNAs with oligo dT beads. Then, the libraries were prepared with NEBNext UltraII RNA Library Prep Kit according to the manufacturer's instructions.

treatment_protocol: For the induction of differentiation, cells were plated on fibronectin coated plates with serum-free N2B27 medium containing Activin, bFGF and KOSR. Then cells were cultured under this condition for 12h or 24h.

value: Homozygous deletion of 0.7kb Tcf15 regulatory region


title: 3217

city: Vancouver

first: Wan

middle: L

last: Lam

address: 675 West 10th Ave

institute: BC Cancer Research Centre

data_processing:
Library strategy: 16S rRNA seq
Sequencing data was processed as forward, single-end reads. Forward reads were trimmed to a total length of 210 bases, such that 75% of reads at each base had a PHRED score greater than 25.
Amplicon sequence variants (ASVs) were denoised using the DADA2 denoising algorithm (v2019.1.0)
Taxonomy was assessed in relation to the SILVA reference database (version 132) using BLAST on the QIIME2 software platform
Assembly: SILVA reference database (v.132)
Supplementary files format and content: CSV file containing relative frequencies of each bacterial species identified within each sample (sample ID, Kingdom, Phylum, Class, Order, Family, Genus, Species, Relative Frequency)

source_name: oral swab

extract_protocol:
DNA isolation was performed on Lesion cytology brush samples using the DNeasy Blood & Tissue Kit (QIAGEN, Hilden Germany). An enzymatic lysis buffer preparation was followed by two centrifugation/wash steps with PBS. The pellet was resuspended in PBS with 20 µl proteinase K and 4 µl of RNase A (100 mg/ml), followed by vortex and incubation. Extraction steps were conducted as per the manufacturer’s kit instructions. DNA was eluted using 50 µl nuclease free distilled water and stored at −20 °C.
A custom16S rRNA gene sequencing approach was employed. A single round of PCR (25 cycles) was done using Platinum SuperFi II DNA Polymerase–High-Fidelity PCR Enzyme for pre-amplification and custom primers targeting the V1-V3 region (515FB forward primer = GTGYCAGCMGCCGCGGTAA; 926R reverse primer= CCGYCAATTYMTTTRAGTTT) of the 16S rRNA gene. PCR products were verified visually by gel electrophoresis. Amplicon fragments were then sent to the Integrated Microbiome Resource, at Dalhousie University (https://imr.bio) and PCR-amplified using high-fidelity Phusion Plus® polymerase (New England Biolabs Inc.). Amplified DNA concentrations were then normalized, pooled, and sequenced via 6 runs on an Illumina MiSeq using 300 bp paired-end read chemistry. The sequencing runs yielded an average of at least 50,000 reads per sample.

tag: age at baseline (years)

tag: Sex

value: female

tag: ethnicity

value: white

tag: smoking status

value: ever smoker

tag: grade

value: mild dysplasia

tag: lesion site

value: tongue


title: delta0.7 12h rep1


title: HL60-D-2

description: HL60 treated with DZNep

value: DZNep treatment


title: Ctrl-Tissue-directRT [rna-17]

value: breast cancer tissue section


title: 3223

value: south asian

value: never smoker


title: RNA-seq of Dmrt1 +/+ P28 Gonad rep 3

description:
Dmrt1 +/+ p28 Gonad rep 3
Gene_Expression_Count_Table.csv.gz

value: gonad

value: Mixed 129Sv and C57Bl/6J


title: delta0.7 2iL rep1


title: HL60-V-D-2

description: HL60 treated with VC and DZNep


title: delta0.7 24h rep2


title: Uninfected rep1

city: Kunming

first: Deng-Feng

last: Zhang

address: No.32 Jiaochang Donglu Kunming 650223 Yunnan, Chin

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw reads were trimmed to remove sequencing adapters and low-quality reads with Trimmomatic
Clean reads were then aligned to the standard mouse reference genome (GRCm38) using STAR
RSEM was then used to count aligned reads that mapped to the annotated mouse genes
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text with TPM values for each gene of each sample

source_name: Uninfected rep1

extract_protocol:
Hippocampous were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

value: 30-day post PBS infection

value: hACE2 transgenic mice

tag: agent

value: Control


title: 3213

value: male

value: moderate dysplasia


title: HL60-2

description: HL60 treated with PBS

value: PBS treatment


title: Ctrl-MCF7-NV13 [rna-43]

value: breast cancer


title: Kidney_SIKCTRLD2_CBP_Veh_rep1

source_name: kidney tissue

extract_protocol:
The kidneys were isolated, rinsed with cold 1× phosphate-buffered saline, and subjected to a cross-linking reaction for 10 min with 1.5% formaldehyde. After the fixative was neutralized for 5 min with glycine (0.125 m final concentration), the kidney tissue was homogenized briefly in phosphate-buffered saline using a loose fitting Dounce pestle, and the cells were collected via 70-μm nylon cell strainers (BD Falcon). Cells were then subjected to ChIP analysis as described previously (Yamamoto H, 2003, Journal Biol Chem).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA kit (NEB, #E7645S) with the NEBNext Multiplex Oligos for Illumina (NEB, #E6440S) according to the manufacturer’s protocols. Libraries were submitted to the University of Wisconsin – Madison Biotechnology Center’s DNA Sequencing Facility (Research Resource Identifier – RRID:SCR_017759). Libraries were sequenced on a NovaSeq 6000. Paired end, 250 bp sequencing with a target of 20+ million reads was performed.

value: vehicle (EtOH, PBS)

tag: antibody

value: CBP (Cell Signaling, D6C5, 7389, lot# 7)


title: Kidney_SIKCTRLD2_CBP_Veh_rep2


title: Kidney_SIKCTRLD2_CBP_Veh_rep3


title: Uninfected rep3

source_name: Uninfected rep3

tag: age


title: 3222

value: female

value: white

value: ever smoker

value: mild dysplasia

value: tongue


title: Patient2_I1_L002_121307

city: Seattle

first: Miranda

last: Lahman

state: WA

address: 1100 Fairview Ave N

department: CRD

institute: Fred Hutchinson Cancer Research Center

data_processing:
Alignment and quantification have been done following the Cell Ranger Software Suite (2.1.0). The Cell Ranger Single-Cell Software Suite (version 2.1.0) was used to perform sample demultiplexing, barcode processing and single-cell 3' gene counting (http://10xgenomics.com/). First, raw base BCL files were demultiplexed using the cellranger mkfastq pipeline into sample-specific FASTQ files. Second, these FASTQ files were processed with the cellranger count pipeline. Each sample was analyzed separately. The Cell Ranger pipeline uses the STAR alignment software (Dobin et al., 2013) to align cDNA reads to the GRCh38 human reference genome and transgene. Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads. cellranger aggr was then used to aggregate the two samples together (Patient 1). A correction for sequencing depth was performed during the aggregation. Patient 2 data integration was performed with Seurat.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv-delimitated table

source_name: PBMC - Patient 2

extract_protocol: 10X genomics

tag: cellranger id

tag: time point


title: HL60-V-2

description: HL60 treated with VC

value: VC treatment


title: 3173

value: other

value: never smoker


title: Uninfected rep2

source_name: Uninfected rep2

tag: tissue

value: Hippocampus

value: 30-day post PBS infection


title: RNA-seq of Dmrt1 +/+ P28 Gonad rep 2

description:
Dmrt1 +/+ p28 Gonad rep 2
Gene_Expression_Count_Table.csv.gz

value: gonad

value: Mixed 129Sv and C57Bl/6J

value: Dmrt1 +/+


title: delta0.7 2iL rep2

value: Homozygous deletion of 0.7kb Tcf15 regulatory region

tag: time


title: HL60-V-1

description: HL60 treated with VC

tag: cell line


title: Infected rep1

source_name: Infected rep1

value: 30-day post viral infection

tag: genotype

value: hACE2 transgenic mice


title: 8876

value: male

value: moderate dysplasia

value: buccal or labial mucosa


title: 3046

value: white


title: delta0.7 12h rep2


title: 3012

value: soft palate


title: HL60-1

description: HL60 treated with PBS

tag: treatment

value: PBS treatment


title: E14Tg2a 24h rep1

tag: strain

value: WT


title: E14Tg2a 24h rep2


title: 3201

tag: age at baseline (years)


title: E14Tg2a 12h rep2


title: 3052

tag: Sex

value: female

value: ever smoker

value: floor of mouth


title: Infected rep3

source_name: Infected rep3

value: Hippocampus


title: E14Tg2a 12h rep1


title: Ezh2 Y641F - 234D

city: St. Louis

first: George

middle: P.

last: Souroullas

state: MO

address: 660 S. Euclid Av

department: Medicine

institute: Washington University School of Medicine

data_processing:
Encode ChIPseq pipeline 2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Melanoma

growth_protocol: Melanoma cell lines were grown in DMEM media supplemented withj 10% FBS and 1% Pen/Strep

extract_protocol:
10 million melanoma cells were harvested from tissue culture, washed and fixed with paraforaldehyde according to standard protocol. Nuclei were isolated and sonicated to shear chromatin to approximately 200bp.
Illumina Truseq ChIPseq kit

treatment_protocol: Not treated

tag: cell type

value: Melanoma

tag: chip antibody

value: Ezh2 (cell sign. 5246)


title: Infected rep2

source_name: Infected rep2


title: E14Tg2a 2iL rep1


title: Ezh2 WT - 234


title: Patient2_I1_L001_005_1213


title: Patient2_I1_L001_121307


title: Patient2_I1_L001_004_1213


title: 2108

tag: ethnicity

tag: smoking status

value: never smoker

tag: grade

value: tongue


title: 1864

value: asian

tag: lesion site


title: Patient2_I1_L001_002_1213


title: R9 progenitor cells_DAY7.5

city: Guangzhou, China

first: yunqing

last: Lin

address: Building 3, No.188 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Center for Cell Lineage and Atlas (CCLA)

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

data_processing:
Droplet-based scRNA-seq datasets were aligned and quantified using the CellRanger software package (version 4.0.0)
Datasets were subjected to Seurat3(version 3.2.3) for further analysis
To pass quality control, cells were required to have at least 200 and no more than 7500 genes detected, and less than 5% of mapped reads mapping to mitochondrial genes
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: bone marrow

growth_protocol: We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of generating  ILC-related progenitors including iLP, iILCP, iILC1/3P and iILC2P, which could further developing into mature ILCs in the Rag2-/-Il2rg-/- recipients.

extract_protocol:
Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture’s instruction.
Novaseq PE150

treatment_protocol: At day 7.5 after iHPC transplantation, we sorted the GFP+CD45.2+ Lin- cells from the bone marrow of recipients for Droplet-based scRNA-seq.  Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture’s instruction.

value: day 7.5 after iHPC transplantation

value: bone marrow of recipients

value: GFP+CD45.2+ Lin- cells


title: Patient2_I1_L001_003_1213


title: E14Tg2a 2iL rep2


title: Donor 2

city: Stanford

first: Kristina

last: Maas-Bauer

state: California

address: 269 Campus Drive

department: Blood and Marrow Transplantation

institute: Stanford University

description:
KMB2R-HWV2NBBXX
5 day old male

data_processing:
Sample demultiplexing, barcode processing, alignment to the GRCh38 assembly of the human genome, and single-cell 3′ gene counting were performed using the Cell Ranger Suite version 2.1.
The gene-barcode matrix contained 397 cells, with 383784 mean reads per cell and 1099 (984-1203) median genes per cell. Cells with unique gene counts <200 or >2500, as well as cells with >5% of mitochondrial genes were excluded from the analysis.
scRNA-sSeq analysis was performed using the Seurat R package, version 4.
Pseudotime analysis was performed using the Monocle3 package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, genes.tsv, matrix.mtx).

source_name: Thymus

extract_protocol:
Thymocytes were thawed at room temperature in RPMI 1640 containing FCS 30%, Penicillin-Streptomycin 1%, DNase I (10 ug/ml, Sigma), and heparin 20 U/ml. After washing, FACS surface staining was performed on ice, after FC blockage, using the following antibodies: Vα24 (FITC, Beckman Coulter), Vβ11 (APC, Beckman Coulter), CD3 (BV605, Biolegend), CD14 (APC Cy7, Biolegend), CD19 (APC Cy7, Biolegend), LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (Invitrogen). CD3+, Vα24+, Vβ11+, CD14-, CD19- live cells were FACS-sorted on a FACS Aria-III (BD Biosciences).
Single-cell libraries were generated from FACS-sorted human thymic iNKT cells using the Chromium Controller Single-Cell Instrument and Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x Genomics).

treatment_protocol: Thymi were obtained after being removed from 3 newborn/infant donors undergoing cardiac surgery between 5 days and 13 months of age for cardiac diseases without evidence of immunological diseases. Single cell suspensions were obtained by mechanical dissociation, washed, cryopreserved in fetal calf serum and 10% DMSO and stored in liquid nitrogen until use.

value: Thymus

value: Invariant natural killer T cells

tag: age

value: 5 days

value: male


title: 2137

value: south asian

value: mild dysplasia


title: Donor 1

description:
KMB1-HWV2NBBXX
13 month old male

value: 13 months


title: Stat3 Y641F - 234D

value: Stat3 (cell sign. 9139)


title: Patient1_I1_L001_0615

source_name: PBMC - Patient 1

tag: cellranger id


title: Donor 3

description:
KMB3-HWV2NBBXXX
5 day old child, gender unknown


title: HL60-D-1

description: HL60 treated with DZNep

value: DZNep treatment


title: Patient1_I1_L002_0615

tag: time point


title: Stat3 WT - 234

value: Melanoma

value: WT


title: 1799

value: female

value: ever smoker

value: moderate dysplasia


title: Patient2_I1_L001_001_1213


title: Regulatory small RNA CRISPR flamΔZAM-RevIH2i2 chr III

city: CLERMONT-FERRAND

first: Emilie

last: BRASSET

address: 28 place Henri dunant

country: France

institute: CNRS 6293 INSERM U1103 Université Clermont Auvergne

description: Enriched-small-RNA

data_processing: Adapters were trimmed and size selection was performed to retain only 18-29 nucleotide reads.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Argonaute-bound sRNAs were isolated with the TRApR kit according to Grentzinger et al. (2020)
gel-free protocol without size selection - Library preparation using QIAseq-miRNA kit

tag: tissue

value: ovaries

value: CRISPR flam-delta-ZAM-RevIH2i2 chr III

value: 3-6 day old female


title: Regulatory small RNA white-sKD

description: Enriched small RNA

value: Tj-Gal4-expressed dsRNA-white BDSC_3605

tag: time


title: S47_D190125_N

city: Beijing

first: Zemin

address: 5 Yiheyuan Rd, Haidian

institute: Peking University

description:
scgex.txt.gz
metadata.txt.gz

data_processing:
Cell Ranger 3.0.0 was used to quantify gene expression level and to identify TCR sequences.
A set of quality thresholds was applied to filter out low-quality cells, including detection of 200-7500 genes, 500-75000 UMI counts, and less than 10% mitochondrial reads.
UMI counts were then normalized using SCTransform with default parameters.
Assembly: GRCh38
Supplementary files format and content: text files for expression matrices and cell metadata

source_name: stomach

extract_protocol:
Tumors and adjacent non-cancer tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, GIBCO), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% fetal bovine serum (FBS, Gibco)).  Single cell suspensions were stained with antibodies against CD326 (EPCAM, BioLegend, Cat #324207) and 7-AAD (eBioscience, Cat# 00-6993-50) for FACS sorting, performed on a BD Aria SORP instrument. Expression levels of EPCAM and permeability of 7-AAD were gated by their negative controls of unstained cells and positive controls of beads stained by each antibody. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul.
Cells were loaded to the 10x Chromium Microfluidic Chips for single-cell RNA and TCR library preparation. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq-4000 sequencer with 150-bp paired-end reads.

value: stomach

tag: tissue type

value: Adjacent non-tumor normal Sample from individual D190125


title: 1608

value: white

value: floor of mouth


title: S46_D190124_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D190124


title: Regulatory small RNA CRISPR flamΔZAM-RevIH2i2 chr II

description: Enriched-small-RNA

tag: genotype

value: CRISPR flam-delta-ZAM-RevIH2i2 chr II


title: Kidney_WT_BRD4_125_rep1

city: Madison

first: Mark

last: Meyer

address: 1415 Linden Dr.

institute: University of Wisconsin-Madison

data_processing:
Data was processed from NovaSeq 6000 with bcl2fastq
ChIP-seq raw files were mapped using bowtie2 with standard parameters ( -x input file) with sam file output.
Sam files were converted with samtools into sorted and indexed bam files
HOMER was used to process the bam files, find peaks, and create the bigWig files.
bigWig files were averaged using the wiggletools mean function: wiggletools mean file1.bigWig file2.bigWig, file3.bigWig | wigToBigWig stdin chrom.sizes *_averaged.bigWig
Assembly: mm9
Supplementary files format and content: bigWig

value: wild type C57BL6

tag: treatment

tag: antibody

value: BRD4 (Bethyl Labs, A700-004, lot# 3)


title: 1512

tag: age at baseline (years)

value: male

value: tongue


title: PM9_BE2C_KO_WT3

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
RNA-seq reads were trimmed for adaptor sequence using Trimmomatic and aligned to the human genome hg38 using Bowtie/Tophat
Counts were generated using featureCounts
Normalization was performed with DESeq2
Classification of samples was performed using a customized script to train random forest classifiers based on transcriptome data from neuroblastoma studies
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated text file containing gene expression counts

source_name: LIN28B knockout

growth_protocol: BE2C (ATCC #CRL-2268) were maintained in 1:1 DMEM/F12:MEM media with 10% inactivated fetal calf serum, 1ug/ml penicillin, and 1U/ml streptomycin. Cell lines were purchased for the purposes of this study, are not among commonly misidentified cell lines (per ICLAC), and tested negative for mycoplasma contamination

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Invitrogen # 15596018) and RNeasy Plus Mini Kit (Qiagen # 74136). RNA concentration was assessed with Quant-iT™ Qubit RNA BR Assaykit (Invitrogen # Q10210)
PolyA selection with NEBNext® Poly(A) mRNA Magnetic Isolation Module. Paired-end libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to manufacturer's protocol

treatment_protocol: No specific treatment applied

tag: cell line

value: LIN28B knockout


title: Patient1_I1_L002_0214


title: S45_D190124_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D190124


title: PM8_BE2C_KO_WT2


title: S42_D190118_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D190118


title: PM7_BE2C_KO_WT1


title: 3191

tag: Sex

value: south asian

value: never smoker

value: mild dysplasia

value: soft palate


title: S44_D190123_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D190123


title: Regulatory small RNA vret-sKD

description: Enriched small RNA

value: ovaries

value: 3-6 day old female


title: Regulatory small RNA  CRISPR flamΔZAM- 2 actives ZAM copies of the X chromosome of RevIH2i2

description: Enriched-small-RNA

value: CRISPR flam-delta-ZAM- 2 actives ZAM copies of the X chromosome of RevIH2i2


title: S43_D190123_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D190123


title: 8288

value: female

value: white

value: ever smoker

value: moderate dysplasia


title: Patient1_I1_L001_0214


title: Piwi-bound small RNA yb-sKD

description: Enriched-small-RNA

extract_protocol:
Small RNA from Piwi-Immunoprecipitation and Trizol extraction
gel-free protocol without size selection - Library preparation using QIAseq-miRNA kit

value: Tj-Gal4-expressed dsRNA-Yb VDRC_110056


title: Piwi-bound small RNA Vret-sKD

description: Enriched-small-RNA


title: S48_D190125_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D190125


title: Regulatory small RNA CRISPR flamΔZAM

description: Enriched small RNA

value: CRISPR flam-delta-ZAM


title: S41_D190118_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D190118


title: PM1_BE2C_WT1

source_name: LIN28B wild type

value: LIN28B wild type


title: 3087

source_name: oral swab

value: south asian

value: never smoker

value: tongue


title: 3128


title: BE2C_KO_3

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Invitrogen # 15596018) and RNeasy Plus Mini Kit (Qiagen # 74136). RNA concentration was assessed with Quant-iT™ Qubit RNA BR Assaykit (Invitrogen # Q10210)
Paired-end libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to manufacturer's protocol

value: KO BE2C


title: PM2_BE2C_WT2


title: Small RNA CRISPR flamΔZAM

extract_protocol:
Total RNA extraction with TRIzol
Polyacrylamide gel size selection of 18-35 nucleotides, Library preparation using illumina TruSeq small RNA kit, Specific treatment anti 2S

value: ovaries


title: BE2C_KO_2


title: S40_D190103_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D190103


title: S39_D190103_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D190103


title: 1457

value: male


title: 3162

value: female

value: white


title: 3090

value: moderate dysplasia


title: BE2C_KO_1


title: PM3_BE2C_WT3


title: 3086


title: Small RNA vret-sKD

value: 3-6 day old female


title: Small RNA white-sKD

value: Tj-Gal4-expressed dsRNA-white BDSC_3605


title: 3080

value: mild dysplasia


title: Piwi-bound small RNA white-sKD

description: Enriched-small-RNA


title: S37_D181227_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D181227


title: BE2C_WT_3

value: WT BE2C


title: BE2C_WT_2


title: 3063


title: 3073

value: ever smoker


title: S34_D181026_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D181026


title: S35_D181217_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D181217


title: S38_D181227_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D181227


title: 3059

value: tongue


title: S32_D181025_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D181025


title: Small RNA RevIH2i4

value: ovaries


title: BE2C_WT_1


title: Small RNA RevI-H2i2- piwi GLKD

value: RevI-H2i2- nos-Gal4- expressed dsRNA-Piwi BDSC_37483


title: S36_D181217_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D181217


title: Small RNA yb-sKD

value: Tj-Gal4-expressed dsRNA-Yb VDRC_110056


title: S30_D181019_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D181019


title: Small RNA RevI-H2i2- ago3 GLKD

value: RevI-H2i2- nos-Gal4- expressed dsRNA Ago3 BDSC_35232

value: 3-6 day old female


title: HT-29 IMP1-OE rep 2

city: PORTLAND

first: Sarah

middle: F

last: Andres

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: OHSU

data_processing:
Raw fastq files were simultaneously demultiplexed and had their adapters removed using cutadapt v3.5
Additional adapter sequences of 4nt at the 5' end and 5nt at the 3' end were removed with cutadapt v3.5
Quality control on demultiplexed fastq files was performed using fastp v0.21
in silico rRNA/tRNA depletion was performed using hisat v2.1.0 and non-rRNA/tRNA reads were retained
Processed fastq files were quantified using kallisto v0.46.2 against an index generated based on principal isoforms from the APPRIS database.
Assembly: gencode v39
Supplementary files format and content: kallisto_results.csv contains read counts for all samples and deseq_results.csv contains the desults of differential expression analysis.

source_name: colorectal cancer cell line

growth_protocol: Cell lines were maintained in DMEM-H, 10% FBS, 1% penicillin/streptomycin, and 2ug/mL puromycin.

extract_protocol:
Cells were lysed in 20mM Tris, pH7.4, 150 mM NaCl, 5 mM MgCl2, 100 ug/ml cycloheximide, 1% v/v Triton X-100, 25 U/ml Turbo DNase I on ice. Lysate was passed 10 times through a 26 gauge needle and clarifed by centrifugation for 10 minutes at 20,000 x g, 4°C. Supernatant was snap frozen in liquid nitrogen for sequencing.
Separate 5′ and 3′ linkers were ligated to the RNA fragment instead of 3′ linker followed by circularization (Subtelny et al. 2014). 5′ linkers contained four random nucleotide unique molecular identifiers (UMIs), similar to a 5-nucleotide (nt) UMI in 3′ linkers. RNA-seq libraries were prepared using RNA that was randomly fragmentated by incubating for 15 min at 95°C in 1 mM EDTA, 6 mM Na2CO3, and 44 mM NaHCO3 (pH 9.3). RNA-seq fragments were restricted to 18–50 nt. Ribosomal RNA (rRNA) were removed from pooled RNA-seq samples using RiboZero. cDNA for the pooled library were PCR-amplified for 15 cycles.

value: colorectal cancer cell line

tag: tumor-derived

value: mouse liver metastasis

tag: crispr treatment

value: CRISPR/Cas9 - IMP1

tag: piggybac vector

value: PB*-FLAG-IMP1-short UTR


title: S31_D181025_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D181025


title: Small RNA RevIH2i3


title: S33_D181026_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D181026


title: HT-29 null rep 1

value: PB*-empty


title: 3060

value: female

tag: ethnicity

value: white

tag: smoking status

value: never smoker

tag: grade

value: mild dysplasia

value: tongue


title: S28_D180611_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D180611


title: 3053

value: male

value: ever smoker

tag: lesion site

value: hard palate or gingiva


title: DU145-WD 03

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description:
L1HFC120654_WD03.R1
processed data file: WCD.gene.count.matrix.annot

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to h38.p10 whole genome using bowtie v 0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Matrix table with raw gene counts  and tpm for every gene and every sample.

source_name: DU145 treated by EREG-CM

growth_protocol: Prostate cancer cells were routinely cultured and passaged (typically 0.5–1 × 106 cells in a T25 flask) in DMEM media supplemented with 10% FBS.

extract_protocol:
At the end of cell culture, media were removed, cells were lysed with Trizol reagent and total RNA was harvested. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101, RS-122-2102) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Upon 80% confluency, cancer cells were treated for 3 days with conditioned media derived from prostate stromal cells, either naive (control) or ectopically expressing human epiregulin (EREG).

tag: cell type

value: Human prostate cancer cells

value: Grade IV, adenocarcinoma, derived from the metastatic site, brain of a prostate cancer patient

tag: passage

value: treated by EREG-CM


title: D.melanogaster trachea, air control male, rep. 3

city: Borstel

first: Susanne

last: Krauss-Etschmann

address: Parkallee 1-44

department: Early Life Origins of Chronic Lung Diseases

institute: Resarch Center Borstel, Leibniz Lung Center

data_processing:
For analysis of gene expression, reads were mapped to ENSEMBL annotated transcripts from the human genome assembly hg38 with STAR 2.6.0c.
Analysis on differentially expressed genes, moderated estimation of fold change and dispersion for RNA sequencing data were performed using DESeq2 (v. 1.22.2)
Specifically, a generalized linear model using a negative binomial distribution was built to estimate the effects of the factors group (smoke versus control), sex, and their interaction.
To identify enriched biological processes due to CSE in larval epithelial cells, the DAVID software was used.
To have a look which pathways and processes play a role in the response to CS, GOs were taken including an enrichment p-value <0.1.
Assembly: hg38

source_name: trachea

extract_protocol:
RNA isolation was performed using the NucleoSpin RNA kit (Macherey-Nagel, Dueren, Germany) following manufacturer`s protocol and finally eluted in 40 µl RNase-free H2O.
RNA sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer´s recommendations.  All samples were normalized to 2nM and pooled equimolar. The library pool was sequenced on the NextSeq500 (Illumina) with 1x75bp, with 17 to 22 mio reads per sample.

treatment_protocol:
Mainstream cigarette smoke (CS) served as a surrogate for active smoking and was generated using the inExpose exposure system (SCIREQ, Canada) with 3R4F Research Cigarettes (Tobacco Research Institute, University of Kentucky, USA).
All exposure experiments were performed with a smoke intensity of 4 puffs/min for a duration of 60 min.

tag: tissue

value: trachea

value: Canton S

value: air control


title: 3049


title: D.melanogaster trachea, air control male, rep. 2


title: DU145-WD 02

description:
L1HFC120653_WD02.R1
processed data file: WCD.gene.count.matrix.annot


title: 3068

value: moderate dysplasia


title: S27_D180611_N

description:
scgex.txt.gz
metadata.txt.gz

tag: tissue type

value: Adjacent non-tumor normal Sample from individual D180611


title: HT-29 null rep 2

department: Pediatrics

value: colorectal cancer cell line

value: mouse liver metastasis

value: CRISPR/Cas9 - IMP1

value: PB*-empty


title: D.melanogaster trachea, air control male, rep. 1

tag: genotype


title: 3048

value: female

value: white

value: never smoker

value: tongue


title: HT-29 IMP1-OE rep 1

value: PB*-FLAG-IMP1-short UTR


title: 3024

value: mild dysplasia


title: S29_D181019_N

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Adjacent non-tumor normal Sample from individual D181019

tag: treatment


title: D.melanogaster trachea, air control male, rep. 4

value: trachea

value: male


title: 3036


title: 3022


title: S24_D180606_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D180606


title: Small RNA RevIH2i2

value: ovaries

tag: time

value: 3-6 day old female


title: 3040

tag: age at baseline (years)

value: asian

value: ever smoker


title: DU145-WD 01

description:
L1HFC120652_WD01.R1
processed data file: WCD.gene.count.matrix.annot

tag: cell line

value: Human prostate cancer cells

value: Grade IV, adenocarcinoma, derived from the metastatic site, brain of a prostate cancer patient

value: treated by EREG-CM


title: DU145-WC 01

description:
L1HFC120649_WC01.R1
processed data file: WCD.gene.count.matrix.annot

source_name: DU145 control (DMEM)

value: control (DMEM)


title: S25_D180608_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180608


title: 3031

tag: Sex

value: female

value: white

value: never smoker

value: tongue


title: D.melanogaster trachea, cigarette smoke exposed male, rep. 4

value: Canton S

value: cigarette smoke exposed


title: S26_D180608_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D180608


title: D.melanogaster trachea, cigarette smoke exposed male, rep. 2

value: trachea

value: male


title: DU145-WC 02

description:
L1HFC120650_WC02.R1
processed data file: WCD.gene.count.matrix.annot


title: 3003

value: mild dysplasia


title: DU145-WC 03

description:
L1HFC120651_WC03.R1
processed data file: WCD.gene.count.matrix.annot


title: D.melanogaster trachea, cigarette smoke exposed male, rep. 3


title: PC3-WB 01

description:
L1HFC120646_WB01.R1
processed data file: WAB.gene.count.matrix.annot

source_name: PC3 treated by EREG-CM

value: Carcinoma, derived from the metastatic site, bone of a prostate cancer patient


title: S21_D180605_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180605


title: PC3-WB 03

description:
L1HFC120648_WB03.R1
processed data file: WAB.gene.count.matrix.annot

value: Human prostate cancer cells


title: S20_D180308_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D180308


title: D.melanogaster trachea, cigarette smoke exposed male, rep. 1


title: S22_D180605_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D180605


title: S23_D180606_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180606


title: PC3-WA 02

description:
L1HFC120644_WA02.R1
processed data file: WAB.gene.count.matrix.annot

source_name: PC3 control (DMEM)

value: control (DMEM)


title: 3011

value: white

value: ever smoker


title: S18_D180305_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D180305


title: D.melanogaster trachea, air control female, rep. 4

value: female

value: Canton S

value: air control


title: PC3-WA 03

description:
L1HFC120645_WA03.R1
processed data file: WAB.gene.count.matrix.annot


title: S19_D180308_N

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Adjacent non-tumor normal Sample from individual D180308


title: 2074

value: never smoker

value: moderate dysplasia

value: buccal or labial mucosa


title: S17_D180305_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180305


title: D.melanogaster trachea, air control female, rep. 2

value: trachea


title: 2088

value: male

value: asian

value: tongue


title: PC3-WA 01

description:
L1HFC120643_WA01.R1
processed data file: WAB.gene.count.matrix.annot

value: Human prostate cancer cells

value: Carcinoma, derived from the metastatic site, bone of a prostate cancer patient

value: control (DMEM)


title: PC3-WB 02

description:
L1HFC120647_WB02.R1
processed data file: WAB.gene.count.matrix.annot

value: treated by EREG-CM


title: 3021

value: female

value: white

value: ever smoker

value: floor of mouth


title: S16_D180129_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D180129


title: D.melanogaster trachea, cigarette smoke exposed female, rep. 3

value: Canton S

value: cigarette smoke exposed


title: SO_8069_YSCCC_RNAseq

city: Bangkoknoi

first: Somponnat

last: Sampattavanich

state: Bangkok

address: 2 Wanglang Road

department: Department of Pharmacology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital, Mahidol University

data_processing:
Transcriptome sequencing was performed using Illumina Hiseq2000 (Illumina, San Diego, CA) with 150x2 paired-end chemistry reads and sequencing at depth 20-25 million reads per sample.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The STAR (v2.5.3a) was used to align reads to human reference genome (hg19 release).
Other pipelines were used including sambamba (v0.6.6) for sorting the BAM files, samtools (v1.6): for indexing the BAM files, fastp (v0.19.4) for the read trimming and QC and subread (v1.6.2) for the gene/isoform quantification.
The expression levels for each gene were normalized to transcripts per million (TPM) to facilitate the comparison of transcript levels among samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

source_name: cholangiocarcinoma cell lines

growth_protocol: We cultured KKU-055, KKU-156, KKU-213, KKU-214, KKK-D068, KKK-D131, KKK-D138 HuCCT-1 and HuH-28 in DMEM (Gibco) supplemented with 10% FBS (Biochrom) and 1% penicillin-streptomycin (Gibco). Four of CCA cell lines which are RBE, SSP-25, TFK-1, YSCCC were cultured in RPMI (Gibco) supplemented with 10% FBS (Biochrom) and 1% penicillin-streptomycin (Gibco). KKU-100 and HuCCA1 were grown in Ham-F12 (Gibco) supplemented with 10% FBS (Biochrom) and 1% penicillin-streptomycin (Gibco). MMNK-1 were growth in 2 mM L-glutamin from Gibco (Ham-F12) supplemented with 10% FBS (Biochrom) and 1% Penicillin-Streptomycin (Gibco). All cell lines were tested mycoplasma before perform an experiment.

extract_protocol:
RNA were extracted from cell lines byTrizol reagent (Invitrogen). RNA purification using Ambion RNA isolation kit (Invitrogen) and perform on-column DNA treatement using PureLink DNase set (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 24 hours after plating cell at 80% confluent, we performed drug treatment using inhibitors from Selleckchem Which are Src/Abl inhibitor(Dasatinib) and MEK inhibitor (PD-0325901). All cell lines were individually treated with inhibitors for 24 hours in 0.5%DMSO at a concentration of 10uM.

value: YSCCC

value: cholangiocarcinoma cell lines

tag: rrid

value: Japanese


title: SO_8069_TFK-1_RNAseq


title: 2028

extract_protocol:
DNA isolation was performed on Lesion cytology brush samples using the DNeasy Blood & Tissue Kit (QIAGEN, Hilden Germany). An enzymatic lysis buffer preparation was followed by two centrifugation/wash steps with PBS. The pellet was resuspended in PBS with 20 µl proteinase K and 4 µl of RNase A (100 mg/ml), followed by vortex and incubation. Extraction steps were conducted as per the manufacturer’s kit instructions. DNA was eluted using 50 µl nuclease free distilled water and stored at −20 °C.
A custom16S rRNA gene sequencing approach was employed. A single round of PCR (25 cycles) was done using Platinum SuperFi II DNA Polymerase–High-Fidelity PCR Enzyme for pre-amplification and custom primers targeting the V1-V3 region (515FB forward primer = GTGYCAGCMGCCGCGGTAA; 926R reverse primer= CCGYCAATTYMTTTRAGTTT) of the 16S rRNA gene. PCR products were verified visually by gel electrophoresis. Amplicon fragments were then sent to the Integrated Microbiome Resource, at Dalhousie University (https://imr.bio) and PCR-amplified using high-fidelity Phusion Plus® polymerase (New England Biolabs Inc.). Amplified DNA concentrations were then normalized, pooled, and sequenced via 6 runs on an Illumina MiSeq using 300 bp paired-end read chemistry. The sequencing runs yielded an average of at least 50,000 reads per sample.

value: moderate dysplasia


title: S14_D180124_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D180124


title: 2104

value: male

value: other

value: never smoker

value: tongue


title: 2118


title: SO_8069_SSP-25_RNAseq


title: D.melanogaster trachea, air control female, rep. 3

value: trachea

value: female

value: air control


title: SO_8069_RBE_RNAseq

value: RBE


title: D.melanogaster trachea, cigarette smoke exposed female, rep. 4


title: SO_8069_MMNK-1_RNAseq

source_name: immortalized cholangiocyte cell lines

value: immortalized cholangiocyte cell lines


title: S12_D180123_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D180123


title: 1972

value: white

value: ever smoker


title: 1973


title: D.melanogaster trachea, cigarette smoke exposed female, rep. 2

value: Canton S

value: cigarette smoke exposed


title: D.melanogaster trachea, air control female, rep. 1


title: D.melanogaster trachea, cigarette smoke exposed female, rep. 1


title: SO_8069_KKU-213_DAS_RNAseq

value: cholangiocarcinoma cell lines

value: dasatinib

value: Thai


title: S8_D180116_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D180116


title: 1825

value: never smoker

value: mild dysplasia


title: S15_D180129_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180129


title: 1876

value: male

value: moderate dysplasia

value: tongue


title: S13_D180124_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180124


title: SO_8069_KKU-213_MEK_RNAseq


title: S6_D171218_T

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Tumor Sample from individual D171218


title: S9_D180118_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180118


title: 1913

value: female

value: white


title: 1871

value: buccal or labial mucosa


title: 2024

value: asian


title: 1822


title: SO_8069_KKU-213_RNAseq

value: cholangiocarcinoma cell lines


title: S7_D180116_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180116


title: S10_D180118_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D180118


title: SO_8069_KKU-156_RNAseq

value: Thai


title: SO_8069_KKU-100_RNAseq


title: S5_D171218_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D171218


title: 1758

value: ever smoker

value: mild dysplasia


title: SO_8069_KKU-214_RNAseq


title: S11_D180123_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D180123


title: iR9-CHILP-6-3

data_processing:
Bcl2fastq (version 2.16.0.10) convert .bcl files into fastq files.
Fastq files were aligned to mm10 genome. *.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Assembly: mm10
Supplementary files format and content: CHILP_TPM_Matrix.txt: Matrix table with TPM value for every gene and every cell.

source_name: common helper innate lymphoid progenitors

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2 (Vazyme, N711).
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme, TD503).

treatment_protocol: The single CHILPs were sorted for RNAseq analysis.

tag: strain


title: SO_8069_KKU-055_MEK_RNAseq


title: SO_8069_KKU-055_DAS_RNAseq

value: dasatinib


title: 1774

value: never smoker

value: moderate dysplasia

value: tongue


title: SO_8069_KKU-055_RNAseq


title: 1806

value: male


title: 1818

value: female


title: S3_D171116_N

description:
scgex.txt.gz
metadata.txt.gz

value: stomach

value: Adjacent non-tumor normal Sample from individual D171116


title: S2_D171012_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D171012


title: 1655

value: white

value: floor of mouth


title: 1650

value: hard palate or gingiva


title: iR9-CHILP-8-3


title: SO_8069_HuCCA-1_RNAseq

value: cholangiocarcinoma cell lines

value: Thai


title: SO_8069_KKK-D138_DAS_RNAseq


title: SO_8069_HuH-28_RNAseq

value: Japanese


title: 1667

value: ever smoker

value: mild dysplasia


title: 1639

value: buccal or labial mucosa


title: S1_D171012_N

description:
scgex.txt.gz
metadata.txt.gz

value: Adjacent non-tumor normal Sample from individual D171012


title: S4_D171116_T

description:
scgex.txt.gz
metadata.txt.gz

value: Tumor Sample from individual D171116


title: SO_8069_HuCCT-1_RNAseq


title: iR9-CHILP-34-3


title: 1730


title: 1607

value: never smoker

value: tongue


title: 1661

value: female

value: moderate dysplasia


title: iR9-CHILP-25-3


title: iR9-CHILP-27-3


title: iR9-CHILP-30-3


title: SO_8069_KKK-D131_RNAseq


title: iR9-CHILP-32-3


title: SO_8069_KKK-D138_RNAseq


title: iR9-CHILP-24-3


title: SO_8069_KKK-D138_MEK_RNAseq


title: iR9-CHILP-33-3


title: 14387_cystic_P4_RNA-seq

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

description: LinNEG organoids RNA-seq

data_processing:
Illumina 1.9 software used for conventional basecalling.
Reads were trimmed using TrimGalore v0.4.1.
Reads were mapped using STAR v2.5.2a.
Number of reads that map to genomic features is calculated using HTSeq v0.6.0. Reads with a mapping quality less than 10, or those that map to multiple loci or to overlapping gene regions are discarded to avoid ambiguity and false positives.
PCA  plots and heatmaps are based on normalised and rlog transformed counts obtained with DESeq2 version 1.14.1 (R version 3.4.1). Differential Gene Expression Analysis was done using the counted reads and the R package edgeR version 3.16.5 (R version 3.4.1), for the 3 pairwise comparisons.
Genome_build: Ensembl Homo_sapiens.GRCh38 (release 92)
Supplementary_files_format_and_content: A text file (csv format) includes FPKM values for each sample

source_name: Human fetal lung

growth_protocol: Fetal lung tip organoids were cultured in Matrigel  in self-renweing (SN) culture medium.

extract_protocol:
Total RNA was harvested from lung organoids using Rneasy Kit (Quiagen, 74004) and  Illumina TruSeq RNA Sample Prep Kit (Illumina, 20020594) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After complete removal of Matrigel, TripLE (Thermo Fisher Scientific, 12605010) were treated to dissociate organoids into single cells.

tag: sample id

tag: developmetal age

value: 20 pcw

tag: passage number

value: Human fetal lung

value: LinNEG organoids

value: Cystic


title: iR9-CHILP-28-3


title: 1585

tag: ethnicity

value: asian

tag: smoking status

tag: grade


title: 1574

value: white

tag: lesion site


title: 14387_folded_P3_RNA-seq

description: LinPOS organoids RNA-seq

tag: tissue

tag: cell type

value: LinPOS organoids

value: Folded


title: iR9-CHILP-20-3


title: SO_8069_KKK-D068_DAS_RNAseq

value: cholangiocarcinoma cell lines

value: dasatinib

value: Thai