title: 92-1,IDE196,24h, biol rep3

data_processing:
Sequencing reads were aligned to version hg38 of the human genome using gencode v30 gene annotations.
Differential gene expression was calculated using limma-voom R package.
Geneset enrichment analysis and Gene ontology term overrepresentation analysis was performed using clusterProfiler and DOSE R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited excel files for read counts for each gene

extract_protocol:
Total RNA was extracted from frozen cell pellets previously washed with PBS. 1 μg RNA per sample was used as input material.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, index codes were added to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter). Then 3 μl USER Enzyme (NEB) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

value: uveal melanoma

value: PKC inhibition


title: AML_blood_time0_01_021

status: Public on Sep 11 2023

type: SRA

city: San Diego

first: Peter

last: Croucher

state: CA

address: 11055 Flintkote Avenue

country: USA

institute: Cardiff Oncology Inc

library_source: transcriptomic

data_processing:
Raw fastq files were pseudo-mapped to GRCh38 (Gencode v36) using Salmon v0.14
Salmon transcript counts were converted to genes using tximport (v1.18)
Genes were library size factor normalized and variance-stabilizing transformed (VST) using DESeq2.
The gene counts (VST) data were subject to principal components analysis (PCA). PCs were weighted by their degree of association with the percentage of peripheral leukemic blasts in the samples. The most strongly associated PCs were removed and the data backtransformed, controling for the influence of varying leukemic blast percentages on the data.
Subsequent differential gene expression analyses were based on moderated T-tests as implemented in Limma. For machine learning regression analyses data were Blom (inverse normal transformed).
Assembly: hg38
Supplementary files format and content: comma delimited text file (.csv) containing size-factor normalized gene counts for each sample
Supplementary files format and content: comma delimited text file (.csv) variance-stabilizing transformed and percent peripheral blast corrected gene counts for each sample
Supplementary files format and content: comma delimited text file (.csv) containing Blom (inverse normal) transformed  and percent peripheral blast gene counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Blood samples were collected on day 1 of the trial prior to treatment with onvansertib and decitabine. RNA samples were collected in Paxgene tubes and total RNA extracted using the PAXgene blood RNA kit (Qiagen).
Samples were pre-treated with ezDNase (ThermoFisher). cDNA synthesis used the SMART-Seq v.4 Ultra-Low Input RNA Kit (Takara Bio). NGS libraries were generated using the Nextera XT DNA Library Preparation kit (Illumina) and sequenced (paired-end 100bp) on a HiSeq4000 (Illumina).

tag: tissue

value: Blood

tag: cell type

value: leukemic blasts and WBC

tag: disease

value: AML

tag: percent peripheral_blasts

tag: response group

tag: treatment


title: HCC44 treated with DMSO at day 0, Replica 2

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

library_source: genomic

data_processing:
sgRNA count table and important genes identificantion were all done by using MAGeCK (https://sourceforge.net/p/mageck/wiki/Home/)
Assembly: hg38
Supplementary files format and content: Matrix table with raw single-guide RNA counts for every sample
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: lung

growth_protocol: RPMI 10%FBS

extract_protocol:
Cells were lysed with Tris/SDS buffer supplemented with protease inhibitor, and DNA was precipitated with 40% isopropanol
Region contatining sgRNA sequence was amplified with two sequenctial PCR and final product was gel purified--genomic library is recovered

treatment_protocol: MRTX849 (2X IC50) and TNO155  (IC50) value

value: DMSO at day 0

value: lung

tag: cell line

tag: genotype

value: KRAS G12C mut STK11 mut KEAP1 mut


title: 72hr, scRNA_seq

city: Baltimore

first: Kellie

middle: N

last: Smith

state: MD

address: 1650 Orleans Street

institute: Johns Hopkins University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger v6.0.0 was used to demultiplex the FASTQ reads, align them to the mm10 mouse transcriptome, and extract their cell and unique molecular identifier (UMI) barcodes. The output of this pipeline is a digital gene expression (DGE) matrix for each sample, which records the number of UMIs for each gene that are associated with each cell barcode.
To generate the single-cell V(D)J sequences and annotate each library, we aligned TCR FASTQ reads to human mm10 V(D)J reference (v6.0.0 from 10X Genomics) using “cellranger vdj” function from Cell Ranger (v6.0.0). The filtered contig annotations, which contained high-level annotations of each high-confident cellular contig,
Assembly: mm10
Supplementary files format and content: Tab separated files and matrix files

organism: Mus musculus

source_name: MC38GP Tumor

extract_protocol:
DNA was extracted from each CD8-enriched culture condition using the Qiamp micro-DNA kit according to the manufacturer’s instructions
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX, feature barcode, and V(D)J TCR (Version 1)

value: MC38GP Tumor

value: T cell


title: HCC44 treated with MRTX after 8 doublings, Replica 2

value: MRTX after 8 doublings


title: 7day, scRNA_seq

description: 10X Genomics


title: 92-1,IDE196,24h, biol rep2

city: Cambridge

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

value: WT

tag: time


title: HCC44 treated with MRTX after 8 doublings, Replica 1


title: H2122 treated DMSO for 48 hrs Replica 1

data_processing:
NovaSeq 6000 System
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: RPMI 10% FBS

extract_protocol:
RNA extraction
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit and sequenced on an Illumina NovaSeq 6000 machine using 150bp paired end reads.

treatment_protocol: MRTX-849 IC50 treatment 48 hrs

value: Lung

value: DMSO treated 48 hrs


title: 7day, scTCR_seq

description: 10X Genomics


title: 72hr, scTCR_seq

description: 10X Genomics


title: RNA-Seq-WT-eIF3d-DMSO-2

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

data_processing:
For RNA-Seq and Subunit-Seq, reads were trimmed with Cutadapt and mapped to GRCh38 using STAR. Differential enrichment was performed using DESeq2
For m6A-eCLIP, UMIs were extracted using UMItools, reads were trimmed with Cutadapt and mapped to GRCh38 using bwa. m6A site identification was performed using CTK and CIMS/CITS analysis.
Assembly: GRCh38
Supplementary files format and content: For RNA-Seq and Subunit-Seq: RPKM; for m6A-eCLIP: m6A sites

growth_protocol: All cell lines were grown in DMEM with 10% FBS and 500 U mL-1 penicillin-streptomycin.

extract_protocol:
Cells were lysed in 50 mM HEPES-KOH pH 7.4, 150 mM KCl, 5 mM Mg(OAc)2, 1 % v/v NP-40, 0.25 mM DTT.
For RNA-Seq, polyadenylated RNA was purified and libraries were made using NEBNext Ultra II RNA Library Prep Kit for Illumina. For m6A-eCLIP, libraries were constructed using the m6A-eCLIP kit from Eclipse Bio. For Subunit-Seq, eIF3d was immunoprecipitated using anti-HA beads, the cap-binding domain was isolated by TEV protease digestion, contaminating RNAs were removed by enzymatic treatment and libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were seeded to be at ~80 % confluency at time of treatment and then treated with 600 nM thapsigargin or equal volume of DMSO vehicle for 16 h.

value: Human embryonic kidney

value: DMSO


title: 24hr, scTCR_seq

description: 10X Genomics


title: AML_blood_time0_05_043


title: RNA-Seq-WT-eIF3d-DMSO-1


title: KCL GEMM tumor nodule control vehicle for combo replica 2

data_processing:
NovaSeq 6000 System
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung nodule

extract_protocol:
Tumor nodules were harvested from the treated mice, and dissociated into single cell suspensions. Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit and sequenced on an Illumina NovaSeq 6000 machine using 150bp paired end reads.
RNA library was prepared using SMARTER mRNA seq library prep kit following manufacturer's kit

treatment_protocol: Tumor-bearing mice were treated MRTX849 100mpk and or SHP099 75 mpk daily

value: lung nodule

value: lung tumor cell

value: KRAS G12C STK11 null

value: vehicle for combo replica


title: 92-1,IDE196,24h, biol rep1

value: uveal melanoma

value: PKC inhibition


title: TM2c80

city: IZMIR

first: Duygu

last: Sag

address: Dokuz Eylül Üniversitesi 15 Temmuz Sağlık ve Sanat Yerleşkesi, Mithatpaşa Cad. 58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
The quality control of reads from sequencing libraries was performed with FASTQC tool (v0.11.9).
Adapter removal and quality trimming of reads were done with Trimmomatic (v0.39).
Sequencing libraries were aligned to the human reference genome with Rusbread v2.0.3 package of R v3.5.1.
Assembly: GRCh38
Supplementary files format and content: To measure the expression levels of genomic features, the featureCounts function of Rsubread package.

source_name: blood

growth_protocol: Primary human monocytes were differentiated into macrophages for 7 days in RPMI1640 media containing 10 ng/ml MCSF, 5% fetal bovine serum (FBS) and 1% pen/strep in humidified atmosphere with 5% CO2 at 37C. After differentiation, macrophages were maintained and treated in RPMI1640 media supplemented with 5% fetal bovine serum (FBS) and 1% pen/strep.

extract_protocol:
Total RNA was harvested using NucleoSpin RNA isolatin kit (MN). 0.4 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol:
In the control group, macrophages were left untreated (M0) or treated with 100 ng/ml LPS+20 ng/ml IFN gamma (M1 polarized), 20 ng/ml (M2a polarized) or 10 ng/ml IL-10 (M2c polarized) for 6 hours.
In the TRAIL-treated group, macrophages were pre-treated with 200 ng/ml soluble TRAIL for 2 hours and then either left unpolarized (M0) or polarized into M1, M2a and M2c macrophages for 6 hours.

value: blood

value: primary human monocyte derived macrophages

value: TRAIL and IL-10 treated macrophages (TRAIL+M2c polarized)


title: 24hr, scRNA_seq

description: 10X Genomics

value: MC38GP Tumor


title: HCC44 treated with DMSO after 8 doublings, Replica 2

value: DMSO after 8 doublings

value: lung

value: KRAS G12C mut STK11 mut KEAP1 mut


title: 12hr, scTCR_seq

description: 10X Genomics

value: T cell


title: M2c80

value: WT

value: IL-10 treated macrophages (M2c polarized)


title: 12hr, scRNA_seq

description: 10X Genomics


title: 92-1,IDE196,4h, biol rep2


title: 92-1,IDE196,4h, biol rep3


title: M2a80

value: IL-4 treated macrophages (M2a polarized)


title: PreAT-2, scTCR_seq

description: 10X Genomics

source_name: Spleen

value: Spleen


title: TM2a80

value: TRAIL and IL-4 treated macrophages (TRAIL+M2a polarized)


title: HCC44 treated with DMSO after 8 doublings, Replica 1


title: 92-1,DMSO,24h, biol rep6

value: negative control for IDE196


title: T80

value: TRAIL treated macrophages


title: PreAT-2, scRNA_seq

description: 10X Genomics


title: H23 treated with DMSO at day 0, Replica 2

value: DMSO at day 0

value: KRAS G12Cmut STK11mut  KEAP1 WT


title: 92-1,DMSO,24h, biol rep5

value: uveal melanoma


title: H23 treated with TNO155 after 8 doublings, Replica 2

value: TNO155 after 8 doublings


title: TM180

value: blood

value: primary human monocyte derived macrophages

value: TRAIL and LPS+IFN gamma treated macrophages (TRAIL+M1 polarized)


title: PreAT-1, scTCR_seq

description: 10X Genomics


title: 92-1,IDE196,4h, biol rep1

value: PKC inhibition


title: 92-1,DMSO,24h, biol rep4


title: H23 treated with DMSO at day 0, Replica 1

value: lung


title: H23 treated with TNO155 after 8 doublings, Replica 1


title: H23 treated with MRTX after 8 doublings, Replica 2

value: MRTX after 8 doublings


title: 92-1,DMSO,4h, biol rep6

value: WT


title: M180

value: LPS+IFN gamma treated macrophages (M1 polarized)


title: CD8_WT, scTCR_seq

description: 10X Genomics

value: MC38GP Tumor

value: T cell


title: UT80

value: untreated/unpolarized macrophages (M0)


title: H23 treated with MRTX after 8 doublings, Replica 1


title: CD8_WT, scRNA_seq

description: 10X Genomics


title: 92-1,DMSO,4h, biol rep5

value: negative control for IDE196


title: 92-1,DMSO,4h, biol rep4


title: H23 treated with DMSO after 8 doublings, Replica 2

value: DMSO after 8 doublings


title: T_81

value: TRAIL treated macrophages


title: TM2c81

value: TRAIL and IL-10 treated macrophages (TRAIL+M2c polarized)


title: H23 treated with DMSO after 8 doublings, Replica 1

value: KRAS G12Cmut STK11mut  KEAP1 WT


title: MP41,FHT-1015, 24h, biol rep 2

value: uveal melanoma

value: dual SMARCA4/SMARCA2 inhibition


title: MP41,FHT-1015, 24h, biol rep 1


title: H23 treated with MRTX+TNO after 8 doublings, Replica 2

value: MRTX+TNO after 8 doublings


title: WT, scRNA_seq

description: 10X Genomics


title: CD8Dep, scRNA_seq

description: 10X Genomics


title: H2122 treated with TNO155 after 8 doublings, Replica 2

value: TNO155 after 8 doublings

value: KRAS G12C mut STK11 mut KEAP1 mut


title: PreAT-1, scRNA_seq

description: 10X Genomics

value: Spleen


title: WT, scTCR_seq

description: 10X Genomics


title: CD8Dep, scTCR_seq

description: 10X Genomics


title: TM2a81

value: blood

value: primary human monocyte derived macrophages

value: TRAIL and IL-4 treated macrophages (TRAIL+M2a polarized)


title: MP41,FHT-1015, 4h, biol rep 3

value: WT


title: rip, scTCR_seq

description: 10X Genomics

value: MC38GP Tumor

value: T cell


title: M2c81

value: IL-10 treated macrophages (M2c polarized)


title: M2a81

value: IL-4 treated macrophages (M2a polarized)


title: rip, scRNA_seq

description: 10X Genomics


title: MP41,FHT-1015, 4h, biol rep 2


title: H23 treated with MRTX+TNO after 8 doublings, Replica 1

value: lung


title: H2122 treated with TNO155 after 8 doublings, Replica 1


title: T83

value: TRAIL treated macrophages


title: H2122 treated with DMSO at day 0, Replica 2

value: DMSO at day 0


title: MP41,FHT-1015, 4h, biol rep 1

value: uveal melanoma


title: TM2c83

value: TRAIL and IL-10 treated macrophages (TRAIL+M2c polarized)


title: GEX_2-8_ENWTSP, scTCR_seq

description: 10X Genomics


title: MP41,FHT-1015, 24h, biol rep 3

value: dual SMARCA4/SMARCA2 inhibition


title: H2122 treated with DMSO at day 0, Replica 1


title: GEX_2-8_ENWTSP, scRNA_seq

description: 10X Genomics


title: M2c83


title: UT_81

value: untreated/unpolarized macrophages (M0)


title: H2122 treated with MRTX after 8 doublings, Replica 2

value: MRTX after 8 doublings

value: KRAS G12C mut STK11 mut KEAP1 mut


title: GEX_2-7_SMWTSP, scTCR_seq

description: 10X Genomics

value: Spleen


title: MP41,DMSO,24h, biol rep2

value: negative control


title: H2122 treated with MRTX after 8 doublings, Replica 1


title: MP41,DMSO,24h, biol rep1


title: M2a83

value: blood

value: primary human monocyte derived macrophages


title: GEX_2-7_SMWTSP, scRNA_seq

description: 10X Genomics


title: H2122 treated with DMSO after 8 doublings, Replica 2

value: DMSO after 8 doublings


title: GEX_2-6_ENGPSP, scTCR_seq

description: 10X Genomics

value: T cell


title: MP41,DMSO,4h, biol rep2

value: WT


title: GEX_2-6_ENGPSP, scRNA_seq

description: 10X Genomics


title: MP41,DMSO,4h, biol rep3


title: H2122 treated with DMSO after 8 doublings, Replica 1


title: TM2a83

value: TRAIL and IL-4 treated macrophages (TRAIL+M2a polarized)


title: H2122 treated with MRTX+TNO after 8 doublings, Replica 2

value: MRTX+TNO after 8 doublings

value: lung


title: GEX_2-5_ENGPSP, scTCR_seq

description: 10X Genomics


title: MP41,DMSO,4h, biol rep1


title: H2122 treated with MRTX+TNO after 8 doublings, Replica 1


title: UT83


title: T84

value: TRAIL treated macrophages


title: MEL202,FHT-1015, 24h, biol rep 2

value: uveal melanoma


title: GEX_2-5_ENGPSP, scRNA_seq

description: 10X Genomics


title: GEX_2-4_SMGPSP, scTCR_seq

description: 10X Genomics


title: H2030 treated with TNO155 after 8 doublings, Replica 2

value: TNO155 after 8 doublings


title: TM2c84

value: TRAIL and IL-10 treated macrophages (TRAIL+M2c polarized)


title: H2030 treated with TNO155 after 8 doublings, Replica 1


title: GEX_2-4_SMGPSP, scRNA_seq

description: 10X Genomics


title: M2c84

value: IL-10 treated macrophages (M2c polarized)


title: TM2a84


title: H2030 treated with DMSO at day 0, Replica 2

value: DMSO at day 0


title: M183

value: LPS+IFN gamma treated macrophages (M1 polarized)


title: TM183

value: TRAIL and LPS+IFN gamma treated macrophages (TRAIL+M1 polarized)


title: MEL202,FHT-1015, 4h, biol rep 2

value: dual SMARCA4/SMARCA2 inhibition


title: GEX_2-3_ENGPLN, scTCR_seq

description: 10X Genomics

source_name: Lymph node

value: Lymph node


title: H2030 treated with DMSO at day 0, Replica 1

value: KRAS G12C mut STK11 mut KEAP1 mut


title: MEL202,FHT-1015, 4h, biol rep 3


title: GEX_2-2_SMGPLN, scTCR_seq

description: 10X Genomics


title: MEL202,FHT-1015, 24h, biol rep 3


title: GEX_2-3_ENGPLN, scRNA_seq

description: 10X Genomics


title: MEL202,FHT-1015, 4h, biol rep 1


title: MEL202,DMSO,24h, biol rep3

value: negative control


title: TM184

value: blood

value: primary human monocyte derived macrophages


title: M2a84

value: WT

value: IL-4 treated macrophages (M2a polarized)


title: H2030 treated with MRTX after 8 doublings, Replica 2

value: MRTX after 8 doublings

value: lung


title: H2030 treated with MRTX after 8 doublings, Replica 1


title: GEX_2-2_SMGPLN, scRNA_seq

description: 10X Genomics

value: T cell


title: H2030 treated with DMSO after 8 doublings, Replica 2

value: DMSO after 8 doublings


title: MEL202,DMSO,24h, biol rep2

value: uveal melanoma


title: GEX_2-1_ENWTTU, scTCR_seq

description: 10X Genomics

source_name: MC38WT Tumor

value: MC38WT Tumor


title: M184


title: UT84

value: untreated/unpolarized macrophages (M0)


title: MEL202,FHT-1015, 24h, biol rep 1


title: H2030 treated with DMSO after 8 doublings, Replica 1


title: MEL202,DMSO,24h, biol rep1


title: GEX_2-1_ENWTTU, scRNA_seq

description: 10X Genomics


title: C4-2_PAR_ST

city: San Antonio

first: Tim

middle: Hui-Ming

last: Huang

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health at San Antonio

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were pseudo-aligned to hg38+mm10 genome assembly using kallisto bus command with -x 0,0,16:0,16,28:1,0,0. Gencode primary assembly v32 annotation model were supplied in GTF format.
bustools was used to error correct barcodes and produce gene count matrices.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files containing genes by barcode counts matrices

molecule: polyA RNA

source_name: C4-2 prostate cancer cells

growth_protocol: C4-2 prostate cancer cells were cultured in RPMI-1640 with 10% FBS and 1% penicillin/streptomycin aired with 5%CO2 at 37℃. U937 were cultured in RPMI 1640 supplemented with 10% heat shocked FBS and 100 units/mL penicillin and 100 µg/mL streptomycin (Gibco) aired with 5% CO2 at 37°C. U937 monocytes were differentiated into macrophages by 100 ng/mL phorbol 12-myristate 13-acetate (PMA)

extract_protocol: Libraries were construct with 10X genomic Visium library kits with Dual Index Plate TT Set A- B1 and C1

treatment_protocol: C4-2 prostate cancer cells and U937 derived macrophages were co-cultured in ultra-low adhesion plate for 7 days to generate tumor-macrophage hybrid cells. Then, 3*10^6 cells of mixed cells were harvested for transplantation.

tag: host

value: Mus musculus

value: Xenograft tumor

tag: mouse treatment

value: C4-2 prostate cancer cells


title: MEL202,DMSO,4h, biol rep3


title: GEX_1-8_ENWTTU, scTCR_seq

description: 10X Genomics


title: H2030 treated with MRTX+TNO after 8 doublings, Replica 1

value: MRTX+TNO after 8 doublings


title: C4-2_MTF_ST

value: hybrid cells derived from cultured C4-2 prostate cancer cells and U937 derived macrophages


title: Mouse testes, RAD51 ChIP-SSDS, Spo11 KO Fignl1 cKO, rep2

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

data_processing:
A published bioinformatic pipeline (https://nf-co.re/ssds/dev) was run for the resulting reads for the identification of single-stranded sequences.
The bigWig files were generated from the BAM files using bamCoverage in Deeptools.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: testes

extract_protocol:
A pair of testes from Spo11 KO and Spo11 KO Fignl1 cKO mice (9-20 weeks, except a Spo11 KO mouse at 31 weeks) were dissected, the tunica albuginea was removed, and seminiferous tubules were transferred into 10 ml of 1% formaldehyde (Pierce, 28908) in PBS (Nakarai, 14249-24) and immediately homogenized in a Dounce homogenizer with 20 strokes of the tight-fit pestle. The homogenate was passed through a 70 μm cell strainer (Falcon, 352350), and after a total of 10 min of incubation at room temperature, crosslinking was quenched by adding 2.5 M glycine to a final concentration of 125 mM. After 5 min of incubation at room temperature, cells were pelleted by centrifugation at 900 x g for 5 min at 4℃, washed once with 10 ml of cold PBS, and suspended in 1 ml of cold PBS. The cell suspension was transferred to a 1.5 ml tube, centrifuged at 900 x g for 5 min at 4℃, and after removal of the supernatant, the cell pellet was snap-frozen on liquid nitrogen and stored at -80℃. The frozen cell pellet was suspended in 500 μl of cell lysis buffer (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0) supplemented with protease inhibitor (Roche, 04693159001), incubated for 10 min on ice, centrifuged at 300 x g for 3 min at 4℃, and the nuclei pellet was resuspended in 500 μl of lysis wash buffer (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0) supplemented with protease inhibitor. After centrifugation at 300 x g for 3 min at 4℃, the nuclei pellet was resuspended in 200 μl of RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 140 mM NaCl) supplemented with protease inhibitor and split into two ~130 μl aliquots and sonicated on the Covaris M220 for 5 min 30 sec at 5-9oC with a setting of Peak Power 50.0, Duty Factor 20.0, and Cycles/Burst 200. Sheared nuclei were combined, and after adding 700 μl of RIPA buffer, centrifuged at 15,000 rpm for 15 min at 4℃ to remove insoluble debris. 800 μl of the chromatin-containing supernatant was mixed with 50 μl of Dynabeads protein G bound to 9.7 μg of RAD51 antibody (Novus, NB100-148) and incubated overnight on a rotating wheel at 4℃ for immunoprecipitation. Beads were washed once with 1 ml of cold ChIP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), 1 ml of cold ChIP wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), 1 ml of cold ChIP wash buffer 3 (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and twice with 1 ml of cold TE (1 mM EDTA and 10 mM Tris-HCl pH 8.0), followed by elution with 100 μl of elution buffer (0.1 M NaHCO3 and 1% SDS) for 30 min at 65℃ with vortexing every 10 min. The elutes were incubated overnight at 65℃ for de-crosslinking, neutralized by adding 4 μl of 1M Tris-HCl (pH 6.5) and 2 μl of 0.5 M EDTA, and RNA was digested by adding 2 μl of 10 mg/ml RNase-A and incubation for 15 min 37oC. After adding 5 μl of 10 mg/ml Proteinase-K (Wako, 165-21043) and incubation for 1 h at 55℃, DNA was purified using QIAquick PCR Purification Kit (QIAGEN).
7-10 ng of ChIP DNA was further sonicated on the Covaris M220 for 8 min 30 sec at room temperature with a setting of Peak Power 75.0, Duty Factor 10.0, and Cycles/Burst 200, followed by end-repair and dA-tailing using ChIP-Seq Library Prep Reagent Set for Illumina (NEB, E6200L). DNA was incubated for 3 min at 95℃ and returned to room temperature for kinetic enrichment for single-stranded DNA. After adapter ligation using IDT for Illumina TruSeq DNA UD Indexes (Illumina, 20022370), SSDS libraries were amplified during 15 cycles of PCR using TruSeq DNA Nano LP (Illumina, 20016328) and purified with AMPureXP beads (Beckman Coulter, A63880).

tag: strain background

value: testes

tag: age

value: adult (9-20 weeks)

value: Stra8-Cre +; Fignl1 flox/-; Spo11 -/-

tag: antibody lot

tag: read length

value: 50 bp


title: MEL202,DMSO,4h, biol rep2

value: WT

value: negative control


title: 92-1,FHT-1015, 24h,RNA-seq,biol rep 3

value: dual SMARCA4/SMARCA2 inhibition


title: Mouse testes, RAD51 ChIP-SSDS, Spo11 KO Fignl1 cKO, rep1


title: GEX_1-8_ENWTTU, scRNA_seq

description: 10X Genomics

value: T cell


title: Mouse testes, RAD51 ChIP-SSDS, Spo11 KO, rep2

value: adult (31 weeks)

value: Stra8-Cre +; Fignl1 +/+; Spo11 -/-


title: MEL202,DMSO,4h,RNA-seq,biol rep1

value: uveal melanoma


title: GEX_1-7_ENGPTU, scTCR_seq

description: 10X Genomics

value: MC38GP Tumor


title: GEX_1-6_SMGPTU, scTCR_seq

description: 10X Genomics


title: 92-1,FHT-1015, 24h,RNA-seq,biol rep 2


title: GEX_1-7_ENGPTU, scRNA_seq

description: 10X Genomics


title: 501mel cells in shNT keratinocyte CM #2

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library
library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data ( clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end cleanreads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: hg38
Supplementary files format and content: Text file include fpkm value for each sample for batch 1
Supplementary files format and content: Text file include fpkm value for each sample for batch 2

source_name: skin

growth_protocol: Keratinocytes at confluence were cultured for 72 hours in 0.07mM Calcium containing M154 media + HKGS + gentamycin and amphotericin

extract_protocol:
RNA was harvested using Quick-RNA miniprep kit (Zymo).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP

treatment_protocol: Keratinocytes were treated with conditioned media from melanoma cells for 48 hours

value: skin

value: Melanoma cell line

value: shNT keratinocyte conditioned media


title: 501mel cells in shNT keratinocyte CM #3


title: 501mel cells in shNT keratinocyte CM #1


title: 501mel cells in shDsg1 keratinocyte CM #3

value: shDsg1 keratinocyte conditioned media


title: 92-1,FHT-1015, 24h,RNA-seq,biol rep 1


title: GEX_1-6_SMGPTU, scRNA_seq

description: 10X Genomics


title: 501mel cells in shDsg1 keratinocyte CM #2


title: 92-1,FHT-1015, 4h,RNA-seq,biol rep 3


title: GEX_1-5_SMWTTU, scTCR_seq

description: 10X Genomics

source_name: Lung tumor

value: Lung tumor


title: H2030 treated with MRTX+TNO after 8 doublings, Replica 2

value: MRTX+TNO after 8 doublings

value: lung

value: KRAS G12C mut STK11 mut KEAP1 mut


title: maxillary process, e11.5

city: Berkeley

first: Laura

middle: E

last: Cook

state: California

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

data_processing:
RNA-seq data was analyzed using the ENCODE RNA-Seq (Long) Pipeline-1 implemented at DNAnexus.
Sequence reads were mapped to the reference genome using STAR align (V2.12). Genome wide coverage plots were generated using bam to signals (v2.2.1), and gene expression counts were generated using RSEM (v1.4.1).
Mouse datasets were analyzed using mouse reference genome version mm10 and GENCODE M4 gene annotations.
Assembly: mm10
Supplementary files format and content: genes.results.counts

source_name: Maxillary Process (Mx)

extract_protocol:
Freshly dissected mouse embryonic face tissue.
Tissue was dissociated with TRIzol, DNase treated and assessed for quality.  TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat kit (Illumina) was used to prepare RNA-seq libraries according to manufacturer’s protocol.

value: Maxillary Process (Mx)

value: mixed

tag: developmental stage


title: 501mel cells in shDsg1 keratinocyte CM #1


title: medial nasal process, e11.5

source_name: Medial Nasal Process (LNP)

value: Medial Nasal Process (LNP)

value: WT


title: GEX_1-5_SMWTTU, scRNA_seq

description: 10X Genomics

value: T cell


title: WM1341D cells in shNT keratinocyte CM #3


title: 92-1,FHT-1015, 4h, RNA-seq,biol rep 2

value: dual SMARCA4/SMARCA2 inhibition


title: GEX_1-4_ENGPLN, scTCR_seq

description: 10X Genomics

value: Lymph node


title: WM1341D cells in shNT keratinocyte CM #2


title: 92-1,DMSO,24h,RNA-seq,biol rep3

value: uveal melanoma

value: negative control


title: WM1341D cells in shNT keratinocyte CM #1

value: skin


title: 92-1,DMSO,24h, RNA-seq,biol rep2


title: face_hs746_e11.5_rep1

data_processing:
BCL files from Illumina were processed into FASTQ format, individual sample libraries were de-multiplexed as necessary, reads were aligned to mm10 reference genome where mCherry sequence was added as an additional chromosome.
Cell Ranger was used to process the raw sequence files to generate feature-barcode matrices, and to aggregate data from multiple samples after correcting for batch effects.
Seurat package was used for filtering and clustering cells. A combination of auto-referencing and manual annotations was used to assign cell type identies to resulting clusters.
Assembly: mm10
Supplementary files format and content: rds file that contains all scRNA-seq data samples intergrated. Includes features counts, barcodes and matrix.

source_name: face

extract_protocol:
Embryonic mouse face tissue was dissected, embryos with positive mCherry reporter activity wwre selected where applicable, and immediately processed for downstream experiments. Fresh mouse embryonic face tissue was mechanically dissociated by pipetting gently into a single-cell suspension using Accumax, assessed for viability of cells and cell density using Trypan Blue staining.
Tha standard protocol for 10X Genomics Chromium Next GEM Single Cell 3’ was followed for transcript capture and library preparation for single-cell gene expression. Samples were either processed individually or pooled using a previously described Multi-seq strategy78 upstream of the 10X Genomics Chromium protocol. The resulting libraries were sequenced on an Illumina HiSeq2500 or NovaSeq 10X.
10X Genomics Chromium Next GEM Single Cell 3’

value: face


title: GEX_1-3_SMGPLN, scTCR_seq

description: 10X Genomics


title: mandibular process, e11.5

source_name: Mandibular Process (Md)

value: Mandibular Process (Md)


title: Mouse testes, RAD51 ChIP-SSDS, Spo11 KO, rep1

value: testes

value: adult (9-20 weeks)

value: Stra8-Cre +; Fignl1 +/+; Spo11 -/-

value: 50 bp


title: 92-1,DMSO,24h, RNA-seq,biol rep1


title: WM1341D cells in shDsg1 keratinocyte CM #2

value: Melanoma cell line

value: shDsg1 keratinocyte conditioned media


title: GEX_1-4_ENGPLN, scRNA_seq

description: 10X Genomics


title: WM1341D cells in shDsg1 keratinocyte CM #3


title: GEX_1-2_ENWTLN, scTCR_seq

description: 10X Genomics


title: GEX_1-3_SMGPLN, scRNA_seq

description: 10X Genomics


title: WM1341D cells in shDsg1 keratinocyte CM #1


title: 92-1,DMSO,4h, RNA-seq,biol rep3


title: 92-1,DMSO,4h, RNA-seq,biol rep2


title: face_WT_e11.5

value: mixed


title: GEX_1-2_ENWTLN, scRNA_seq

description: 10X Genomics


title: 92-1,FHT-1015, 4h,RNA-seq,biol rep 1


title: Keratinocytes in melanocyte CM #3

value: human keratinocyte

value: primary keratinocyte

value: melanocyte conditioned media


title: GEX_1-1_SMWTLN, scTCR_seq

description: 10X Genomics

value: T cell


title: face_hs1431_e11.5_rep1


title: 92-1,DMSO,4h, RNA-seq,biol rep1

value: WT


title: lateral nasal process, e11.5

source_name: Lateral Nasal Process (LNP)

value: Lateral Nasal Process (LNP)


title: face_hs746_e11.5_rep2


title: Keratinocytes in 501mel CM #3

value: 501mel conditioned media


title: face_WT_e12.5


title: Keratinocytes in 1341D CM #3

value: skin

value: 1341D conditioned media


title: face_hs521_e11.5

value: face


title: GEX_1-1_SMWTLN, scRNA_seq

description: 10X Genomics

value: Lymph node


title: face_hs746_hs1431_hs521_e13.5


title: Cranial bone marrow far away from suture, 18-month-old, scRNAseq, replicate 1

city: Chengdu

first: Bo

last: Li

state: Sichuan

address: No. 14, 3rd Section, Renminnan Road

department: Department of Orthodontics

country: China

institute: West China School of Stomatology

description: 10x Genomics

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format by using bcl2fastq software (Illumina, version 2.20). The Cell Ranger Single-Cell Software Suite (version 5.0.1) was used to perform sample demultiplexing, barcode processing, and single-cell 3’ gene counting. All scRNA-seq data were aligned to Ensembl genome GRCm38 reference genome.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cranial bone marrow

extract_protocol:
To isolate the cranial bone marrow, the entire calvarium was harvested and processed to prepare cranial bone marrow single-cell suspensions, which was adopted from a peer-reviewed high-profile publication (Cugurra et al. 2021). In brief, the calvarium was dissected under a stereomicroscope, with the removal of dura mater and periosteum, and transferred into a 60 mm RNase-free culture dish on ice, containing an appropriate amount of calcium-free and magnesium-free 1× PBS (0.04% BSA). The sagittal sutures and adjacent parietal bones were collected for CBMA groups, and meanwhile, the parietal bones distant from cranial sutures were collected for CBMD groups. The collected cranial tissues were then cut into 0.5 mm2 pieces using sterile scissors and mechanically dissociated in 1× PBS (0.04% BSA) with a pestle, followed by enzymatic digestion (1 mg/mL collagenase I + 3 mg/mL collagenase II + 2 mg/mL dispase II in 10 mL MEM) for 15 min at 37℃ with brief vortexing every 5 min. The digestion process was terminated with 3 mL MEM containing 10% FBS and then pipetting 5-10 times. The resulting cell suspension was filtered through a 70 μm cell strainer and centrifuged at 420g for 4 min at 4°C. The cell pellet was resuspended in 100 μL 1× PBS (0.04% BSA) and added with 1 mL 1× Red Blood Cell Lysis Solution (Miltenyi Biotec, 130-094-183) and incubated on ice for 5-10 min. After incubation, the suspension was centrifuged at 420g for 4 min at 4°C and processed to remove dead cells by using MACS® Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101), followed by washing in 1× PBS (0.04% BSA) and centrifuging at 420g for 4 min at 4°C. The cell pellet was resuspended in 50 μL of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion (Thermo Fisher Scientific, SV3008401), which was no less than 85%. Finally, the concentration of single-cell suspensions was determined using the automated cell counter (Invitrogen, Countess II) and adjusted to 700-1200 cells/μL.
The CBMA and CBMD single-cell suspensions were loaded to 10x Chromium single cell platform (10x Genomics) to capture around 5,000 single cells, which was performed with the 10x Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics, 1000092) according to the manufacturer’s instructions. Next, the cDNA amplification and library construction steps were conducted according to the standard protocol. Libraries were paired-end sequenced on a NovaSeq 6000 Sequencing System (Illumina) by LC-Bio Technology Co. Ltd. (HangZhou, China) at a minimum depth of 20,000 reads per cell.

value: Cranial bone marrow

value: Wild-type C57BL/6


title: Keratinocytes in melanocyte CM #2


title: face_hs746_hs1431_e12.5


title: CS23, face, rep 4

data_processing:
RNA-seq data was analyzed using the ENCODE RNA-Seq (Long) Pipeline-1 (single-end) replicate pipeline (https://www.encodeproject.org/pipelines/ENCPL002LSE/) implemented at DNAnexus (https://www.dnanexus.com). Briefly, reads were mapped to the reference genome using STAR align (V2.12). Genome wide coverage plots were generated using bam to signals (v2.2.1). Gene expression counts were generated using RSEM (v1.4.1). Human datasets were analyzed using human reference genome version hg19, and GENCODE v24 gene annotations.
Assembly: hg19
Supplementary files format and content: genes.results.gz

extract_protocol:
Human embryonic face tissue (dissected) was received as de-identified, frozen samples from the Human Developmental Biology Resource (Newcastle University, UK).
RNA was isolated from dissociated tissue using TRIzol Reagent and samples were treated to remove DNase. RNA-seq libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Kit (Illumina). after depleting high moelcular weight prducts, RNA was eluted, and the quality and RNA concentration of samples was assessed on an Agilent Bioanalyzer.


title: CS22, face, rep 5


title: nose, e13.5, input

data_processing:
ChIP-seq data was analyzed using the ENCODE histone ChIP-seq Unary Control Unreplicated pipeline (https://www.encodeproject.org/pipelines/ENCPL841HGV/) implemented at DNAnexus (https://www.dnanexus.com).
Reads were mapped to the mouse reference genome version mm10 using BWA (v0.7.7) and sorted bam file generated using samtools (v0.1.19). Peak calling was performed using MACS2 (v2.2.4; --broad flag, q-value < 0.05), and overlapping peaks identified using overlap_peaks.py.
Assembly: mm10
Supplementary files format and content: broadPeak, bigWig

source_name: nose

extract_protocol:
Freshly dissected mouse embryonic face tissue.
Tissue was dissociated and crosslinked, cells lyzed and chromatin was sonicated to obtain DNA fragments ranging between 100-600bp. Chromatin was immunoprecipitated with an anti-H3K27ac antibody (Active Motif, Cat#39133), reverse crosslinked  and the samples were assessed for DNA concentration and fragment size distribution. Sequencing libraries were prepared with Illumina TruSeq kit.

value: nose

tag: antibody


title: Keratinocytes in 501mel CM #2

tag: tissue


title: Cranial bone marrow far away from suture, 12-month-old, scRNAseq, replicate 1

description: 10x Genomics


title: Keratinocytes in 1341D CM #2

tag: cell type


title: CS22, face, rep 4


title: face_hs1431_e11.5_rep2


title: Cranial bone marrow far away from suture, 2-month-old, scRNAseq, replicate 1

description: 10x Genomics


title: Cranial bone marrow and sutures, 18-month-old, scRNAseq, replicate 1

description: 10x Genomics

source_name: Cranial bone marrow and sutures

value: Cranial bone marrow and sutures


title: maxillary process, e13.5, input

source_name: maxillary process

value: maxillary process


title: CS22, face, rep 2

value: mixed


title: Keratinocytes in 501mel CM #1

value: human keratinocyte


title: CS22, face, rep 3


title: Cranial bone marrow and sutures, 2-month-old, scRNAseq, replicate 1

description: 10x Genomics


title: Keratinocytes in melanocyte CM #1

value: primary keratinocyte


title: Cranial bone marrow and sutures, 12-month-old, scRNAseq, replicate 1

description: 10x Genomics


title: CS23, face, rep 3


title: CS23, face, rep 1


title: maxillary process, e13.5, H3K27ac


title: Keratinocytes in 1341D CM #1


title: CS19, face, rep 1


title: segment 3, control, rep 1

city: Washington

first: Danielle

last: Sosnicki

state: DC

address: 3001 Connecticut Ave NW

institute: Smithsonian's National Zoo and Conservation Biology Institute

data_processing:
reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt and fastQC. Parameters: -j 1 -e 0.1 --nextseq-trim=20 -O 1 -a AGATCGGAAGAGC --length 50 --fastqc
unwanted reads were removed with STAR v 2.7.0e Parameters: --outReadsUnmapped Fastx
reads were mapped to the reference genome/transcriptome using STAR v2.7.0e
Assembly: GRCm38/mm10 with ENSEMBL annotations
Supplementary files format and content: tab-delimited text file include raw counts for each sample in sequencing run 3017
Supplementary files format and content: tab-delimited text file include raw counts for each sample in sequencing run 3097

source_name: epididymis segment 3

extract_protocol:
RNA extraction was performed using TRI Reagent LS (Molecular Research Center, Inc., Cincinnati, OH, USA)
DirectionalRNA-seq libraries were prepared from500ngtotal RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initialpolyA+ isolation. Each sample is a pool from two mice

treatment_protocol: Efferent duct ligation procedures were performed by tying 4-0 PDS suture around efferent ducts just prior to entering caput epididymis

value: epididymis segment 3

value: control (no ligation)


title: segment 3, control, rep 2

value: WT


title: mandibular process, e13.5, H3K27ac

source_name: mandibular process

value: mandibular process


title: MXRA8 knockout clone V grown as tumor in NCG mice, sample 3

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

data_processing:
adapters removed, reads containing N>10% removed, Qscore<=5 removed by Novogene
data was provided by Novogene as .fq.gz files
data was analyzed using Genialis software and the standard RNA-seq pipeling
Assembly: hg19
Supplementary files format and content: xlsx file containing CPM values for each sample

source_name: human TNBC cell line

growth_protocol: 231MXRA8Con and knockout clones were maintained in DMEM media (GIBCO, Burlington, ON) supplemented with 10% FBS, 2% glutamine, 1% sodium pyruvate, 1% 4-(2-hydroxyethyl)-1-piper- azineethanesulfonic acid (HEPES), and 1% antibiotic/antimycotic. Cells cultures were maintained in media containing 1µl/ml puromycin (ant-pr-1, InvivoGen, San Diego, CA) and 2µl/ml blasticidin (sc-495389, Santa Cruz Biotechnology, Dallas, TX) for selection.

extract_protocol:
Total RNA was extracted using the miRVana miRNA extraction kit from Thermo Fisher Scientific
libraries were created by Novogene using Illumina kits

treatment_protocol: MDA-MD-231 cells were initially infected with a hEF1a Blast-Cas9 lentiviral vector (cat# VCAS10126, Horizon/Dharmacon, Cambridge, UK). MDA-231Cas9 cells were selected with 20µg/ml of blasticidin and Cas9 protein was confirmed. MDA-231Cas9 cells were transduced with lentivirus that contained MXRA8 gRNA targeting hg38:chr1:1354815-1354837 of MXRA8 (VSGH10142-246490800, Horizon/Dharmacon, Cambridge, UK) or a control guide RNA (cat# VSGC10215, Horizon/Dharmacon, Cambridge, UK). Cells underwent selection using Puromycin (ant-pr-1, InvivoGen, San Diego, CA) and single cell clones were seeded in 96-well plates and expanded. Clones V (231MXRA8KO-V) and O (231MXRA8KO-O) and were selected due to the lowest MXRA8 expression compared to MDA-231 cells containing control gRNA (231MXRA8Con).

value: human TNBC cell line

value: MXRA8KO clone V tumor

value: MXRA8 gRNA


title: CS18, face, rep 4

value: face


title: CS18, face, rep 3


title: MXRA8 knockout clone V grown as tumor in NCG mice, sample 2


title: MXRA8 knockout clone V grown as tumor in NCG mice, sample 1


title: medial nasal plate, e11.5, input

source_name: medial nasal plate

value: medial nasal plate


title: CS22, face, H3K27ac, rep 2

data_processing:
ChIP-seq data was analyzed using the ENCODE histone ChIP-seq Unary Control Unreplicated pipeline (https://www.encodeproject.org/pipelines/ENCPL841HGV/) implemented at DNAnexus (https://www.dnanexus.com).
Reads were mapped to the human reference genome version hg38 using BWA (v0.7.7) and sorted bam file generated using samtools (v0.1.19). Peak calling was performed using MACS2 (v2.2.4; --broad flag, q-value < 0.05), and overlapping peaks identified using overlap_peaks.py.
Assembly: hg38
Supplementary files format and content: broadPeak, bigWig

extract_protocol:
Human embryonic face tissue (dissected) was received as de-identified, frozen samples from the Human Developmental Biology Resource (Newcastle University, UK).
Frozen tissue was dissociated and crosslinked, cells lyzed and chromatin was sonicated to obtain DNA fragments ranging between 100-600bp. Chromatin was immunoprecipitated with an anti-H3K27ac antibody (Active Motif, Cat#39133), reverse crosslinked  and the samples were assessed for DNA concentration and fragment size distribution. Sequencing libraries were prepared with Illumina TruSeq kit.


title: CS23, face, H3K27ac, rep 1


title: mandibular process, e13.5, input


title: segment 1, control, rep 2

source_name: epididymis segment 1

value: epididymis segment 1


title: segment 2, control, rep 1

source_name: epididymis segment 2

value: epididymis segment 2


title: nose, e13.5, H3K27ac

value: nose


title: CS22, face, H3K27ac, rep 1


title: MXRA8 knockout clone O grown as tumor in NCG mice, sample 2

value: MXRA8KO clone O tumor


title: segment 1, control, rep 1


title: mandibular process, e11.5, input


title: MXRA8 knockout clone O grown as tumor in NCG mice, sample 1


title: maxillary process, e11.5, input

value: maxillary process


title: CS19, face, H3K27ac, rep 1

value: mixed


title: lateral nasal plate, e11.5, H3K27ac

source_name: lateral nasal plate

value: lateral nasal plate


title: segment 3, ligated, rep 2

value: efferent duct ligation


title: segment 2, control, rep 2


title: lateral nasal plate, e11.5, input


title: segment 3, ligated, rep 1

value: epididymis segment 3


title: MDA-MB-231 cells infected with control gRNA and grown as tumor in NCG mice, sample 2

value: control tumor

value: control gRNA


title: medial nasal plate, e11.5, H3K27ac

value: WT


title: MDA-MB-231 cells infected with control gRNA and grown as tumor in NCG mice, sample 3

value: human TNBC cell line


title: segment 2, ligated, rep 2


title: CS18, face, H3K27ac, rep 3


title: maxillary process, e11.5, H3K27ac


title: CS18, face, H3K27ac, rep 1


title: MXRA8 knockout clone O grown as tumor in NCG mice, sample 3


title: MP41,DMSO,24h, biol rep3

data_processing:
Sequencing reads were aligned to version hg38 of the human genome using gencode v30 gene annotations.
Differential gene expression was calculated using limma-voom R package.
Geneset enrichment analysis and Gene ontology term overrepresentation analysis was performed using clusterProfiler and DOSE R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited excel files for read counts for each gene

extract_protocol:
Total RNA was extracted from frozen cell pellets previously washed with PBS. 1 μg RNA per sample was used as input material.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations, index codes were added to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter). Then 3 μl USER Enzyme (NEB) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

value: uveal melanoma

value: negative control


title: CS18, face, H3K27ac, rep 2

value: face


title: segment 2, ligated, rep 1


title: mandibular process, e11.5, H3K27ac

value: mandibular process


title: MXRA8 knockout clone V grown as 2D culture, sample 3

value: MXRA8KO clone V cells

value: MXRA8 gRNA


title: CS23, face, ATAC, rep 1

data_processing:
ATAC-seq data was analyzed using the ENCODE ATAC-seq (unreplicated) pipeline (https://www.encodeproject.org/pipelines/ENCPL344QWT/).
Assembly: hg38
Supplementary files format and content: narrowPeak, bigWig

extract_protocol:
Human embryonic face tissue (dissected) was received as de-identified, frozen samples from the Human Developmental Biology Resource (Newcastle University, UK). Tissues were lysed, centrifuged for 10min at 500 x g, at 4 degree C, and the resulting cell pellet was treated with the Nextera DNA transposase Tagment DNA Enzyme (Catalog number: 20018705) and the transposed DNA was eluted using Qiagen MinElute PCR purification kit.
Samples were PCR amplified using the NEB Next High-Fidelity 2xPCR Master Mix (Catalog number: NEBE6040SEA) with Nextera PCR primers, and DNA was purified. The eluted library was analyzed for quality in a Bioanalyzer High Sensitivity Assay and samples were subsequently deep sequenced on an Illumina HiSeq2500.


title: nose, e15.5, H3K27 input

value: nose


title: segment 1, ligated, rep 2

value: epididymis segment 1


title: maxillary process, e15.5, input

value: maxillary process


title: CS22, face, ATAC, rep 1

value: mixed


title: MXRA8 knockout clone V grown as 2D culture, sample 2


title: segment 1, ligated, rep 1


title: MXRA8 knockout clone V grown as 2D culture, sample 1


title: CS19, face , ATAC, rep 1


title: mandibular process, e15.5, input


title: MXRA8 knockout clone O grown as 2D culture, sample 3

value: MXRA8KO clone O cells


title: CS18, face, ATAC, rep 2


title: MDA-MB-231 cells infected with control gRNA and grown as tumor in NCG mice, sample 1


title: Naive replicate 7 [N7]

city: Boise

first: Javier

last: Ochoa-Reparaz

state: ID

address: 1910 W University Dr, Science 228 MS1515

institute: Boise State University

data_processing:
Indexes of the reference genome were built using STAR
End paired-end clean reads were aligned to the reference genome using STAR (v2.5).
STAR used the Maximal Mappable Prefix (MMP) method. Clean raw reads were calculated into FPKM
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
NEBNext® UltraTM RNA Library Prep Kit for Illumina®
RNA-seq mapped to mouse reference genome (Kallisto STAR)

treatment_protocol:
EAE was induced using Hooke Laboratories Induction kits (Hooke KitTM EK-2110, Hooke Laboratories, Lawrence, MA). The kits use MOG35-55 in emulsion with complete Freund’s adjuvant (CFA) and Pertussis toxin (PTX) in a glycerol buffer. On day 0 of EAE induction, the MOG35-55-CFA emulsion was diluted with PTX in phosphate-buffered saline and injected subcutaneously. PTX toxin injection was repeated the following day (day +1).
FOL and corn oil were administered daily by gavage: 100 mg/kg/day of FOL (trans, trans-farnesol, Sigma-Aldrich, cat. #277,541) solubilized in corn oil, or no treatment.

value: Brain

value: WT C57BL/6

value: Healthy (naïve)


title: Naive replicate 8 [N8]


title: nose, e15.5, H3K27ac


title: MXRA8 knockout clone O grown as 2D culture, sample 2


title: MXRA8 knockout clone O grown as 2D culture, sample 1


title: Naive replicate 6 [N6]


title: maxillary process, e15.5, H3K27ac


title: Naive replicate 5 [N5]


title: MDA-MB-231 cells infected with control gRNA and grown as 2D culture, sample 3

value: control cells

value: control gRNA


title: Naive replicate 4 [N4]


title: Nose, rep2

data_processing:
For read mapping and peak calling, bowtie2 was used  (version 2.2.6), Unmapped failed reads, duplicates, and low-quality reads (MAPQ = 255) were removed using SAMtools, Peak calling was then performed using MACSv2
Assembly: mm10
Supplementary files format and content: narrowPeak, bigWig

extract_protocol:
Freshly dissected mouse embryonic face tissue. Approx. 50’000 nuclei were pelleted at 500 RCF for 10 min at 4°C and resuspended in 50 µL Transposition reaction mix containing 25 µL Nextera 2x TD buffer and 2.5 µL TDE1 (Nextera Tn5 Transposase; Illumina) (cat. no. FC-121-1030) followed by incubation for 30 minutes at 37°C with shaking. The reaction was purified using the Qiagen MinElute PCR purification kit and amplified using defined PCR primers
ATAC-seq libraries were purified using the Qiagen MinElute PCR purification kit (ID: 28004), quantified by the Qubit Fluorometer with the dsDNA HS Assay Kit (Life Technologies) and quality assessed using the Agilent Bioanalyzer high sensitivity DNA analysis assay. Libraries were pooled and sequenced using single end 50 bp reads on a HiSeq 4000 (Illumina).

value: WT


title: Naive replicate 3 [N3]


title: MDA-MB-231 cells infected with control gRNA and grown as 2D culture, sample 2

value: human TNBC cell line


title: MDA-MB-231 cells infected with control gRNA and grown as 2D culture, sample 1


title: 4C K562 WHITE rep2

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description:
Replicate 2 untreated
4C_K562_white.intersect.noDFAM.txt
4C_K562_white.intersect.noDFAM.bedGraph

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed from adaptor sequences and low quality sequences by cutadapt v. 3.5 using the following options:  1. 4C full length adapters (both direct and reverse complement (RC)) were:  >A1D   TTCACTTCTGACATCCCAGATTTGATCTCCCTACAGAATGCTGTACAGAACTGGCGAGTTGATTTCTGGACTT   >A1RC  AAGTCCAGAAATCAACTCGCCAGTTCTGTACAGCATTCTGTAGGGAGATCAAATCTGGGATGTCAGAAGTGAA  >A2D  TCTTTGAAAAAAATCCCAGAAGTGGTTTTGGCTTTTTGGCTAGGAGGCCTAAGCCTGCTGAGAACTTTCCTGCCCAGGATCCT  >A2RC  AGGATCCTGGGCAGGAAAGTTCTCAGCAGGCTTAGGCCTCCTAGCCAAAAAGCCAAAACCACTTCTGGGATTTTTTTCAAAGA  were removed at 5' ends by the options -O 10 (minimal overlap adapter with the read) --trim-n (omit N’s at the ends of reads) --times=4 (search for the adapter up to 4 times in the read consequently) --minimum-length 20 (minimum acceptable read length after trimming) -q 24 (minimal acceptable quality). All untrimmed reads were collected to the separate file.
2. Illumina 3' adapters array from AGATCGGAAGAGC to AGATCGGAAGAGCNNNNNNNNNN and from GATCGGAAGAGC to GATCGGAAGAGCNNNNNNNNNN anchored to 3' end of reads were removed by cutadapt with the following options: -a -O 10 (minimal overlap adapter with the read) --times=4 (search for the adapter up to 4 times in the read consequently) --minimum-length 20 (minimum acceptable read length after trimming) -q 24 (minimal acceptable quality).
3. Incomplete from 5' 4C full length adapters arrays: from TTCACTTCTGACATCCCAGATTTGATCTCCCTACAGAATGCTGTACAGAACTGGCGAGTTGATTTCTGGACTT to TTCACTTCTGACATCCCAGA (minimal length = 20) and from TCTTTGAAAAAAATCCCAGAAGTGGTTTTGGCTTTTTGGCTAGGAGGCCTAAGCCTGCTGAGAACTTTCCTGCCCAGGATCCT to TCTTTGAAAAAAATCCCAGA (minimal length = 20) both direct and reverse complement, anchored to 5' end of reads were removed by cutadapt with the same options as above.
4. Illumina Adapter GATCGGAAGAGC and IlluminaPE adapter AGATCGGAAGAGC were remove by cutadapt from 3' ends of reads with the following options: -a -O 5 (minimal overlap adapter with the read) --times=4 --minimum-length 20 (minimum acceptable read length after trimming) -q 24 (minimal acceptable quality)
5. Incomplete from 3' 4C full length adapters arrays: from TTCACTTCTGACATCCCAGATTTGATCTCCCTACAGAATGCTGTACAGAACTGGCGAGTTGATTTCTGGACTT to GCGAGTTGATTTCTGGACTT (minimal length = 20) and from TCTTTGAAAAAAATCCCAGAAGTGGTTTTGGCTTTTTGGCTAGGAGGCCTAAGCCTGCTGAGAACTTTCCTGCCCAGGATCCT to ACTTTCCTGCCCAGGATCCT (minimal length = 20) both direct and reverse complement were removed by cutadapt from the 3' end of reads with the same options as in points 2 and 3 of this protocol.
6. All untrimmed reads collected at the first step of the described procedure (i.e., the reads without at least 10 nucleotides overlap of adapter and the read) were trimmed again by the described procedure (points 1-5) with the only difference: at the first step the changed set of cudatapt options was applied: -O 15 (instead of -O 10 thus requiring more adapter nucleotides to overlap with the read), -e 0.2 (this option fixes error rate to 0.2 thus enabling to find adapters that were read with a lesser quality).
Trimmed reads were re-paired by BBTools 38.62 repair.sh script with the option “repair” and mapped to hg38p12 by bwa 0.7.17-r1188 using the mem algorithm. All non-aligned reads were removed from the resulting alignment file by samtools 1.14: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.14, BioPerl and in-house Perl scripts.
Each replicate results table was converted to bedGraph file for further processing using reads amount as data value.
Reads intersections with low complexity genome regions that are stored in DFAM database were found by bedtools v.2.29.1 intersect tool with the command line: intersect -sorted -v -f 1.0, i.e. only reads that mapped completely inside low complexity regions are removed from the further consideration.
Intersections between the filtered replicates was found by bedtools v. 2.29.1: bedtools intersect -a 4C_K562_white.rep1.bedGraph -b 4C_K562_white.rep2.bedGraph -wb. bedops v 2.4.40, in-house Perl and bash scripts were applied to convert bedtools output file back to bedGraph file with splitting and averaging in the overlapped regions. Complete processing pipeline is deposited to Github: https://github.com/lokapal/K562.hemin
Assembly: Homo Sapiens hg38/GRCh38.p12 genome with included to chr14 from address 1 Human ribosomal DNA U13369
Supplementary files format and content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence.
Supplementary files format and content: bedGraph files for each replicate and filtered from low complexity regions intersection.
Library strategy: 4C

source_name: blood

growth_protocol: The cells were drown in RPMI 1640 media (PanEco, Russia) supplemented with heat-inactivated fetal calf serum (HyClone, USA), 2 mM glutamine, 250 u/ml penicillin and 250 μg/ml streptomycin (PanEco, Russia) at 37 °C in a humidified atmosphere containing 5% CO2. For a treated samples, hemin (50 μM, neoFroxx, Germany) was added to induce the erythroid differentiation and cells were incubated further for 108 h. At this concentration, the drug did not affect cell proliferation.

extract_protocol:
DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking  To suspension containing about 20x106 of untreated K562 cells in 40 ml of DMEM formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis   The pellet of cells was resuspended at 0°C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI  The nuclei pellet was resuspended in 756 ul of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation  To inactivate the restriction enzyme, 35 l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5 l of BSA (5 mg/ml), 80 l of 100 mM ATP, and 5241 l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification  For isolation of DNA 50 l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40 l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI  About 15 g of DNA was digested in 250 ul solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100 l of 0.1xTE.   Ligation  For circularization 15 g of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50 l of 0.1xTE.   PCR and library preparation  For preparation of 4C-rDNA libraries about 30 ng of 4C DNA preparations were used for 35 cycles of PCR with primers 5' TCTTTGAAAAAAATCCCAGAAGTGGT 3' and 5' AAGTCCAGAAATCAACTCGCCAGT 3' for each biological replicate. Deep sequencing of libraries were performed using HiSeq 2500 Rapid v2 (Illumina) using 150-nt long paired-end reads.
For preparation of 4C-rDNA libraries about 30 ng of 4C DNA preparations were used for 35 cycles of PCR with primers 5' TCTTTGAAAAAAATCCCAGAAGTGGT 3' and 5' AAGTCCAGAAATCAACTCGCCAGT 3' for each biological replicate. Deep sequencing of libraries were performed using HiSeq 2500 Rapid v2 (Illumina) using 150-nt long paired-end reads.

treatment_protocol: K562 cells incubated in the presence of 50 μM hemin (neoFroxx, Germany) for 108 h. At this concentration, the drug did not affect cell proliferation.

value: blood

tag: disease state

value: erythroleukemia

value: untreated

tag: agent


title: 4C K562 RED rep1

description:
Replicate 1 hemin
4C_K562_red.intersect.noDFAM.txt
4C_K562_red.intersect.noDFAM.bedGraph

value: erythroid differentiation

value: hemin


title: Naive replicate 2 [N2]


title: Nose, rep1

value: nose


title: Mandibular Process (Md), rep1

value: mandibular process


title: Naive replicate 1 [N1]


title: 4C K562 WHITE rep1

description:
Replicate 1 untreated
4C_K562_white.intersect.noDFAM.txt
4C_K562_white.intersect.noDFAM.bedGraph


title: MCF7 cells, FOXK2-KD-2

first: Yang

last: Yu

address: 111 Michigan Ave NW

institute: Children's national hospital

data_processing:
RNA-Seq experiments were conducted by using Illumina paired-end sequencing technology.
Raw reads were adaptor removed, and sequencing quality was assessed with the bioinformatics software FastQC (version 0.11.2).
Reads were mapped against the human reference genome (GRCh38.p13 assembly) using the aligner, HISAT2 (v2.1.0).
The mapped reads were subsequently assembled into transcripts or genes using the assembler, StringTie (v1.3.5).
Assembly: Homo_sapiens.GRCh38.dna. primary_assembly.fa.gz
Supplementary files format and content: ReadCounts.xlsx

growth_protocol: MCF7 with FOXK2 knockdown or the control  cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Thermo Fisher). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Breast Cancer


title: Mandibular Process (Md), rep2

value: mixed


title: MCF7 cells, FOXK2-KD-1


title: CS18, face, ATAC, rep 1

value: face


title: FOL treated EAE replicate 9 [EF9]

value: Brain

value: Farnesol treated EAE


title: Maxillary Process (Mx), rep2

value: maxillary process


title: MCF7 cells, Control-3

value: Control


title: 4C K562 RED rep2

description:
Replicate 2 hemin
4C_K562_red.intersect.noDFAM.txt
4C_K562_red.intersect.noDFAM.bedGraph


title: Maxillary Process (Mx), rep1


title: Mammary adipose_surgery_weight_loss rep3

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

data_processing:
Sequence reads were mapped to the mouse genome (mm10) using Bismark Bisulfite Read Mapper.
Assembly: mm10
Supplementary files format and content: raw fastq file (paired end)
Supplementary files format and content: processed data:  normalized read counts in .txt format

source_name: Contralateral normal mammary tissue

growth_protocol: C57BL/6Nmice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain obese or undergo weight loss via 1) low-fat diet, or 2) vertical sleeve gastrectomy with low-fat diet.

extract_protocol:
DNA was isolated by TRIzol
Genomic DNA (1 mg) was digested with MspI, and enrichment for CpG sites in CG-dense and CpG islands was achieved by selective collection and PCR amplification of MspI fragments with sizes of 40-170 bp

treatment_protocol: All mice received either sham surgery or vertical sleeve gastrectomy. 22 weeks after initial randomization mice were orthotopically injected with E0771 cells into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint the contralateral (9th) mammary fat pad was removed and used for nucleic acid extraction.

value: Contralateral normal mammary tissue

value: mouse mammary cancer

value: wt

value: weight loss vertical sleeve gastrectomy


title: FOL treated EAE replicate 8 [EF8]

value: WT C57BL/6


title: MCF7 cells, Control-2


title: FOL treated EAE replicate 10 [EF10]


title: FOL treated EAE replicate 7 [EF7]


title: FOL treated EAE replicate 6 [EF6]


title: mandibular process, e15.5, H3K27ac

value: WT


title: Mammary adipose_surgery_weight_loss rep2


title: FOL treated EAE replicate 5 [EF5]


title: MCF7 cells, Control-1


title: Mammary adipose_surgery_weight_loss rep1


title: H1 cells, SETD7 KO cells, Day2, rep3

city: TianJin

first: Changlu

last: Xu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description:
Day2_KO3
Day2_SETD7_Gene_counts.csv

data_processing:
Clean data were used as input files to map the human reference genome (GRCh38/hg38) using the HISAT2-StringTie analysis pipeline with default parameters.
Assembly: GRCh38/hg38
Supplementary files format and content: Comma-separated files include gene counts and FPKM values for each sample

growth_protocol: H1 cells were maintained in mTESR medium and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Hematopoietic differentiation was induced in Coustom TESR with different selecting factors.

value: Human embryonic stem cell line

value: SETD7 KO

value: hematopoietic differentation


title: MCF7 cells, FOXK2-KD-3


title: FOL treated EAE replicate 4 [EF4]


title: Mammary adipose_Diet_weight_loss rep3

value: weight loss diet


title: H1 cells, SETD7 KO cells, Day2, rep1

description:
Day2_KO1
Day2_SETD7_Gene_counts.csv


title: Mammary adipose_Diet_weight_loss rep2


title: H1 cells, WT cells, Day2, rep3

description:
Day2_WT3
Day2_SETD7_Gene_counts.csv


title: FOL treated EAE replicate 3 [EF3]


title: FOL treated EAE replicate 2 [EF2]


title: Mammary adipose_Diet_weight_loss rep1


title: Mammary adipose_surgery_weight_loss rep4


title: FOL treated EAE replicate 1 [EF1]


title: H1 cells, WT cells, Day2, rep1

description:
Day2_WT1
Day2_SETD7_Gene_counts.csv


title: Mammary adipose_obese rep3

value: obese


title: H1 cells, WT cells, Day2, rep2

description:
Day2_WT2
Day2_SETD7_Gene_counts.csv


title: Mammary adipose_obese rep4


title: H1 cells, SETD7 KO cells, Day0

description:
Day0_KO
Day0_FPKM.csv


title: Vehicle treated EAE replicate 9 [EV9]

value: Vehicle treated EAE


title: H1 cells, SETD7 KO cells, Day2, rep2

description:
Day2_KO2
Day2_SETD7_Gene_counts.csv


title: Vehicle treated EAE replicate 6 [EV6]


title: H1 cells, WT cells, Day0

description:
Day0_WT
Day0_FPKM.csv


title: Mammary adipose_obese rep1


title: Mammary adipose_control rep3

value: control


title: Vehicle treated EAE replicate 8 [EV8]

value: Brain


title: Mammary adipose_obese rep2


title: Vehicle treated EAE replicate 7 [EV7]


title: colorectal cacer  plasma EV 5

city: Shanghai

first: yunjie

last: shi

address: No 800，Xiangyin Road

institute: Naval Medical University

data_processing:
The raw data (raw reads) obtained from Illumina HiSeqTM 2500 sequencing.
The connectors at both ends of the reads, and the reads with fragment length less than 17nt and low-quality read were removed to complete the preliminary filtering of data and obtain high-quality data (clean reads).
C++and R languages were used to control the quality of raw data to obtain clean and high-quality data.
The expression of microRNA was analyzed with Perl software, and the differential expression of microRNA was obtained with edgeR software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: plasma

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

value: plasma

value: colorectal cancer


title: Vehicle treated EAE replicate 5 [EV5]


title: Mammary adipose_control rep1


title: Mammary adipose_control rep2


title: colorectal cacer  plasma EV 6


title: Vehicle treated EAE replicate 4 [EV4]


title: colorectal cacer  plasma EV 3


title: colorectal cacer  plasma EV 2


title: Vehicle treated EAE replicate 3 [EV3]


title: Mammary adipose_control_rep4

data_processing:
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.7).
The aligned reads were counted using HTSeq-count from HTSeq package (version 0.5.3p9).
Differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: raw fastq file (paired end)
Supplementary files format and content: processed data: DESeq2 normalized read counts in .txt format

growth_protocol: C57BL/6Nmice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain obese or undergo weight loss via 1) low-fat diet, or 2) verticle sleeve gastrectomy with low-fat diet.

extract_protocol:
DNA was isolated by TRIzol
Illumina TruSeq Stranded Total RNA Library Preparation Kit, sequenced using a 2x76 bases paired-end protocol on the Illumina HiSeq 2000 instrument

treatment_protocol: All mice recieved either sham surgery or verticle sleeve gastrectomy. 22 weeks after initial randomization mice were orthotopically injected with E0771 cells into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint the contralateral (9th) mammary fat pad was removed and used for nucleic acid extraction.

tag: group


title: colorectal cacer  plasma EV 4


title: Vehicle treated EAE replicate 2 [EV2]

tag: treatment


title: colorectal cacer  plasma EV 1


title: Vehicle treated EAE replicate 1 [EV1]


title: Mammary adipose_control_rep2

tag: cell line


title: advanced adenoma plasma EV 6

value: advanced adenoma


title: Untreated EAE replicate 9 [EU9]

tag: genotype

value: Untreated EAE


title: Mammary adipose_control_rep3

value: Contralateral normal mammary tissue

value: mouse mammary cancer


title: advanced adenoma plasma EV 5


title: Mammary adipose_control_rep1

value: wt


title: Mammary adipose_surgery_weight_loss_rep4


title: Untreated EAE replicate 8 [EU8]

value: WT C57BL/6


title: Untreated EAE replicate 6 [EU6]


title: advanced adenoma plasma EV 4


title: Mammary adipose_surgery_weight_loss_rep3


title: Mammary adipose_surgery_weight_loss_rep2


title: advanced adenoma plasma EV 3


title: Untreated EAE replicate 4 [EU4]


title: advanced adenoma plasma EV 1


title: Untreated EAE replicate 7 [EU7]


title: advanced adenoma plasma EV 2


title: Untreated EAE replicate 3 [EU3]


title: Untreated EAE replicate 2 [EU2]


title: Mammary adipose_Diet_weight_loss_rep3


title: healthy donor plasma EV  6

value: Ctrl


title: healthy donor plasma EV  5


title: Mammary adipose_Diet_weight_loss_rep2


title: healthy donor plasma EV  4


title: Untreated EAE replicate 1 [EU1]


title: healthy donor plasma EV  3


title: Mammary adipose_Diet_weight_loss_rep1


title: KO-3,KO replicate3

city: Guangzhou

first: Xinpeng

last: Liu

state: Guangdong

address: 157 health care road, nangang district, Harbin

department: StomatologicalHospital

institute: Southern Medical University

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
ATAC-seq reads were aligned to the mm10 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: osteoblasts

growth_protocol: αMEM, 10% fetal bovine serum, 1% penicillin-streptomycin, cells  were cultured at 37°C with 5% CO2.

extract_protocol:
cells were harvested from cell culture and lysed in lysis buffer. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃.
The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen).

value: osteoblasts

value: cell line

value: Musmusculus osteoblasts

value: Fam20c-deficient osteoblasts

value: Fam20c knockout


title: Mammary adipose_obese_rep4

value: obese


title: healthy donor plasma EV  2


title: KO-2,KO replicate2


title: Mammary adipose_obese_rep3


title: Mammary adipose_surgery_weight_loss_rep1


title: Untreated EAE replicate 5 [EU5]


title: KO-1,KO replicate1


title: healthy donor plasma EV  1


title: Mammary adipose_Diet_weight_loss_rep4


title: WT3P2 INPUT

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: single-stranded RNA, tri-phopshorylated TAATACGACTCACTATAGGAAACTAAAAGGGAGAAGTGAAAGTG and CACTTTCACTTCTCCCTTTTAGTTTCCTATAGTGAGTCGTATTA

data_processing:
Data was processed using the eCLIP pipeline and available at: http://github.com/yeolab/eclip
Reads were demultiplexed and umi-extracted according to their inline barcode (sequences available on github in: yeolabbarcodes_20170101.fasta) with custom scripts (available at: https://github.com/YeoLab/eclipdemux)
Post-umi-extracted reads were trimmed of adapter sequences using cutadapt 1.14
Trimmed reads were mapped against RepBase with STAR v2.4.0j to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were uniquely mapped to the appropriate genome build (hg19) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Uniquely mapped reads were removed of PCR duplicates with custom scripts available on github (barcodecollapsepe.py)
PCR-deduped BAM files from data with multiple inline barcodes were merged with samtools merge.
R2 was extracted from aligned reads using samtools view (-f 128)
Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Overlapping enriched clusters (peaks) were merged with a custom perl script, available in the main eCLIP repository as: compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl
Assembly: hg19
Supplementary files format and content: bigwigs contain RPM-normalized read densities of uniquely-mapped reads
Supplementary files format and content: BED files contain CLIPper peak clusters. Columns 4 and 5 describe the -log10(p-value) and log2(fold) enrichment IP over corresponding SMInput.

source_name: human embryonic kidney

growth_protocol: 1X Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37°C in a 5% CO2

extract_protocol:
N/A
eCLIP Standard Operating Procedure v1.P 20151108 (van Nostrand et al, Nat. Methods 2016)
Bound RNA isolation - 3'  adapter ligation - revese transcription - 5' adapter ligation - cDNA amplification by PCR

treatment_protocol: 2.5 μL Lipofectamine 2000 and 125 μL Opti-MEM medium were combined with a mixture of 1 μg RNA (either ssRNA or 3p-RNA) and 125 μL Opti-MEM per well of a 6-well plate. After 5 min at room temperature, the solution was added drop-wise to cells grown to 70-90% confluence in 2 mL DMEM

value: human embryonic kidney

value: embryonic kidney

value: wildtype

value: transfection

tag: inline barcodes


title: Mammary adipose_obese_rep2


title: WT3P2


title: Mammary adipose_obese_rep1


title: OB-2,OB replicate2

value: control


title: OB-3,OB replicate3


title: BDL [8_S180_R1_001]

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

country: Germany

institute: University Hospital Bonn

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
DEseq2 normalization
Flooring
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized gene counts

source_name: BDL_T cells

extract_protocol:
RNA was isolated via Qiagen RNeasy micro kit
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)
1x 50bp single reads, 15mio reads deep per sample, Illumina HiSeq2500

tag: strain

tag: treatment/group

value: BDL

value: primary liver T cells

tag: passages


title: S_OGM_bio3

city: South San Francisco

first: Kimberly

last: Homan

address: 1 DNA Way

institute: Genentech

description: Colon organoid grown as BOBAs in OGM

data_processing:
Base-calling and quality control were performed by Novogene, Inc.
Gene mapping was performed by Novogene, Inc.
Assembly: GRCm38
Supplementary files format and content: gene_count.xls is a tab-delimited file containing gene counts for all genes in reference genome for all conditions. The gene_id header refers to the Ensembl gene ID. The sample name headerss refer to the readcounts for that sample. The gene_name header refers to the gene symbol. The gene_chr header refers to the chromosome/scaffold ID. The gene_start header refers to the chromosomal start coordinate, and gene_end refers to the end coordinate. The gene_strand header refers to the strand specificity of the gene. The gene_length header provides the gene length in bp. The gene_biotype header provides the gene type. The gene_description header provides a description from PFAM Annotation. The tf_family header provides the TF family for the gene if applicable.
Supplementary files format and content: gene_fpkm.xls is a tab-delimited file containing gene counts in FPKM for all genes in reference genome for all conditions. The gene_id header refers to the Ensembl gene ID. The sample name headerss refer to the readcounts for that sample. The gene_name header refers to the gene symbol. The gene_chr header refers to the chromosome/scaffold ID. The gene_start header refers to the chromosomal start coordinate, and gene_end refers to the end coordinate. The gene_strand header refers to the strand specificity of the gene. The gene_length header provides the gene length in bp. The gene_biotype header provides the gene type. The gene_description header provides a description from PFAM Annotation. The tf_family header provides the TF family for the gene if applicable.

source_name: Colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and extracted using the QiaCube Connect (Qiagen). At least 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

value: Colon

value: Colon Stem Cell Organoids

value: WT

value: BOBA + OGM growth


title: WT3P1 INPUT


title: BDL [7_S179_R1_001]


title: S_OGM_bio2

description: Colon organoid grown as BOBAs in OGM


title: OB-1,OB replicate1

value: osteoblasts


title: S_OGM_bio1

description: Colon organoid grown as BOBAs in OGM


title: WTSS2 INPUT

description: single-stranded RNA, unphosphorylated CACUUUCACUUCUCCCUUUUAGUUUCC


title: BDL [5_S177_R1_001]


title: BDL [6_S178_R1_001]


title: WTSS2


title: Sham [4_S176_R1_001]

source_name: Sham_T cells

value: Sham


title: S_DAPT_bio1

description: Colon organoid grown as BOBAs, DAPT differentiated, day 5

value: BOBA + DAPT differentiation


title: Sham [3_S175_R1_001]


title: S_DAPT_bio2


title: WTSS1


title: Sham [2_S174_R1_001]


title: D_OGM_bio3

description: Colon organoid grown as Domes in OGM

value: Dome + OGM


title: WTSS1 INPUT


title: Sham [1_S173_R1_001]


title: YAP_2

city: Shang Hai

first: Ping

middle: Ping

last: Nie

address: Songhu Road 2005

institute: Fudan University

data_processing:
Sequencing raw reads were preprocessed by filtering out sequencing adapters, short-fragment reads and other low-quality reads.
Bowtie (version 0.12.8) was then used to map the clean reads to the human hg19 reference genome.
Peak detection was performed by MACS2 (version 2.2.7.1; https://pypi.python.org/pypi/MACS/2.2.7.1).
The protein-binding motifs were identified using HOMER software (http://homer.ucsd.edu/homer/).
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: Blood

growth_protocol: neutrophils cells were isolated from the peripheral blood of gastric cancer patient using positive selection of CD15+ cells with microbeads according to the manufacturer’s instructions (Miltenyi Biotec Inc.).

extract_protocol:
DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation as well as RNase A treatment.
For library amplification, 24 μl of DNA was mixed with 1 μl of TruePrep Amplify Enzyme , 10 μl of 5× TruePrep Amplify Enzyme buffer and 5 μl of ddH2O, as well as 5 μl of uniquely barcoded i5 and i7 primers from TruePrep Index Kit V2 for Illumina (Vazyme).
The DNA fragments were then isolated and sequenced using the Illumina HiSeq X-ten platform (Shanghai Biotechnology Co., China).

treatment_protocol: 1 μg of primary antibody (YAP (Abcam, ab39361; Santa Cruz, A2319) or normal mouse IgG (Abcam, ab171870)) was added and incubated overnight at 4 °C with slow rotation.

value: neutrophils

tag: chip antibody

value: YAP (Abcam ab39361)


title: D_OGM_bio2

description: Colon organoid grown as Domes in OGM


title: M-K-SM-2

city: Changsha

first: Yanxia

last: Guo

address: 100 Fubuhe Street, Yuelu District

institute: Hunan University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were processed using fastp 1 and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: StringTie2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor tissue

extract_protocol:
RNA was harvested using  TRIzol reagent (Invitrogen, CA, USA)
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: tumor tissue

value: colon cancer cells

value: TLR4 knockout C57BL/6 mice

value: Salmonella i.v. injection post 1 day


title: YAP_4

value: YAP (Santa Cruz A2319)


title: IgG

value: IgG (Abcam ab171870)


title: WT3P1

value: human embryonic kidney

value: embryonic kidney

value: wildtype

value: transfection


title: M-K-SF-1


title: Skin, Adalimumab, day00, rep3, pair1

city: Worcester

first: Jing

last: Wang

address: 100 Research Drive

institute: AbbVie

description:
count data column name: YC04-8BLA
cao_mouse_skin_genesymbol_count

data_processing:
RNA-seq reads were aligned to the mouse genome (GRCm39) with STAR
Assembly: GRCm39
Supplementary files format and content: .txt file containing raw counts for all samples

source_name: skin

growth_protocol: HTNFki/kiLeprdb/db mice (8~12 weeks) were placed in a chamber and anesthetized with 5% isoflurane to prepare the animals. The fur on the dorsal skin was removed with an electric shaver, followed by the application of NairTM hair removal cream for no more than 1 min. The dorsal skin was cleaned and sterilized with iodine solution. After depilation, four 6-mm diameter full-thickness skin punches extending through the panniculus carnosus were made on the dorsa of mice with skin biopsy punches, and dressed by TegadermTM transparent film. Mice were administrated with tramadol (5 mg/kg, single dose) and indicated TNF inhibitors or vehicle control (twice a week by subcutaneous injection). Wounds were measured by caliper and photographed every other day and visually monitored for possible signs of infection. The wound area was quantified by tracing wound margins and calculated as a percent of the original wound size, with scaling normalized to the original wound. Secondary 8-mm full-thickness skin punches overlaying the original wounds were harvested on indicated days for RNA sequencing.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions.
RNA library preparation from total RNA was conducted following the manufacturer’s protocol for the SMARTer Stranded Total RNA-Seq Kit V2-Pico
Final libraries were assessed using the Agilent Tapestation and Qubit assay methods, then sequenced on an Illumina NextSeq500 sequencer using 1x50bp read length for a depth of 50M reads

treatment_protocol: Wounded mice were administrated with either vehicle control (PBS) or adalimumab (20mg/kg, twice a week on days 0, 3, 7, and 10 by subcutaneous injection).

value: skin

tag: biological replicate

tag: time

value: Day 0

value: Adalimumab


title: D_DAPT_bio3

description: Colon organoid grown as Domes, DAPT differentiated, day 5

value: Colon

value: Colon Stem Cell Organoids

value: WT

value: Dome + DAPT


title: mouse antrum scRNA-seq

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
Raw reads were aligned to the different species genome (Human: GRCh38/hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: GRCm38/mm10), and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs).
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Assembly: Human: hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: mm10
Supplementary files format and content: text files

organism: Sus scrofa

source_name: antral epithelium

extract_protocol:
Gastric glands were isolated and digested with EDTA and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

value: antral epithelium

tag: strategy

value: scRNA-seq

value: Wild type

value: Untreated


title: D_DAPT_bio2


title: M-K-SM-1

value: tumor tissue

value: colon cancer cells

value: TLR4 knockout C57BL/6 mice

value: Salmonella i.v. injection post 1 day


title: S_DAPT_bio3

value: BOBA + DAPT differentiation


title: Skin, Adalimumab, day03, rep2, pair1

description:
count data column name: YC04-7-D3A
cao_mouse_skin_genesymbol_count

value: Day 3


title: Skin, Adalimumab, day00, rep2, pair1

description:
count data column name: YC04-7BLA
cao_mouse_skin_genesymbol_count

value: skin


title: D_DAPT_bio1


title: TNFa treated pig gastric antral organoids-2

description: pig-TNFa-con.csv

data_processing:
RNA-seq reads were aligned to the human, pig, rat or mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Assembly: Human: hg38, Pig: Sscrofa11.1, Rat: Rnor_6.0, Mouse: mm10
Supplementary files format and content: csv

source_name: Gastric antral organoids

growth_protocol: Organoids were embedded in Matrigel and seeded on 48- or 24- well plate. After Matrigel polymerization, the CM medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX, N2, B27, and N-acetylcysteine containing 50 ng/mL EGF, 100 ng/mL Noggin, 500 ng/mL R-spondin1, 5 μM CHIR, 10 nM Gastrin, 10 μM SB431542, 100 ng/mL FGF10 and 10 μM Y27632) was added and refreshed every 2 days.

extract_protocol:
Organoids were digested with Tryple and alive cells were sorted by flow cytometry. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
The library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina.

treatment_protocol: Organoids derived from antral glands of 4 kinds of species were treated with Tnfa 10 ng/ml for 2 days.

value: RNA-Seq

value: Treated with TNFa 2 days


title: M-K-PM-2

value: PBS i.v. injection post 1 day


title: TNFa treated pig gastric antral organoids-1

description: pig-TNFa-con.csv


title: M-K-PM-1


title: Skin, Adalimumab, day03, rep1, pair1

description:
count data column name: YC04-6-D3A
cao_mouse_skin_genesymbol_count

value: Adalimumab


title: human antrum scRNA-seq repeat 4

source_name: antral epithelium and stromal cells

value: antral epithelium and stromal cells

value: Sleeve gastric surgery


title: WT pig gastric antral organoids-2

description: pig-TNFa-con.csv


title: human antrum scRNA-seq repeat 3


title: D_OGM_bio1

description: Colon organoid grown as Domes in OGM

value: Colon

value: Colon Stem Cell Organoids

value: WT

value: Dome + OGM


title: Skin, Adalimumab, day03, rep3, pair1

description:
count data column name: YC04-8-D3A
cao_mouse_skin_genesymbol_count


title: WT pig gastric antral organoids-1

description: pig-TNFa-con.csv

value: Wild type

value: Untreated


title: Skin, Adalimumab, day00, rep1, pair1

description:
count data column name: YC04-6BLA
cao_mouse_skin_genesymbol_count

value: Day 0


title: M-W-SM-2

value: tumor tissue

value: colon cancer cells

value: WT C57BL/6 mice

value: Salmonella i.v. injection post 1 day


title: M-K-PF-1

value: TLR4 knockout C57BL/6 mice


title: human antrum scRNA-seq repeat 2

value: scRNA-seq


title: bulk RNA-seq of pig gastric antral organoids

description: pig-exp.csv

value: RNA-Seq


title: M-W-SM-1


title: Skin, control, day00, rep3, pair1

description:
count data column name: YC04-17BLA
cao_mouse_skin_genesymbol_count

value: skin

value: control


title: human antrum scRNA-seq repeat 1

value: antral epithelium and stromal cells

value: Sleeve gastric surgery


title: Skin, control, day03, rep3, pair1

description:
count data column name: YC04-17-D3A
cao_mouse_skin_genesymbol_count

value: Day 3


title: TNFa treated human gastric antral organoids-2

description: human-TNFa-con.csv

value: Treated with TNFa 2 days