title: RPA_ChIP_siRAD51_sg1_rep2

description: Related to Fig 3D


title: Control replicate 1

status: Public on Jun 11 2025

type: SRA

city: Memphis

first: Douglas

middle: R

last: Green

state: TN

address: 262 Danny Thomas Place

department: Immunology

country: USA

institute: St. Jude Children's Research Hospital

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse mm10 assembly plus ERCC spike-in sequences using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function (version 2.19.0).
Transcript quantification was calculated using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: CD8+ T cells

growth_protocol: Tumor infiltrating CD8+ T cells were isolated from tumors at D9 post T-cell injection.

extract_protocol:
Total-RNA was isolated using RNAqueous-Micro Total RNA isolation kit (Catalog-AM1931, Thermo).
Libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) (08098131702, Roche) and purified by AMPure SPRI beads (B23318, Beckman-Coulter).

tag: cell type

value: CD8+ T cells

tag: genotype

value: Wild type

tag: treatment

value: 0.1mM Methionine


title: Human_Ulix_1_1

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

country: United Kingdom

institute: Loke Centre for Trophoblast Research

library_source: transcriptomic single cell

data_processing:
Technical replicate fastq files were merged and preprocessed using the nf-core/rnaseq pipeline 3.10.1 with Nextflow 22.10.1. Briefly, reads were trimmed for adaptors and quality using Trimgalore 0.6.7 and cutadapt 3.4. Trimmed reads were pseudoaligned to GRCh38 with salmon 1.9.0.
Assembly: GRCh38
Supplementary files format and content: all_tpm.tsv: TPM normalised counts
Supplementary files format and content: all_counts.tsv: salmon raw count output

organism: Homo sapiens

source_name: human embryo

extract_protocol:
Human and mouse embryos were subject to immunosurgery to remove outer trophectoderm cells and isolate the inner cell mass (ICM), as reported previously(Strawbridge et al., 2002: PMID 34870826;Solter and Knowles 1975 PMID 1108013). The zona pellucida was removed by washing embryos through drops of acid Tyrode’s solution pre-warmed to 37°C. Embryos were then washed briefly and incubated at 37°C for 30min in 20% anti-mouse serum (Sigma) or 20% anti-human serum (Sigma), depending on the species, in Global media + 10% HSA. Embryos were then washed briefly in Global medium + 10% HSA, before incubation with 20% Guinea Pig Serum Complement (Merk) at 37°C for 10-15min until trophectoderm began to lyse. Embryos were then moved to a drop of medium and triturated with 100µm STRIPPER tip (Cooper Surgical) to remove lysed trophectoderm and isolate the inner cell mass.Isolated ICMs were then briefly washed, then incubated at 37°C for 3 min in 0.5% Trypsin, 1mM EDTA in PBS. Then, ICMs were transferred to 4% BSA, 0.5mM EDTA in PBS for fine manual dissociation into single cells with pulled (Sutter Instruments) glass capillaries (World Precision Instruments). Cells were then picked manually with pulled glass capillaries for downstream single-cell RNA-seq. cDNA kit lot number 2109360A
Single-cell cDNA synthesis was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) according to the manufacturers protocol with some modifications as previously described(Blakeley et al., PMID 26293300). Briefly, single-cells were manually picked after dissociation and snap frozen on dry ice in 5µl 10x Reaction Buffer in low-bind 0.2ml PCR tubes and stored at -80°C until processing. Samples were subject to first strand cDNA synthesis, then cDNA was amplified by LD PCR for 23 cycles. Amplified cDNA was purified on AMPure XP beads, using a 96-well magnetic stand (ThermoFisher), and eluted in 17µl of elution buffer. Single-cell RNA-seq libraries were prepared using a Nextera XT DNA Library Preparation Kit (Illumina) using according to the manufacturers protocol. Sequencing was carried out as paired-end 50bp read on Novaseq 6000 to a depth of 12 million reads.

treatment_protocol: Human blastocysts were cultured in Global media (Cooper Surgical) supplemented with 10% Human Serum Albumin (HSA, Cooper Surgical) in Embryo+ slide dishes (Vitrolife) overlaid with Mineral oil (Cooper Surgical). Embryos were incubated at 37°C 5% CO2 in an EmbryoScope time-lapse imaging system (Vitrolife). For treatments, immediately after thawing embryos were incubated in Global media, 10% HSA supplemented with; 250 FGF: 250ng/ml FGF4 (R&D) and 250ng/ml Heparin (Sigma); 500 FGF: 500ng/ml FGF4 and 500ng/ml Heparin; 750 FGF: 750ng/ml FGF4 and 750ng/ml Heparin; 1000 FGF: 1000ng/ml FGF4 and 1000ng/ml Heparin; 5µM Ulixertinib (Cambridge Bioscience); 1% DMSO. Day 5 embryos were treated with cytokines and inhibitors for 36 hours to Day 6.5.

tag: tissue

value: human embryo

tag: sample collection

tag: cdna prep

tag: embryo stage

value: Ulixertinib


title: Human_DMSO_2_10

value: DMSO


title: MCF10A_RPA_ChIP_sg1_siRAD51_R1

city: Bethesda

first: Ajith

last: Viswanathan Asari Pankajam

address: Building 37

institute: National Institutes of Health

description: Related to Fig 3D

library_source: genomic

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction

molecule: genomic DNA

extract_protocol:
For END-seq, Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
For ChIP-seq, Live cells were fixed using 1% Formaldehyde. After cell lysis, DNA was sonicated and captured using specific antibodies.
For TrAEL-seq, Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
For EdU-seq, Live cells were fixed with methanol 90%. Genomic DNA was extracted after Click-IT reaction.
Libraries were constructed and sequenced following Illumina standard protocols and were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences)
END-seq, EdU-seq, Amplicon-seq, ChIP-seq, TrAEL-seq

tag: cell line

value: mammary epithelial cells

value: WT RAD51KD by siRNA

value: siRAD51 for 24h


title: IgG control for histone modification experiment

description: Library name: Sample 18

data_processing:
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid reference of mouse mm10 and E. coli ASM584v2 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq6 to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions, or have more than 4 mismatches (-F 0x004 -F 0x008 -F 0x0100 -F 0x0400 -f 0x001 -q 1).
MACS (version 2.1.2) was used to call peaks from the BAM file with IgG control and recommended mappable genome size (default value for other parameters). NarrowPeak mode was used for NFAT1 and H3K4me3, broadPeak mode for H3K27me3.
Signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters.
Assembly: mm10
Supplementary files format and content: BigWig files scaling tag count to 1 million mapped reads to spike-in E. coli genome.
Supplementary files format and content: Bed files of peaks called using MACS2.
Library strategy: CUT&Run

growth_protocol: OT-I CD8+ T cells were activated in 0.1mM methionine or 0.03mM methionine with 2.5ng/ml SIINFEKL. Methioinine was restored to control (0.1mM) levels in 0.03mM after 30 min of activation. Cells were cultured for 24 hrs.

extract_protocol:
CUT&RUN ChIP-seq experiments were performed as previously described (Meers et al. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019)) with modifications as needed.
CUT&RUN ChIP-seq experiments were performed as previously described (Meers et al. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019)) with modifications as needed.

value: Control


title: Control - H3K4me3 modification replicate 3

description: Library name: Sample 17

treatment_protocol: OT-I CD8+ T cells were activated in 0.1mM methionine or 0.03mM methionine with 2.5ng/ml SIINFEKL. Methioinine was restored to control (0.1mM) levels in 0.03mM after 30 min of activation. Cells were cultured for 24 hrs.


title: MCF10A_S1-END-seq_sg1_sgblocking_guides

description: Related to Fig 3D

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction
Library strategy: S1-ENDseq

value: WT


title: Human_DMSO_2_9


title: Control - H3K4me3 modification replicate 2

description: Library name: Sample 16


title: Human_DMSO_2_8


title: MCF10A_siBRCA2_RPA_ChIP_R6h

description: Related to Fig 3C

value: WT BRCA2KD by siRNA

value: siBRCA2 for 48h


title: Control - H3K4me3 modification replicate 1

description: Library name: Sample 15


title: RPE1_BRCA1KO_RPA_ChIP_R8h

description: Related to Fig 3B

value: retinal pigment epithelial cells


title: Human_DMSO_2_7


title: MCF10A_RPA_ChIP_siRAD51_6h

description: Related to Fig3 A and S8


title: MCF10A_RPA_ChIP_control_6h

description: Related to Fig 3A and S8


title: 30uM - H3K4me3 modification replicate 3

description: Library name: Sample 14

value: 0.03mM Methionine


title: MCF10A_END-seq_siRAD51_12h_Lagging_Rep3

description: Related to Fig 2 and S6

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction
Library strategy: ENDseq


title: Human_DMSO_2_6


title: MCF10A_END-seq_siRAD51_6h_Lagging_Rep3

description: Related to Fig 2 and S6


title: 30uM - H3K4me3 modification replicate 2

description: Library name: Sample 13


title: MCF10A_END-seq_siRAD51_12h_Lagging_Rep2

description: Related to Fig 2 and S6


title: Human_DMSO_2_5


title: MCF10A_END-seq_siRAD51_6h_Lagging_Rep2

description: Related to Fig 2 and S6


title: 30uM - H3K4me3 modification replicate 1

description: Library name: Sample 12


title: MCF10A_END-seq_siRAD51_12h_Lagging

description: Related to Fig 2 and S6


title: Human_DMSO_2_4


title: Control - H3K27me3 modification replicate 3

description: Library name: Sample 11


title: MCF10A_END-seq_WT_12h_Lagging_Rep3

description: Related to Fig 2 and S6


title: Human_DMSO_2_3


title: MCF10A_END-seq_WT_6h_Lagging_Rep3

description: Related to Fig 2 and S6


title: MCF10A_END-seq_siRAD51_6h_Lagging

description: Related to Fig 2 and S6


title: RPE1_BRCA1KO_RPA_ChIP_R16h

description: Related to Fig3B


title: Human_DMSO_2_2


title: Control - H3K27me3 modification replicate 1

description: Library name: Sample 9


title: MCF10A_END-seq_WT_12h_Lagging

description: Related to Fig 2 and S6


title: Human_DMSO_2_1


title: MCF10A_END-seq_WT_6h_Lagging

description: Related to Fig 2 and S6


title: MCF10A_END-seq_siRAD51_12h_Leading_Rep3

description: Related to Fig 2 and S6


title: Control - H3K27me3 modification replicate 2

description: Library name: Sample 10


title: MCF10A_END-seq_siRAD51_6h_Leading_Rep3

description: Related to Fig 2 and S6


title: MCF10A_END-seq_WT_6h_Lagging_Rep2

description: Related to Fig 2 and S6


title: 30uM - H3K27me3 modification replicate 2

description: Library name: Sample 7


title: Human_DMSO_1_17


title: Human_DMSO_1_18


title: 30uM - H3K27me3 modification replicate 3

description: Library name: Sample 8


title: 30uM - H3K27me3 modification replicate 1

description: Library name: Sample 6


title: MCF10A_END-seq_siRAD51_12h_Leading_Rep2

description: Related to Fig 2 and S6


title: Human_DMSO_1_16


title: MCF10A_END-seq_siRAD51_12h_Leading

description: Related to Fig 2 and S6


title: MCF10A_END-seq_siRAD51_6h_Leading

description: Related to Fig 2 and S6


title: MCF10A_END-seq_siRAD51_6h_Leading_Rep2

description: Related to Fig 2 and S6


title: Human_DMSO_1_15


title: MCF10A_END-seq_WT_6h_Leading_Rep3

description: Related to Fig 2 and S6


title: 30uM - NFAT1 binding replicate 1

description: Library name: Sample 4


title: MCF10A_END-seq_WT_12h_Leading_Rep2

description: Related to Fig 2 and S6


title: Human_DMSO_1_14


title: MCF10A_END-seq_WT_6h_Leading_Rep2

description: Related to Fig 2 and S6


title: MCF10A_END-seq_WT_12h_Lagging_Rep2

description: Related to Fig 2 and S6


title: MCF10A_END-seq_WT_12h_Leading_Rep3

description: Related to Fig 2 and S6


title: Control - NFAT1 binding replicate 3

description: Library name: Sample 3


title: Human_DMSO_1_13


title: Human_DMSO_1_12


title: MCF10A_END-seq_WT_12h_Leading

description: Related to Fig 2 and S6


title: MCF10A_sg4_sg5_LaggingD10A_6h_ENDseq

description: Related to Fig 1B


title: Control - NFAT1 binding replicate 1

description: Library name: Sample 2


title: MCF10A_sg6_LaggingD10A_6h_ENDseq

description: Related to Fig S3A


title: IgG control for NFAT1 experiment

description: Library name: Sample 1


title: MCF10A_sg1sg2sg3_LeadingD10A_6h_ENDseq

description: Related to Fig 1B and S3A


title: MCF10A_siBRCA2_RPA_ChIP_R12h

description: Related to Fig3C


title: Library_1, gRNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
10x Genomics
gRNA

data_processing:
Alignment of reads from the single cell RNA-seq library and unique molecular identifiers (UMI) counting, as well as oligonucleotides tags (HTOs) counting, were performed with 10X Genomics Cell Ranger tool (v6.0.2). Reads of the gRNA library were counted with CITE-seq-Count (v1.4.2).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files of raw counts

growth_protocol: A549-KRAB-MeCP2 cells were transduced with different amounts of the viral stock containing the library of pooled, selected gRNA. After six hours, the virus-containing medium was replaced by fresh complete culture medium.

extract_protocol:
Cells were trypsinized
Samples were then stained for multiplexing using cell hashing, using the Cell Hashing Total-Seq-ATM protocol (Biolegend) following the protocol provided by the supplier, using 4 distinct Hash Tag Oligonucleotides-conjugated mAbs. Briefly, for each condition, 1.106 cells were resuspended in 100µL of PBS, 2% BSA, 0.01% Tween and incubated with 10µL Fc Blocking reagent for 10 minutes at 4°C then stained with 0.5µg of cell hashing antibody for 20 minutes at 4°C. After washing with PBS, 2% BSA, 0.01% Tween, samples were counted and merged at the same proportion, spun 5 minutes 350 x g at 4°C and resuspended in PBS supplemented with 0.04% of bovine serum albumin at final concentration of 500 cells/µL. Samples were then adjusted to the same concentration, mixed in PBS supplemented with 0.04% of bovine serum albumin at a final concentration of 100 cells/µl and pooled sample were immediately loaded onto10X Genomics Chromium device to perform the single cell capture. After single-cell capture on the 10X Genomics Chromium device (3' V3), libraries were prepared as recommended, following the Chromium Next GEM Single Cell  3' Reagent  Feature Barcoding V3.1 kit (10X Genomics) and a targeted gRNA amplification with respectively 6, 8 and 10 PCR cycles. Libraries were then quantified, pooled (80% RNA libraries, 10% gRNA libraries and 10% hashing libraries) and sequenced on an Illumina NextSeq 2000.

treatment_protocol: Puromycin selection (1µg/ml) was started at 48 h post-transduction, and two days later, the plate with about 30% surviving cells was selected, corresponding roughly to a MOI=0.3. The cells were then amplified under puromycin selection for 5 days. The cells were then plated and further cultured in normoxia or in hypoxic condition (1% O2) for 3h, 6h or 24h.


title: Kcnn4 WT ATAC-seq replicate 3

description: Library name: Sample 12

data_processing:
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid genome of reference mouse mm10 assembly and drosophila Ensembl r97 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive -X 2000.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions; only reads mapped in proper pair were kept (-F 1804 -f 2 -q 30).
The alignments were shifted by deepTools alignmentSieve (version 3.5.1) with --ATACshift and default parameters. Nucleosome-free reads (fragment length < 109 bp) were separated from the BAM files with SAMtools (version 1.9).
Peaks were called using MACS (version 2.1.2) with narrowPeak setting, --extsize 200, and recommended mappable genome size (default value for other parameters).
Chromatin accessibility signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters.
Assembly: mm10
Supplementary files format and content: BigWig files scaling tag count to 1 million mapped reads.
Supplementary files format and content: Bed files of peaks called using MACS2

growth_protocol: 1. OT-I CD8+ T cells were activated in 0.1mM or 0.03mM methionine with 2.5ng/ml SIINFEKL. Methioinine was restored to control (0.1mM) levels in 0.03mM after 30 min of activation. Cells were cultured for 24 hrs. 2: KCa3.1WT and KCa3.1R350A mutant OT-I CD8+ T cells were activated with 2.5ng/ml SIINFEKL. Cells were processed 24 hrs post activation.

extract_protocol:
50,000 cells were pelleted at 500 x g for 5 min at 4°C. Samples were washed in 1 ml cold PBS and resuspended in 50 ul cold cell lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei were pelleted at 1000 x g for 10 min and resuspended in 50 ml transposition reaction mixture (25 ml TD buffer, 2.5 ml TDE1, 22.5 ml ddH2O) (20034197, Illumina).
Samples were incubated at 42°C for 45 min. DNA was then purified using MiniElute PCR Purification Kit (28004, Qiagen). Libraries were barcoded and amplified with Q5 High-Fidelity 2x Master Mix (M0492S, NEB).

value: Kcnn4 WT

value: KCa3.1 WT


title: Library_2, HTOs

description:
10x Genomics
oligonucleotides tags


title: 30uM - NFAT1 binding replicate 3

description: Library name: Sample 5

value: CD8+ T cells


title: Library_1, HTOs

description:
10x Genomics
oligonucleotides tags


title: Kcnn4 WT ATAC-seq replicate 2

description: Library name: Sample 11

treatment_protocol: 1. OT-I CD8+ T cells were activated in 0.1mM or 0.03mM methionine with 2.5ng/ml SIINFEKL. Methioinine was restored to control (0.1mM) levels in 0.03mM after 30 min of activation. Cells were cultured for 24 hrs. 2: KCa3.1WT and KCa3.1R350A mutant OT-I CD8+ T cells were activated with 2.5ng/ml SIINFEKL. Cells were processed 24 hrs post activation.


title: Library_2

description:
10x Genomics
total RNA


title: Human_DMSO_1_8


title: Kcnn4 mutant ATAC-seq replicate 3

description: Library name: Sample 9

value: Kcnn4 mutant


title: Kcnn4 WT ATAC-seq replicate 1

description: Library name: Sample 10


title: MCF10A_END-seq_WT_6h_Leading

description: Related to Fig 2 and S6


title: CAF Kang4_002 | 027

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th Ave NE

institute: Hormel Institute

description: Desmin

data_processing:
FASTQ fileswere processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2. Briefly, reads were trimmed to remove low quality bases and adapter sequences. Paired end reads were stitched and aligned, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum one mismatch allowed. Reads matching the same barcode were deduplicated by UMI. The number of raw reads was highly linearly correlated with the number of unique UMIs at all AOI sizes, suggesting largely uniform library amplification. However, to correct for any PCR amplification bias, all analyses in this study use UMI deduplicated counts. Data were exported to Excel for further analysis.
Assembly: NA
Supplementary files format and content: xlsx

source_name: Liver metastasis tumor

extract_protocol:
Frozen sections of murine MC38 liver metastasis fixed with formalin overnight were sent to the University of Minnesota Genomics Center for probe hybridization, immunofluorescence staining, and selection of ROIs for analysis. 1x Tris-EDTA (pH9.0) solution and steaming the solution to 95⁰C method were used for antigen retrieval followed by Proteinase K digestion at 37⁰C for 5 minutes (1 µg/mL) to expose RNA targets.
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep manual. The DSP aspirate was dried and resuspended in 10 μL DEPC-treated water, and 4 μL was used in a PCR reaction. NanoString SeqCode primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled either in equal volumes or in proportion relative to AOI size, depending on the experiment, and purified with two rounds of AMPure XP beads (Beckman Coulter).Libraries were sequenced on an Illumina NextSeq 2000, according to the manufacturer’s instructions, with at least 27 × 27 paired end reads.
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep manual.

value: Liver metastasis tumor

value: CAF in CMTM6 knockdown MC38 liver metastases


title: Human_DMSO_1_7

value: human embryo


title: CAF Kang4_002 | 026

description: Desmin


title: Human_DMSO_1_11

value: DMSO


title: Human_DMSO_1_6


title: CAF Kang4_002 | 024

description: Desmin


title: CAF Kang4_002 | 025

description: Desmin


title: CAF Kang4_002 | 023

description: Desmin


title: Kcnn4 mutant ATAC-seq replicate 1

description: Library name: Sample 7


title: Kcnn4 mutant ATAC-seq replicate 2

description: Library name: Sample 8


title: CAF Kang4_002 | 022

description: Desmin


title: Library_2, gRNA

description:
10x Genomics
gRNA


title: CAF Kang4_002 | 021

description: Desmin


title: Human_DMSO_1_10


title: 30uM ATAC-seq experiment 1 replicate 3

description: Library name: Sample 6

value: Wild type


title: Human_DMSO_1_4


title: Human_DMSO_1_9


title: CAF Kang4_002 | 020

description: Desmin


title: CAF Kang4_002 | 019

description: Desmin


title: 30uM ATAC-seq experiment 1 replicate 2

description: Library name: Sample 5


title: Human_DMSO_1_3


title: Library_1

description:
10x Genomics
total RNA


title: 30uM ATAC-seq experiment 1 replicate 1

description: Library name: Sample 4


title: CAF Kang4_002 | 028

description: Desmin


title: CAF Kang4_002 | 017

description: Desmin


title: Control ATAC-seq experiment 1 replicate 3

description: Library name: Sample 3

value: 0.1mM Methionine


title: CAF Kang4_002 | 015

description: Desmin

value: CAF in Control MC38 liver metastases


title: Human_DMSO_1_2


title: Human_DMSO_1_1


title: CAF Kang4_002 | 011

description: Desmin


title: UMUC3_ROSA26_KO_No3_RNAseq

city: Urbana

first: Jun

middle: S

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

data_processing:
Paired-end reads were aligned to the human genome (hg38) with HISAT2 using the command hisat2 -X 1000
Aligned reads were filtered using Samtools using the command samtools view -h -F 4 -q 10
Read duplicates were removed
Gene and transcript abundances were determined using StringTie2 using the command stringtie -e -A. Samples corresponding to knockout of exon 2, exon 9, exons 2-9, and no exons of the B1 subunit were mapped to their corresponding reference transcriptomes. Expression levels for samples iwth multiple technical replicates were determined by taking the average of gene abundance across replicates.
Differential expression was determined using DESeq2
Assembly: hg38
Supplementary files format and content: Differential expression results returned by DESeq2. Comma delimited text file. Columns are: mean of all samples after normalization, log2(treatment/control), standard error of log2 fold change, Wald statistic, p-value, Benjamini-Hochberg corrected p-value, q-value

source_name: urinary bladder

growth_protocol: Cell lines were cultured in their respective media and supplements. All cell lines were maintained at 37 °C in a humidified incubator with 5% CO2. Cell culture medium was changed every 3-5 days depending on cell density. For routine passage, cells were split at a ratio of 1:3-10 when they reached 80% to 90% confluence. Cell lines were authenticated by short tandem repeat (STR) analysis at the University of California Berkeley Sequencing Facility and confirmed to be Mycoplasma free by PCR using a previously published method.

extract_protocol:
RNA was isolated with the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (Cat.80224)
300 ng good quality RNA (RIN>7) was used to construct RNA-seq libraries with KAPA Stranded mRNA-Seq Kit (Cat. KK8421)

treatment_protocol: CRISPR-mediated knockouts were performed as previously described. Single guide RNAs (sgRNAs) were designed using the Genetic Perturbation Platform Web Portal (https://portals.broadinstitute.org/gpp/public/) and the highest scoring guide RNAs were then cloned into PX458 (Cas9 expressing plasmid, Addgene #48138) and combinations of guide RNAs were empirically tested in HEK293T cells for their cutting efficiency. Finally, gRNAs were transfected into cells and clonal cells were isolated with fluorescence-activated cell sorting (FACS) (Sony SH800 or FACSAria3) followed by plating of GFP positive cells into 96-well dishes for clonal growth. Cells were replica plated for clonal expansion and genotyping. DNA was isolated from clones with Lucigen Corporation QuickExtract DNA extraction solution 1.0 (FisherScientific, #NC9904870). Genotyping was performed with primer pairs listed in supplementary table S3. Primers were designed with NCBI Primer-BLAST then empirically tested by gradient end-point PCR to optimize the specificity and sensitivity.

value: bladder


title: CAF Kang4_002 | 013

description: Desmin


title: Control ATAC-seq experiment 1 replicate 2

description: Library name: Sample 2


title: CAF Kang4_002 | 010

description: Desmin


title: CAF Kang4_002 | 009

description: Desmin


title: UMUC3_ROSA26_KO_No2_RNAseq


title: UMUC3_ROSA26_KO_No1_RNAseq


title: CAF Kang4_002 | 007

description: Desmin


title: CAF Kang4_002 | 018

description: Desmin


title: Human_DMSO_1_5


title: CAF Kang4_002 | 008

description: Desmin


title: CAF Kang4_002 | 005

description: Desmin


title: Tissue array well B1

city: San Francisco

first: Ken

last: Nakamura

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: YS-3499_02
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (GqCNO 801, GqCNO 804, GqVEH 802, CNOAlone C2W2) within regions of interest (SNc, VTA, TH)

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate fastq files.
Sequences were aligned to the mm10 genome to gene expression count using Space Ranger's default settings.
Gene expression level of Refseq coding genese were quantified using space ranger's default settings.
The 10X Loupe Browser software (RRID: SCR_018555) was used to identify six anatomical regions of interest: (1) SN, (2) VTA, and (3) thalamus (TH) in the midbrain, and (4) CP, (5) LSX, and (6) white matter tracts in the striatum. RNA capture areas corresponding to each anatomical region were selected for analysis based on their spatial proximity to the anatomical regions and on the expression of known genetic markers. SN and VTA genetic markers included tyrosine hydroxylase, DAT, and VMAT2; thalamus markers included Prkcd, Ptpn3, and Synpo2; CP was identified with DARPP32; the LSX was identified with PRKCD; white matter was identified with MBP. Capture areas from mice injected with virus (GqCNO, GqVeh) expressed mCherry based on histology. Capture areas that expressed high levels of astrocyte markers (Gfap, Aldh1l1) and microglia markers (Aif1, P2ry12) were excluded. SN and VTA capture areas also had to contain at least one complete DA neuron soma.
Assembly: mm10 2020 A
Supplementary files format and content: barcodes.csv: list of spatial barcodes
Supplementary files format and content: Features.csv: list of gene IDs and gene expression count data
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: scalefactors.json: scalefactors in json format
Supplementary files format and content: lowresimage.png: low-res image of tissue
Supplementary files format and content: highresimage.svg: high-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Midbrain tissue

growth_protocol: 3-4mo male GqCNO and GqVeh DATCre mice were bilaterally injected with a conditional AAV-hM3Dq(Gq)-mCherry virus in the midbrain.

extract_protocol:
Fresh frozen tissues were OCT embedded, and 10µm frozen sections were cut with a cryostat. Slides were immunostained for tyrosine hydroxylase (green), mCherry (red), NeuN (magenta), and DAPI (blue).
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression v1 Slides & Reagent kit according to the manufacturer's instruction.

treatment_protocol: GqCNO and CNOAlone mice were administered CNO and 2% sucrose via their drinking water for one week. GqVeh mice were administered 2% sucrose for one week. All mice were single housed and had access to a running wheel during treatment. After treatment, brains were collected and spatial transcriptomics was performed.

value: Midbrain tissue

value: DAT (iCre/iCre)


title: Tissue array well C1

description:
Library name: YS-3499_03
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (CNOAlone C1W7, GqCNO 781, GqVEH 785, GqVEH 784) within regions of interest (CP, white matter, LSX)

source_name: Striatal brain tissue

value: Striatal brain tissue


title: CAF Kang4_002 | 004

description: Desmin


title: UMUC3_parental_RNAseq

value: parental


title: Tissue array well D1

description:
Library name: YS-3499_04
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (CNOAlone C1W7, GqCNO 781, GqVEH 785, GqVEH 784) within regions of interest (SNc, VTA, TH)


title: CAF Kang4_002 | 006

description: Desmin


title: CAF Kang4_002 | 003

description: Desmin


title: UMUC3_B1X2KO_No4_RNAseq


title: CAF Kang4_002 | 002

description: Desmin


title: Tissue array well A1

description:
Library name: YS-3499_01
Fresh frozen Spatial transcriptome sequencing; processed data file lists median normalized average for each tissue section (GqCNO 801, GqCNO 804, GqVEH 802, CNOAlone C2W2) within regions of interest (CP, white matter, LSX)


title: M1702_PBMC_TCR

city: Houston

first: Sung Wook

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

description:
Library name: M1702_PBMC_TCR
FFPE

data_processing:
Sequencing reads were aligned to the mouse reference transcriptome (mm10) using the Cell Ranger multi pipeline (10x Genomics, v9.0.0) with default parameters. This pipeline enables the joint processing of gene expression and TCR V(D)J profiling data from the same cellular libraries, allowing for the simultaneous quantification of transcriptomic profiles and immune receptor sequences.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 -> scRNA data
Supplementary files format and content: filtered_contig_annotations.csv -> immuno profiling results
Library strategy: TCR-seq

source_name: PBMC

extract_protocol:
Single-cell suspensions from each heart tissue and matched PBMC sample were loaded into separate wells of a Chromium Next GEM Chip N (10X Genomics, Cat# 2000418) to generate gel beads-in-emulsion (GEMs), each containing uniquely barcoded beads for downstream single-cell capture and indexing. Cell concentration was adjusted to approximately 700-2,000 cells/µL to target recovery of up to 20,000 cells per sample. Sequencing libraries for 5’ gene expression and T cell receptor (TCR) V(D)J profiling were prepared using the Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (10X Genomics, Cat# 1000356), the Mouse Chromium Single Cell V(D)J Amplification Kits (10X Genomics, Cat#1000254) and the Library Construction Kit (10X Genomics, Cat# 1000190) according to the manufacturer’s instructions.
All libraries were sequenced on the Illumina NovaSeq 6000 system using paired-end reads with dual indexing 26 cycles for Read 1, 10 cycles for i7 Index, 10 cycles for i5 Index, and 90 cycles for Read 2), targeting 400 million reads per gene expression library and 100 million reads per TCR amplification library.

value: PBMC


title: CAF Kang4_002 | 001

description: Desmin


title: Control ATAC-seq experiment 1 replicate 1

description: Library name: Sample 1


title: UMUC3_B1X2KO_No3_RNAseq


title: Kang4_002 | 028

description: Remainder

value: CMTM6 knockdown MC38


title: CAF Kang4_002 | 016

description: Desmin


title: Kang4_002 | 026

description: Remainder


title: Kang4_002 | 027

description: Remainder


title: CAF Kang4_002 | 014

description: Desmin


title: M1702_PBMC_scRNA

description:
Library name: M1702_PBMC_GE
FFPE

data_processing:
Sequencing reads were aligned to the mouse reference transcriptome (mm10) using the Cell Ranger multi pipeline (10x Genomics, v9.0.0) with default parameters. This pipeline enables the joint processing of gene expression and TCR V(D)J profiling data from the same cellular libraries, allowing for the simultaneous quantification of transcriptomic profiles and immune receptor sequences.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 -> scRNA data
Supplementary files format and content: filtered_contig_annotations.csv -> immuno profiling results


title: Kang4_002 | 025

description: Remainder


title: UMUC3_B1X2KO_No1_Rep2_RNAseq


title: UMUC3_B1X2KO_No2_RNAseq


title: M1702_PBMC_BCR

description:
Library name: M1702_PBMC_BCR
FFPE

data_processing:
Sequencing reads were aligned to the mouse reference transcriptome (mm10) using the Cell Ranger multi pipeline (10x Genomics, v9.0.0) with default parameters. This pipeline enables the joint processing of gene expression and TCR V(D)J profiling data from the same cellular libraries, allowing for the simultaneous quantification of transcriptomic profiles and immune receptor sequences.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 -> scRNA data
Supplementary files format and content: filtered_contig_annotations.csv -> immuno profiling results
Library strategy: BCR-seq


title: Kang4_002 | 023

description: Remainder


title: M1702_Heart_TCR

description:
Library name: M1702_Heart_TCR
FFPE

source_name: Heart

value: Heart


title: Kang4_002 | 022

description: Remainder


title: Kang4_002 | 024

description: Remainder


title: UMUC3_B1KO_No4_RNAseq


title: M1702_Heart_scRNA

description:
Library name: M1702_Heart_GE
FFPE


title: UMUC3_B1KO_No3_RNAseq


title: Kang4_002 | 020

description: Remainder


title: Kang4_002 | 019

description: Remainder


title: Kang4_002 | 017

description: Remainder


title: UMUC3_B1KO_No2_RNAseq


title: F234_PBMC_TCR

description:
Library name: F234_PBMC_TCR
FFPE


title: Kang4_002 | 014

description: Remainder

value: Control MC38


title: UMUC3_B1KO_No1_RNAseq


title: M1702_Heart_BCR

description:
Library name: M1702_Heart_BCR
FFPE


title: Kang4_002 | 015

description: Remainder


title: A375_ROSA26_KO_No3_RNAseq

source_name: skin

value: skin


title: F234_PBMC_scRNA

description:
Library name: F234_PBMC_GE
FFPE


title: Kang4_002 | 013

description: Remainder

value: Liver metastasis tumor


title: UMUC3_B1X2KO_No1_Rep1_RNAseq


title: Kang4_002 | 011

description: Remainder


title: Kang4_002 | 009

description: Remainder


title: F234_Heart_scRNA

description:
Library name: F234_Heart_GE
FFPE


title: F234_Heart_TCR

description:
Library name: F234_Heart_TCR
FFPE


title: Kang4_002 | 021

description: Remainder


title: A375_ROSA26_KO_No1_Rep2_RNAseq


title: Kang4_002 | 007

description: Remainder


title: Kang4_002 | 008

description: Remainder


title: A375_ROSA26_KO_No1_Rep1_RNAseq


title: Kang4_002 | 006

description: Remainder


title: F234_Heart_BCR

description:
Library name: F234_Heart_BCR
FFPE


title: Kang4_002 | 005

description: Remainder


title: Kang4_002 | 018

description: Remainder


title: A375_parental_Rep2_RNAseq


title: Kang4_002 | 004

description: Remainder


title: F1863_PBMC_TCR

description:
Library name: F1863_PBMC_TCR
FFPE


title: Kang4_002 | 016

description: Remainder


title: Kang4_002 | 003

description: Remainder


title: A375_parental_Rep1_RNAseq


title: A375_B1X2KO_No5_Rep2_RNAseq


title: A375_ROSA26_KO_No2_RNAseq


title: F1863_PBMC_scRNA

description:
Library name: F1863_PBMC_GE
FFPE


title: F234_PBMC_BCR

description:
Library name: F234_PBMC_BCR
FFPE


title: EdUseq_APH

description: Related to Fig 1B and others

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction
Library strategy: EdU-seq

value: mammary epithelial cells

value: WT


title: Kang4_002 | 002

description: Remainder


title: Kang4_002 | 010

description: Remainder


title: Kang4_002 | 001

description: Remainder


title: F1863_PBMC_BCR

description:
Library name: F1863_PBMC_BCR
FFPE


title: A375_B1X2KO_No5_Rep1_RNAseq


title: A375_B1X2KO_No4_Rep2_RNAseq


title: F1863_Heart_scRNA

description:
Library name: F1863_Heart_GE
FFPE


title: A375_B1X2KO_No4_Rep1_RNAseq


title: F1863_Heart_BCR

description:
Library name: F1863_Heart_BCR
FFPE


title: F127_PBMC_TCR

description:
Library name: F127_PBMC_TCR
FFPE


title: F127_PBMC_scRNA

description:
Library name: F127_PBMC_GE
FFPE


title: A375_B1X2KO_No1_Rep1_RNAseq


title: F1863_Heart_TCR

description:
Library name: F1863_Heart_TCR
FFPE


title: A375_B1X2KO_No1_Rep2_RNAseq


title: F127_PBMC_BCR

description:
Library name: F127_PBMC_BCR
FFPE


title: A375_B1LKO_No2_RNAseq


title: LCC9, BLID control (Scramble), biological replicate 2

type: RNA

city: Washington

first: Usha

last: Kasid

state: DC

address: 3870 Reservoir Rd, NW

institute: Georgetown University Medical Center

hyb_protocol: 21.5 µl biotin-labeled sample was hybridized to miRNA 3.0 array for 16hrs at 48oC. The arrays were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix Fluidics Station 450 User Guide (P/N 080295), the GeneChip Expression Wash, Stain, and Scan User Guide (P/N 702731).

scan_protocol: The arrays were scanned with Affymetrx GeneChip Scanner 3000 7G.

data_processing: The array raw data were generated by Affymetrix GeneChip Command Console & Expression Console software.

label: Biotin

source_name: LCC9 cells

label_protocol: Biotin-labeled samples were prepared according to the Affymetrix FlashTag Biotin HSR RNA Labeling Kit manual (P/N 703095 Rev.3). 300 ng of total RNA was used to synthesize biotin-labeled sample.

growth_protocol: BLID knockdown and control (Scramble) MDA-MB-231 and LCC9 cells were cultured in DMEM with Glutamax, 10% heat-inactivated fetal bovine serum and 2 μg/ml puromycin in a humidified incubator supplied with 5% CO2 air. BLID knockdown and control (Scramble) MCF7 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2 mmol/L glutamine, and 2 μg/ml puromycin.

extract_protocol: Commercially available kit (Qiagen) was used to extract total RNA according to the manufacturer's instructions.

value: Breast cancer cells in vitro


title: F127_Heart_TCR

description:
Library name: F127_Heart_TCR
FFPE


title: A375_B1X2KO_No3_RNAseq


title: MCF7, BLID shRNA, biological replicate 3

source_name: MCF7 cells


title: A375_B1LKO_No1_RNAseq


title: BLID control (Scramble), biological replicate 3


title: A375_B1X2KO_No2_RNAseq


title: MCF7, BLID shRNA, biological replicate 1


title: F127_Heart_BCR

description:
Library name: F127_Heart_BCR
FFPE


title: MCF7, BLID shRNA, biological replicate 2


title: BLID control (Scramble), biological replicate 1


title: BLID control (Scramble), biological replicate 2


title: LCC9, BLID control (Scramble), biological replicate 3


title: LCC9, BLID shRNA, biological replicate 3


title: LCC9, BLID control (Scramble), biological replicate 1


title: LCC9, BLID shRNA, biological replicate 2


title: LCC9, BLID shRNA, biological replicate 1


title: MDA-MB-231, BLID control (Scramble), biological replicate 3

source_name: MDA-MB-231 cells


title: MDA-MB-231, BLID control (Scramble), biological replicate 2


title: MDA-MB-231, BLID control (Scramble), biological replicate 1


title: MDA-MB-231, BLID shRNA, biological replicate 1


title: A375_B1KO_No4_RNAseq


title: MDA-MB-231, BLID shRNA, biological replicate 2


title: Ctcf d/d, replicate 2

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

country: China

institute: South China Agricultural University

description: Library name: Ctcf_dd2

data_processing:
Clean reads were mapped to mouse genome (UCSC mm10) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

molecule: polyA RNA

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Female mice were sacrificed on GD4.

value: whole uterus


title: Ctcf f/f, replicate 3

description: Library name: Ctcf_ff3


title: A375_B1KO_No2_RNAseq


title: Ctcf d/d, replicate 3

description: Library name: Ctcf_dd3


title: MDA-MB-231, BLID shRNA, biological replicate 3


title: F127_Heart_scRNA

description:
Library name: F127_Heart_GE
FFPE


title: HI5

city: Wuhu

first: Huiyun

last: Xu

state: Anhui

address: youyi west road

institute: School of Life Sciences, Northwestern Polytechnical University

description:
Library name: Sample 19
Column name in raw_counts.txt: HI5

data_processing:
fastp(0.22.0) software
Using fastp(0.22.0) remove the sequence with joint at 3'end;  remove reads with average mass fraction lower than Q20.
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Then difference expression of genes was analyzed by DESeq (v1.38.3)
Assembly: Mus_musculus.GRCm38.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: inguinal white adipose

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop  spectrophotometer(Thermo Scientific).3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina(New England Biolabs Inc;Ipswich,Massachusetts,USA).

value: inguinal white adipose

value: adipose cell

value: hypoxia

tag: batch

value: Week 4


title: HI4

description:
Library name: Sample 18
Column name in raw_counts.txt: HI4


title: Male_Heart

description:
Library name: M1702_H1-3DDRG8J_A1_67088
FFPE

data_processing:
Spatial transcriptomic reads were processed using Space Ranger (10X Genomics). Individual nuclei were identified by integrating high-resolution H&E imaging with spatial transcriptomic data captured at 2 µm resolution, enabling single-cell-level spatial analysis. Following cell segmentation, phenotype identification was performed at single-cell level. Segmented cellular features were converted into an AnnData object for downstream analysis.
Assembly: mm10
Supplementary files format and content: barcode.tsv.gz -> list of spatial barcodes
Supplementary files format and content: featrues.tsv.gz -> list of gene IDs
Supplementary files format and content: matrx.mtx.gz -> gene expression mtx format
Supplementary files format and content: aligned_fiducials.jpg -> aligned fiducials tissue images
Supplementary files format and content: aligend_tissue_image.jpg -> image of tissue and spots
Supplementary files format and content: detected_tissue_image.jpg -> image of tissue
Supplementary files format and content: tissue_hires_image.png -> hi-res image
Supplementary files format and content: tissue_lowres_image.png -> low-res image
Supplementary files format and content: tissue_positions.csv -> spatial barcodes and coordinates spots
Library strategy: Spatial Transcriptomics

extract_protocol:
Spatial transcriptomic profiling was performed using the Visium HD Spatial Gene Expression platform (10x Genomics), following the manufacturer’s protocol.
Sequencing libraries were sequenced on the Illumina NovaSeq 6000 system using paired-end reads with dual indexing (43 cycles for Read 1T, 10 cycles for i7 Index, 10 cycles for i5 Index, and 50 cycles for Read 2S)

tag: Sex

value: Male


title: Female_Heart

description:
Library name: F1863_H1-3DDRG8J_D1_67089
FFPE

value: Female


title: A375_B1KO_No3_RNAseq


title: healthy skin from healthy control H8

city: Berlin

first: Alberto

last: Mesas-Fernández

state: Berlin

address: Luisenstraße 2

department: Dermatology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: Library name: I18R029a11_01

data_processing:
Reads were aligned to the GRCh37 (hg19) human reference genome using STAR v2.5.2b with default parameters.
Gene-level counts were generated using Subread v1.5.1 featureCounts.
Raw counts were filtered to retain genes with ≥1 count per million in at least 5 samples.
Assembly: GRCh37 (hg19) — Ensembl reference annotation
Supplementary files format and content: I18R029_Holstein_Expression.xlsx: normalized and raw counts for 15,839 genes across 12 samples
Supplementary files format and content: Files are annotated with gene symbols and Ensembl IDs. Count values are presented as raw and log2-transformed CPM values.

source_name: Skin

growth_protocol: Not applicable. Human skin biopsies were obtained from adult patients with pemphigus and healthy donors. No in vitro cell culture was performed.

extract_protocol:
Total RNA was extracted from skin biopsies using the peqGOLD Total RNA Kit (VWR International). RNA concentration and purity were assessed using NanoDrop and Qubit fluorometry. RNA integrity was determined by Agilent Bioanalyzer; samples with RIN ≥ 8.0 were processed further.
Libraries were prepared using standard polyA enrichment protocols. Sequencing was performed on an Illumina NextSeq 500 platform in single-end mode (1 × 75 bp), targeting ~25 million reads per sample.

treatment_protocol: No experimental treatment was applied. Skin biopsies were taken from patients with active pemphigus prior to any new immunosuppressive therapy. Healthy skin samples were obtained from control individuals undergoing surgery for non-inflammatory conditions.

value: Skin

value: keratinocytes and infiltrating leukocytes


title: HI3

description:
Library name: Sample 17
Column name in raw_counts.txt: HI3


title: Ctcf f/f, replicate 2

description: Library name: Ctcf_ff2


title: healthy skin from healthy control D

description: Library name: I18R029a09_01


title: A375_parental

data_processing:
Paired-end reads were aligned to the human genome (hg38) with Bowtie2 using the command bowtie2 -X 1000
Aligned reads were filtered using Samtools using the command samtools view -h -F 4 -q 10
Read duplicates were removed
Peaks were called using deduplicatd reads with MACS2 using the command macs2 callpeak -g hs --format BAM  -q 0.05
Assembly: hg38
Supplementary files format and content: Narrow peak file returned by MACS2.  Tab delimited text file. Columns are: chromosome, start position (1-based), end position (1-based), peak name, genome-viewer graphic score, strand, average enrichment, p-value, q-value, peak summit relative to start position

extract_protocol:
ChIP DNA was isolated using the Invitrogen GABPA antibody (Cat. #PA5-27735)
About 10-20 ng of ChIP or Input DNA was used to construct ChIP-seq libraries with KAPA Hyper Prep Kit (Cat. KK8502)

value: parental

tag: chip antibody

value: GABPA antibody (Invitrogen Cat. #PA5-27735)


title: Ctcf f/f, replicate 1

description: Library name: Ctcf_ff1


title: lesional skin from pemphigus patient P22

description: Library name: I18R029a06_01


title: HI1

description:
Library name: Sample 15
Column name in raw_counts.txt: HI1


title: A375_parental_input

value: none (input)


title: lesional skin from pemphigus patient P10

description: Library name: I18R029a04_01


title: A375_B1KO_No1_RNAseq

value: skin


title: cortical microglia from adult, KO

first: Wanjing

last: Lai

state: Guangdong

address: Jinan University,601 Huangpu Road West

institute: Key Laboratory of CNS Regeneration

description: Library name: sample 2

data_processing:
CelRanger v6.0 (https://github.com/10XGenomics/cellranger) pre-analyzed the single-cell data (fastq format) that had been downloaded from the machine and compared it with the Mus_musculus GRCm39 reference genome. Next, low-quality cells were filtered out with the conditions of gene median <500 or >5000, mitochondrial gene ratio >30%, and UMI number <500. Then, the expression matrix file of each cell was generated in the format of mx, tsv, etc. Seuratv4.0 (https://satjalab.org/seurat) was used for further follow-up analysis of the single-cell expression matrix. The tSNE clustering algorithm was used to reduce the dimension of the cells and cluster them, and differential analysis was performed on the genes in different clusters. Through these analyses, the characteristics of single-cell subpopulations in different groups were compared.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebral cortex

extract_protocol:
8-week-old mice were sacrificed by cervical dislocation, cerebral cortex from 5-6 mice (for each genotype) were isolated and immersed in 3 mL cooled HBSS, and then digested in 10 mL L15 culture medium supplemented with 80 k unit DNase I, 165 U papain  and 2 mg Cysteine at room temperature for 30 min. L15 culture medium supplemented with 10% fetal bovine serum was used to terminate the ingestion. After filtration through 70 μm cell strainer, cell mixture was centrifugated at 300 ×g at 18°C for 5 min. Cell pellets were resuspended by 4mL 30% Stock Isotonic Percoll (SIP) diluted in HBSS and followed by centrifugation at 300 ×g at 18°C for 40 min. Cell pellets were resuspended by 1 mL 2% FBS in PBS and incubated with Brilliant Violet 421™ anti-mouse CD45 Antibody and FITC anti-mouse CD11b antibodies for 30 min. Followed by rinsed for twice and fluorescence-activated flow cytometry (BD FACSARIASORP), CD45 and CD11b positive cells were obtained in 5% FBS in PBS.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GemCodes were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the Gel bead-in-EMulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Sequenced samples were then processed using the Cell Ranger v6.0 and aligned to the GRCm39 as in RNA-seq. Seurat was used to quality control, filter unwanted cells (gene count<500 per cell; UMI counts > Infinity per cell; the percentage of mitochondrial genes > 25%). Followed by gene expression normalization for each cell via LogNormalize, cells were clustered based on principal component analysis and visualized by Uniform Manifold Approximation and Projection (UMAP). To identify DE genes for a single cluster, likelihood-ratio test was performed with following criteria: p value ≤ 0.01; log2fold change ≥ 0.26; the percentage of cells where the gene is detected in specific cluster > 10%. Top 10 DE genes were identified as the marker genes in specific cluster.

value: cerebral cortex

value: primary cells

value: CD45+ CD11b+ cells

value: Moesin Knockout


title: healthy skin from healthy control H10

description: Library name: I18R029a12_01

value: WT


title: A375_ROSA26_KO_No1

value: ROSA26 knockout


title: A375_ROSA26_KO_No1_input


title: healthy skin from healthy control E

description: Library name: I18R029a10_01


title: lesional skin from pemphigus patient P2

description: Library name: I18R029a02_01


title: A375_B1X2KO_TERT_rescue_input

value: knockout of the exon 2 of the B1 subunit of GABP


title: OA synovial tissues [OA10]

city: ChengDu

first: Tao

last: Li

address: GuoXueXiang street

institute: West China Hospital

data_processing:
RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Read count extraction and normalization were performed using DESeq2 R package (1.20.0).
Assembly: Reference genome and gene model annotation files  downloaded from genome website directly.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: OA synovial tissues

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: OA synovial tissues


title: Ctcf d/d, replicate 1

description: Library name: Ctcf_dd1

value: whole uterus


title: HI2

description:
Library name: Sample 16
Column name in raw_counts.txt: HI2

value: inguinal white adipose

value: adipose cell

value: hypoxia

value: Week 4


title: healthy skin from healthy control C

description: Library name: I18R029a08_01

value: Skin

value: keratinocytes and infiltrating leukocytes


title: healthy skin from healthy control A

description: Library name: I18R029a07_01


title: HB5

description:
Library name: Sample 10
Column name in raw_counts.txt: HB5

source_name: interscapular brown adipose

value: interscapular brown adipose


title: L1236-shH2A.B_Input_Rep2

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

description: Library name: L1236-shH2A.B_Input_Rep2

data_processing:
[CUT&RUN] The CUT&RUN samples were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We obtained the spike-in reads by mapping the reads to the Drosophila melanogaster (dm6) genome assembly.
Supplementary files format and content: [CUT&RUN] bigwig for coverage
[ChIP-seq] BRG ChIP-seq and input raw data in duplicate was adaptor-trimmed using Trimmomatic, and aligned to hg38 human genome assembly using Bowtie2 with the default parameters. High-quality, uniquely mapped reads (MAPQ > 20) were deduplicated and used for further analysis.
Assembly: hg38
Supplementary files format and content: [ChIP-seq] bigwig for coverage

growth_protocol:
[CUT&RUN] The L1236 and L428 cell lines were routinely cultured in RPMI-1640 growth medium supplemented with 10% heat-inactivated foetal bovine serum (HI-FBS), 1% L-glutamine (200 mM stock), and 1% Penicillin-Streptomycin (10,000 units penicillin and 10 mg streptomycin/mL stock). Cells were cultured in T75 flasks and maintained in a humidified cell culture incubator at 37 ˚C and 5% CO2.
[ChIP-seq] The SMARTvector inducible shNTC and shH2A.B transduced L1236 cell lines were routinely cultured in RPMI-1640 growth medium supplemented with 10% heat-inactivated foetal bovine serum (HI-FBS), 1% L-glutamine (200 mM stock), and 1% Penicillin-Streptomycin (10,000 units penicillin and 10 mg streptomycin/mL stock). Cells were cultured in T75 flasks and maintained in a humidified cell culture incubator at 37 ˚C and 5% CO2.

extract_protocol:
[CUT&RUN] The targeted DNA fragments were isolated and purified following the CUT&RUN protocol developed in Henikoff lab (Skene et al. 2018). Drosophila spike-in DNA was added to each sample for normaliztion.
[CUT&RUN] The sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina following the kit manual with modification. During the PCR amplification step, 12 PCR cycles were performed, with a combined annealing and extension step for 10 s, to minimize the large DNA fragments
[ChIP-seq] 1x 108 cells were crosslinked for 11 min at room temperature using 0.1% formaldehyde solution. Chromatin preparation and immunoprecipitation by BRG1 antibody (abcam, ab110641) were performed as previously described (soboleva et al., 2017). 40 μg chromatin and 5 μg BRG1 antibody  were used per ChIP assay. 1% chromatin was used as input for library construction.
[ChIP-seq] The sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina following the kit manual

treatment_protocol: [ChIP-seq] Cells were culutred in growth medium supplemented with 0.1 μg/mL doxycycline for 5 days. 1x 108 cells were collected for chromatin preparation.

value: Hodgkin lymphoma cell line

tag: antibodies


title: L1236-shNTC_BRG1-ChIP_Rep1

description: Library name: L1236-shNTC_BRG1-ChIP_Rep1

value: anti-BRG1 (abcam, ab110641)


title: lesional skin from pemphigus patient P14

description: Library name: I18R029a05_01


title: NI4

description:
Library name: Sample 14
Column name in raw_counts.txt: NI4

value: normoxia


title: OA synovial tissues [OA7]


title: NI3

description:
Library name: Sample 13
Column name in raw_counts.txt: NI3


title: lesional skin from pemphigus patient P4

description: Library name: I18R029a03_01


title: NI2

description:
Library name: Sample 12
Column name in raw_counts.txt: NI2


title: lesional skin from pemphigus patient P1

description: Library name: I18R029a01_01


title: cortical microglia from adult, WT

description: Library name: sample 1

value: cerebral cortex

value: primary cells

value: CD45+ CD11b+ cells

value: Wild-type


title: L1236-shNTC_Input_Rep1

description: Library name: L1236-shNTC_Input_Rep1


title: A375_B1X2KO_TERT_rescue

value: skin

value: knockout of the exon 2 of the B1 subunit of GABP

value: GABPA antibody (Invitrogen Cat. #PA5-27735)


title: L1236-shNTC_BRG1-ChIP_Rep2

description: Library name: L1236-shNTC_BRG1-ChIP_Rep2


title: HB3

description:
Library name: Sample 8
Column name in raw_counts.txt: HB3


title: OA synovial tissues [OA9]

value: OA synovial tissues


title: OA synovial tissues [OA6]


title: NI1

description:
Library name: Sample 11
Column name in raw_counts.txt: NI1

value: inguinal white adipose

value: adipose cell


title: HB2

description:
Library name: Sample 7
Column name in raw_counts.txt: HB2

value: hypoxia

value: Week 4


title: L1236-shH2A.B_Input_Rep1

description: Library name: L1236-shH2A.B_Input_Rep1


title: OA synovial tissues [OA8]


title: HB4

description:
Library name: Sample 9
Column name in raw_counts.txt: HB4


title: L1236-shH2A.B_BRG1-ChIP_Rep2

description: Library name: L1236-shH2A.B_BRG1-ChIP_Rep2


title: L428_H2ABR7me2a_rep2

description: Library name: S3_L428_H2ABR7me2a

data_processing:
[CUT&RUN] The CUT&RUN samples were mapped to the Homo sapiens (hg38) genome assembly using Bowtie2 with the default parameters, after the adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We obtained the spike-in reads by mapping the reads to the Drosophila melanogaster (dm6) genome assembly.
Supplementary files format and content: [CUT&RUN] bigwig for coverage
[ChIP-seq] BRG ChIP-seq and input raw data in duplicate was adaptor-trimmed using Trimmomatic, and aligned to hg38 human genome assembly using Bowtie2 with the default parameters. High-quality, uniquely mapped reads (MAPQ > 20) were deduplicated and used for further analysis.
Assembly: hg38
Supplementary files format and content: [ChIP-seq] bigwig for coverage
Library strategy: CUT&RUN

value: anti-H2A.BR8me2a (in-house)


title: HB1

description:
Library name: Sample 6
Column name in raw_counts.txt: HB1

value: interscapular brown adipose


title: L1236-shH2A.B_BRG1-ChIP_Rep1

description: Library name: L1236-shH2A.B_BRG1-ChIP_Rep1

value: Hodgkin lymphoma cell line


title: OA synovial tissues [OA2]


title: L1236-shNTC_Input_Rep2

description: Library name: L1236-shNTC_Input_Rep2


title: L1236_H2ABR7me2a_rep2

description: Library name: S19_L1236_H2ABR7me2a


title: NB5

description:
Library name: Sample 5
Column name in raw_counts.txt: NB5


title: L428_H2ABS9ph_rep3

description: Library name: S8_L428_H2ABS9ph

value: anti-H2A.BS10ph (in-house)


title: L428_H2ABR7me2a_rep3

description: Library name: S7_L428_H2ABR7me2a


title: L428_H2ABS9ph_rep2

description: Library name: S4_L428_H2ABS9ph


title: OA synovial tissues [OA5]


title: L1236_H2ABS9ph_rep1

description: Library name: S16_L1236_H2ABS9ph


title: Normal Control synovial tissues [N12]

source_name: Normal Control synovial tissues

value: Normal Control synovial tissues


title: L1236_H2ABS9ph_rep2

description: Library name: S20_L1236_H2ABS9ph


title: L1236_H2ABR7me2a_rep1

description: Library name: S15_L1236_H2ABR7me2a


title: L428_H2ABS9ph_rep1

description: Library name: S12_L428_H2ABS9ph


title: L428_H2ABR7me2a_rep1

description: Library name: S11_L428_H2ABR7me2a


title: NB4

description:
Library name: Sample 4
Column name in raw_counts.txt: NB4

value: normoxia


title: NB3

description:
Library name: Sample 3
Column name in raw_counts.txt: NB3


title: NB2

description:
Library name: Sample 2
Column name in raw_counts.txt: NB2


title: Normal Control synovial tissues [N9]


title: Normal Control synovial tissues [N11]


title: Normal Control synovial tissues [N8]


title: NB1

description:
Library name: Sample 1
Column name in raw_counts.txt: NB1


title: Mouse_DMSO_7_1

description: Library name: SIM5111A84

data_processing:
Raw sequencing was processed according to a modified nf-core/scrnaseq pipeline
Reads were trimmed to remove adapter sequences and aligned to the mouse GRCm38 reference genomes using STAR aligner
Transcript abundances, using the Ensembl gene annotations (versions 102 for mouse) were estimated using STAR quantmode, converted into a count matrix and further processed using scanpy. No computational doublet detection was performed. We excluded samples in which more than 15% of total reads aligning to the mitochondrial genome.
Assembly: Mouse GRCm38
Supplementary files format and content: tab delimited .h5ad file

source_name: Mouse pre-implantation embryo

growth_protocol: Embryos were cultured in Global Media + 10% Human serum albumin (Cooper Surgical) .

extract_protocol:
Single-cell cDNA synthesis was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) according to the manufacturer’s instrictions. Briefly, single-cells were manually picked after dissociation and snap frozen on dry ice in reaction buffer in low-bind 0.2 ml PCR tubes and stored at -80°C until processing. Samples were subject to first strand cDNA synthesis, then cDNA was amplified by LD-PCR for 23 cycles. Amplified cDNA was purified on AMPure XP beads, using a 96-well magnetic stand (ThermoFisher), and eluted in 17 µl of elution buffer.
The libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s protocol. Sequencing was carried out as paired-end 50bp read on a Novaseq 6000 sequencer.

treatment_protocol: Day 3.25 mouse embryos were treated for 24 hours with 5µM Ulixertinib (Cambridge Bioscience) or 0.1% DMSO and collected at day 4.25. Mouse embryos were subject to immunosurgery to remove outer trophectoderm cells and isolate the inner cell mass. The zona pellucida was removed by washing embryos through drops of Acidic Tyrode’s solution (Merck) pre-warmed to 37°C and overlaid with mineral oil. Embryos were then washed briefly and incubated at 37°C for 30 min in 20% anti-mouse serum antibody (Sigma) or 20% anti-human serum antibody (Sigma), depending on the species, in Global media + 10% HSA. Embryos were then washed briefly in Global Media + 10% HSA, before incubation with 20% Guinea Pig Serum Complement (Merck) at 37°C for 10-15 min until trophectoderm cell began to lyse. Embryos were then moved to a drop of medium and triturated with 100 µm STRIPPER tip (Cooper Surgical) to remove lysed trophectoderm cells and to isolate the inner cell mass. Isolated inner cell mass were then briefly washed, then incubated at 37°C for 3 min in 0.5% Trypsin, 1 mM EDTA in PBS (Fisher Scientific). Then, were transferred to 4% BSA, 0.5 mM EDTA in PBS for fine manual dissociation into single cells with pulled (Sutter Instruments) glass capillaries (World Precision Instruments). Cells were then picked manually with pulled glass capillaries for downstream single-cell RNA-seq.

value: Mouse pre-implantation embryo

value: Embryo

value: DMSO

tag: time point

value: day 4.25 (24hrs treatment)


title: Mouse_DMSO_6_11

description: Library name: SIM5111A83


title: Normal Control synovial tissues [N4]


title: PVNS synovial tissues [PVNS28]

source_name: PVNS synovial tissues

value: PVNS synovial tissues


title: 171115-14, T2D

city: Changchun

first: Peng

last: Chen

address: Xinmin Street 126

department: Department of genetics

institute: Jilin University

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression. In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned. Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.
Assembly: miRBASE v21
Supplementary files format and content: The processed file is a tab-deliminated text file and contains the miRNA read counts of all samples, with miRNA names in rows and sample names in columns.

source_name: peripheral blood serum

extract_protocol:
Participants were instructed to fast for 8-12 hours, and approximately 5ml of venous blood was collected using vacuum tubes containing citrate anticoagulant at room temperature in the early morning. The whole blood was centrifuged at 1000g for 10 minutes, and the plasma was collected and stored at -80°C for further use.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:  1) 3'-adaptor ligation;  2) 5'-adaptor ligation;  3) cDNA synthesis;  4) PCR amplification;  5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).  The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq 500 per the manufacturer's instructions.

value: peripheral blood serum

tag: disease

value: male

tag: age

tag: bmi


title: 171212-08, T2D


title: 171212-16, T2D


title: 170919-06, T2D


title: 170922-01, T2D

value: female


title: 171103-01, T2D


title: 171115-11, T2D


title: 171220-12, T2D


title: 171205-09, T2D


title: 171212-02, T2D


title: PVNS synovial tissues [PVNS27]


title: 170905-07, T2D


title: Mouse_DMSO_6_10

description: Library name: SIM5111A82


title: 170831-04, T2D


title: 170916-01, T2D


title: Mouse_DMSO_6_9

description: Library name: SIM5111A81


title: 170824-05, T2D


title: Mouse_DMSO_6_8

description: Library name: SIM5111A80


title: 170816-03, T2D


title: PVNS synovial tissues [PVNS24]


title: 170803-11, T2D


title: PVNS synovial tissues [PVNS26]


title: PVNS synovial tissues [PVNS22]


title: Mouse_DMSO_6_7

description: Library name: SIM5111A79


title: Normal Control synovial tissues [N2]


title: 170801-09, T2D


title: 170721-04, T2D


title: 170725-05, T2D


title: Mouse_DMSO_6_6

description: Library name: SIM5111A78


title: PVNS synovial tissues [PVNS21]


title: Mouse_DMSO_6_5

description: Library name: SIM5111A77


title: 170630-02, T2D


title: 170704-15, T2D


title: 170628-02, T2D


title: 170630-06, T2D


title: 170706-03, T2D


title: PVNS synovial tissues [PVNS16]


title: Mouse_DMSO_6_2

description: Library name: SIM5111A74


title: Mouse_DMSO_6_3

description: Library name: SIM5111A75


title: Mouse_DMSO_6_4

description: Library name: SIM5111A76


title: PVNS synovial tissues [PVNS12]


title: PVNS synovial tissues [PVNS17]


title: PVNS synovial tissues [PVNS20]


title: Mouse_DMSO_6_1

description: Library name: SIM5111A73


title: PVNS synovial tissues [PVNS19]


title: 170704-16, T2D


title: Mouse_Ulix_4_12

description: Library name: SIM5111A72

value: Ulixertinib


title: 170627-02, T2D


title: 170428-01, T2D


title: Mouse_Ulix_4_11

description: Library name: SIM5111A71


title: 170425-02, T2D


title: 170621-01, T2D


title: PVNS synovial tissues [PVNS10]


title: PVNS synovial tissues [PVNS11]


title: MCF7, BLID control (Scramble), biological replicate 4

hyb_protocol: 11 µg Fragmented and labeled cRNA were hybridized to HG-U133 Plus 2.0 array for 16 hrs at 45oC. The arrays were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix Fluidics Station 450 User Guide (P/N 080295), the GeneChip Expression Wash, Stain, and Scan User Guide (P/N 702731).

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix GeneChip 3’IVT Plus Reagent Kit manual (P/N 703210 Rev.2 Affymetrix): 250 ng of total RNA was used to synthesize labeled cRNA.

tag: tag

value: Breast cancer cells in vitro


title: 170419-04, T2D


title: PVNS synovial tissues [PVNS9]


title: MCF7, BLID control (Scramble), biological replicate 2


title: Mouse_Ulix_4_9

description: Library name: SIM5111A69

tag: cell type


title: PVNS synovial tissues [PVNS4]


title: Mouse_Ulix_4_8

description: Library name: SIM5111A68


title: 170414-04, T2D


title: 170414-05, T2D


title: Mouse_Ulix_4_7

description: Library name: SIM5111A67


title: MCF7, BLID control (Scramble), biological replicate 1


title: PVNS synovial tissues [PVNS2]


title: 170411-13, T2D


title: 170413-06, T2D


title: Mouse_Ulix_4_6

description: Library name: SIM5111A66


title: PVNS synovial tissues [PVNS]


title: Mouse_Ulix_4_5

description: Library name: SIM5111A65


title: MCF7, BLID control (Scramble), biological replicate 3


title: MCF7, BLID shRNA, biological replicate 3


title: Mouse_Ulix_4_4

description: Library name: SIM5111A64


title: Mouse_Ulix_4_10

description: Library name: SIM5111A70


title: MCF7, BLID shRNA, biological replicate 4


title: MCF7, BLID shRNA, biological replicate 2


title: MCF7, BLID shRNA, biological replicate 1


title: LCC9, BLID control (Scramble), biological replicate 3


title: PVNS synovial tissues [PVNS7]


title: LCC9, BLID control (Scramble), biological replicate 4


title: 170407-03, T2D


title: PVNS synovial tissues [PVNS3]


title: 170330-07, T2D


title: Mouse_Ulix_4_1

description: Library name: SIM5111A61


title: Mouse_Ulix_4_2

description: Library name: SIM5111A62


title: Human_Ulix_7_8

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: Library name: Sample101

data_processing:
Raw sequencing was processed according to a modified nf-core/scrnaseq pipeline
Reads were trimmed to remove adapter sequences and aligned to the human GRCh38 reference genomes using STAR aligner
Transcript abundances, using the Ensembl gene annotations (versions 110 for human) were estimated using STAR quantmode, converted into a count matrix and further processed using scanpy. No computational doublet detection was performed. We excluded samples in which more than 30% of total reads aligning to the mitochondrial genome and fewer than 8,000 unique genes were detected.
Assembly: Human GRCh38
Supplementary files format and content: tab delimited .h5ad file

source_name: day 6.5 (36hrs treatment)

growth_protocol: Embryos were cultured in GT-L culture media (Vitrolife).

extract_protocol:
Single-cell cDNA synthesis was performed using SMART-Seq mRNA (Takara) according to the manufacturer’s instrictions. Briefly, single-cells were manually picked after dissociation and snap frozen on dry ice in 10.5µl 1x reaction buffer in low-bind 0.2 ml PCR tubes and stored at -80°C until processing. Samples were subject to first strand cDNA synthesis, then cDNA was amplified by LD-PCR for 18 cycles. Amplified cDNA was purified on AMPure XP beads, using a 96-well magnetic stand (ThermoFisher), and eluted in 17 µl of elution buffer.
The libraries were prepared using the SMART-Seq mRNA LP kit (Takara) according to the manufacturer’s protocol. Sequencing was carried out as paired-end 150bp read on an AVITI sequencer.

treatment_protocol: Day 5 human embryos were treated with 5µM Ulixertinib (Cambridge Bioscience) or 0.1% DMSO for either 36 hours and collected at day 6.5. Human embryos were then microdissected for single-cell RNA-seq and subjected to laser dissection (Saturn 5 Laser) to remove the mural trophectoderm. Isolated inner cell mass and polar trophectoderm cells were then briefly washed, then incubated at 37°C for 3 min in 0.5% Trypsin, 1 mM EDTA in PBS (Fisher Scientific). Then, were transferred to 4% BSA, 0.5 mM EDTA in PBS for fine manual dissociation into single cells with pulled (Sutter Instruments) glass capillaries (World Precision Instruments). Cells were then picked manually with pulled glass capillaries for downstream single-cell RNA-seq.

value: Human pre-implantation embryo


title: 170411-02, T2D


title: 170328-04, T2D


title: Human_Ulix_7_7

description: Library name: Sample100


title: Human_Ulix_7_5

description: Library name: Sample98


title: Human_Ulix_7_4

description: Library name: Sample97


title: Mouse_Ulix_3_11

description: Library name: SIM5111A59


title: 170322-08, T2D


title: Mouse_Ulix_3_12

description: Library name: SIM5111A60


title: Human_Ulix_7_3

description: Library name: Sample96


title: Mouse_Ulix_4_3

description: Library name: SIM5111A63


title: 170314-21, T2D


title: Mouse_Ulix_3_10

description: Library name: SIM5111A58


title: LCC9, BLID shRNA, biological replicate 2


title: LCC9, BLID shRNA, biological replicate 4


title: Human_Ulix_7_2

description: Library name: Sample95


title: LCC9, BLID control (Scramble), biological replicate 1


title: 170302-08, T2D


title: Human_Ulix_7_6

description: Library name: Sample99


title: Mouse_Ulix_3_9

description: Library name: SIM5111A57


title: 170316-02, T2D


title: 170419-07, T2D


title: LCC9, BLID shRNA, biological replicate 1


title: LCC9, BLID control (Scramble), biological replicate 2


title: MDA-MB-231, BLID control (Scramble), biological replicate 4


title: Human_Ulix_7_1

description: Library name: Sample94


title: Human_DMSO_6_30

description: Library name: Sample93


title: Mouse_Ulix_3_8

description: Library name: SIM5111A56


title: 170226-03, T2D


title: Mouse_Ulix_3_7

description: Library name: SIM5111A55


title: 170301-04, T2D


title: Human_DMSO_6_29

description: Library name: Sample92


title: 170225-02, T2D


title: LCC9, BLID shRNA, biological replicate 3


title: MDA-MB-231, BLID control (Scramble), biological replicate 3


title: Human_DMSO_6_28

description: Library name: Sample91


title: MDA-MB-231, BLID control (Scramble), biological replicate 2


title: 170223-03, T2D


title: Human_DMSO_6_27

description: Library name: Sample90


title: 170221-09, T2D


title: Mouse_Ulix_3_3

description: Library name: SIM5111A51


title: Mouse_Ulix_3_2

description: Library name: SIM5111A50


title: 170218-11, T2D


title: MDA-MB-231, BLID shRNA, biological replicate 4


title: Human_DMSO_6_25

description: Library name: Sample88


title: 170217-09, T2D


title: Pregnant women with GDM-3 [miRNA]

city: Wuhan

first: yin

middle: di

last: Bao

state: Hubei

address: 238 Jiefang Rd

institute: Renmin Hospital of Wuhan

data_processing:
Illumina PE150  software used for basecalling.
remove low quality reads and cut adapter sequences
Compare the clean reads to the miRBase Hisat2 software
Predicting novel miRNAs
Quantitative expression levels of all detected and predicted samples
Assembly: hg38
Supplementary files format and content: provide the miRNA TPM express level and reads count sheet

source_name: placenta

extract_protocol:
Total RNA was isolated from 3 NC and 3 GDM cases using TRIzol reagent (Thermo Fisher Scientific, 15596026) and then treated with DNase I following the manufacturer’s instructions.
sRNA libraries were prepared for sequencing using standard Illumina protocols

value: Pregnant women with GDM


title: Human_DMSO_6_24

description: Library name: Sample87


title: 170214-07, T2D


title: MDA-MB-231, BLID shRNA, biological replicate 3


title: Mouse_Ulix_3_1

first: Loke CTR

address: Downing Street

institute: Loke Centre for Trophoblast Research

description: Library name: SIM5111A49


title: Human_DMSO_6_23

description: Library name: Sample86


title: MDA-MB-231, BLID shRNA, biological replicate 2


title: 170214-06, T2D


title: Mouse_Ulix_3_6

description: Library name: SIM5111A54


title: Mouse_DMSO_5_1

description: Library name: SIM5111A46


title: Pregnant women with GDM-1 [miRNA]


title: Human_DMSO_6_22

description: Library name: Sample85


title: Mouse_Ulix_3_4

description: Library name: SIM5111A52


title: 170210-08, T2D


title: MDA-MB-231, BLID control (Scramble), biological replicate 1


title: Human_DMSO_6_21

description: Library name: Sample84


title: Mouse_DMSO_4_9

description: Library name: SIM5111A45


title: Healthy pregnant women-3 [miRNA]

value: Healthy pregnant women


title: 170113-03, T2D


title: 161117-01, T2D


title: Human_DMSO_6_26

description: Library name: Sample89


title: Mouse_DMSO_4_8

description: Library name: SIM5111A44


title: Human_DMSO_6_20

description: Library name: Sample83


title: Healthy pregnant women-1 [miRNA]


title: Mouse_DMSO_5_2

description: Library name: SIM5111A47


title: Mouse_DMSO_4_6

description: Library name: SIM5111A42


title: Healthy pregnant women-2 [miRNA]


title: Pregnant women with GDM-2 [miRNA]


title: Human_DMSO_6_18

description: Library name: Sample81


title: Human_DMSO_6_19

description: Library name: Sample82


title: Mouse_DMSO_4_7

description: Library name: SIM5111A43


title: Mouse_DMSO_4_5

description: Library name: SIM5111A41


title: 171222-08, NPDR

value: NPDR


title: Human_DMSO_6_17

description: Library name: Sample80


title: 65-Nintedanib

city: Rockville

first: Resat

last: Cinar

state: Maryland

address: 5625 Fishers lane

institute: National Institute on Alcohol Abuse and Alcoholism

description: Library name: 65-Nintedanib

data_processing:
Kallisto with index generated from GRCm39 Protein_coding transcripts were summed to get the gene expression levels
Assembly: GRCm39
Supplementary files format and content: Estimated counts and TPM in tab-separated format

source_name: Lung

extract_protocol: The right middle lobe of the lung tissues was immediately placed in RNAlater solution, then held on ice for 4–5 h, and then stored at -80°C until the RNA extraction procedure. RNA extraction was performed using RNeasy Mini Kits from Qiagen (Valencia, CA). RNA concentrations were measured with a NanoDrop One (ThermoFisher). One microgram of total RNA was reverse transcribed to cDNA using Bio-Rad iScript cDNA synthesis kit (Hercules, CA) according to the manufacturer’s instructions. RNA Quality control, library preparations, sequencing reactions, and initial bioinformatic analysis were conducted at GENEWIZ, LLC (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA-sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (NEB, Ipswich, MA, USA).

value: Lung

tag: genotype

value: WT

value: Nintedanib


title: 171212-12, NPDR


title: 171212-10, NPDR


title: Mouse_DMSO_4_4

last: Bioinformatics

description: Library name: SIM5111A40

value: Mouse pre-implantation embryo

tag: treatment


title: Human_DMSO_6_16

description: Library name: Sample79

tag: tissue

value: Embryo


title: 171209-04, NPDR


title: MDA-MB-231, BLID shRNA, biological replicate 1


title: 80-Control

description: Library name: 80-Control

value: Control


title: Mouse_DMSO_4_2

description: Library name: SIM5111A38

value: DMSO

value: day 4.25 (24hrs treatment)


title: 58-Control

description: Library name: 58-Control


title: Human_DMSO_6_15

description: Library name: Sample78


title: 171209-02, NPDR

value: peripheral blood serum


title: 171209-01, NPDR

value: male


title: 64-Nintedanib

description: Library name: 64-Nintedanib


title: Human_DMSO_6_14

description: Library name: Sample77


title: 71-OPVeh

description: Library name: 71-OPVeh

value: Vehicle


title: Human_DMSO_6_13

description: Library name: Sample76


title: Mouse_Ulix_2_11

description: Library name: SIM5111A35

value: Ulixertinib


title: Human_DMSO_6_12

description: Library name: Sample75


title: 171206-07, NPDR

value: female


title: 57-Control

description: Library name: 57-Control


title: Mouse_Ulix_2_10

description: Library name: SIM5111A34


title: 74-Nintedanib

description: Library name: 74-Nintedanib


title: Human_DMSO_6_11

description: Library name: Sample74

value: Human pre-implantation embryo


title: 60-OPMRI

description: Library name: 60-OPMRI


title: 170914-04, NPDR


title: 63-Nintedanib

description: Library name: 63-Nintedanib


title: Human_DMSO_6_10

description: Library name: Sample73


title: Human_DMSO_6_9

description: Library name: Sample72


title: 170905-02, NPDR


title: 69-OPVeh

description: Library name: 69-OPVeh


title: Mouse_Ulix_2_7

description: Library name: SIM5111A31


title: 170831-06, NPDR


title: 5-Control

description: Library name: 5-Control


title: Human_DMSO_6_7

description: Library name: Sample70


title: Mouse_DMSO_4_1

description: Library name: SIM5111A37


title: Mouse_Ulix_2_12

description: Library name: SIM5111A36


title: Human_DMSO_6_6

description: Library name: Sample69


title: 21-OPVeh

description: Library name: 21-OPVeh


title: 170831-03, NPDR


title: 171114-20, NPDR


title: Human_DMSO_6_4

description: Library name: Sample67


title: 11-OPMRI

description: Library name: 11-OPMRI


title: 170831-01, NPDR


title: Mouse_Ulix_2_9

description: Library name: SIM5111A33


title: Mouse_Ulix_2_3

description: Library name: SIM5111A27


title: 170808-07, NPDR


title: Mouse_DMSO_3_7

description: Library name: SIM5111A23


title: CLKO67

city: Wenzhou

first: Yajiao

last: Wang

address: Chashan Higher Education Zone

institute: Wenzhou Medical College

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: liver

value: Male

value: CL diet


title: Mouse_Ulix_2_8

city: Cambridge

description: Library name: SIM5111A32


title: 170620-08, NPDR

value: NPDR


title: Human_DMSO_6_3

description: Library name: Sample66


title: CLKO66


title: Mouse_DMSO_3_6

description: Library name: SIM5111A22


title: Human_DMSO_6_2

description: Library name: Sample65


title: 170620-07, NPDR


title: CLKO65


title: Mouse_DMSO_3_5

description: Library name: SIM5111A21


title: Mouse_Ulix_2_6

description: Library name: SIM5111A30


title: 170428-05, NPDR


title: Mouse_DMSO_3_3

description: Library name: SIM5111A19


title: Mouse_Ulix_2_5

description: Library name: SIM5111A29


title: Human_DMSO_6_1

description: Library name: Sample64


title: CLWT64

value: WT


title: 170427-03, NPDR


title: 70-OPVeh

description: Library name: 70-OPVeh

value: Lung


title: Mouse_DMSO_3_2

description: Library name: SIM5111A18

value: Mouse pre-implantation embryo


title: Human_DMSO_6_5

description: Library name: Sample68

value: Embryo


title: 170711-08, NPDR


title: CLWT63


title: Human_DMSO_5_22

description: Library name: Sample62


title: 170419-11, NPDR


title: Human_DMSO_5_21

description: Library name: Sample61


title: CLWT62


title: 170318-06, NPDR


title: LKO-CL87


title: Human_DMSO_5_20

description: Library name: Sample60


title: Mouse_DMSO_3_1

description: Library name: SIM5111A17


title: Mouse_Ulix_1_12

description: Library name: SIM5111A12


title: 170314-08, NPDR


title: Human_DMSO_5_19

description: Library name: Sample59


title: 170314-19, NPDR


title: Mouse_DMSO_2_4

description: Library name: SIM5111A16


title: Mouse_Ulix_1_9

description: Library name: SIM5111A9


title: LKO-CL83


title: 170309-07, NPDR


title: Mouse_Ulix_1_8

description: Library name: SIM5111A8


title: LKO-CL85


title: Human_DMSO_5_17

description: Library name: Sample57


title: Human_DMSO_5_23

description: Library name: Sample63


title: WT-CL80


title: Mouse_Ulix_1_7

description: Library name: SIM5111A7


title: WT-CL77


title: Human_DMSO_5_16

description: Library name: Sample56


title: Mouse_Ulix_1_6

description: Library name: SIM5111A6


title: 170309-05, NPDR


title: 170308-07, NPDR


title: WT-CL76


title: Human_DMSO_5_15

description: Library name: Sample55


title: 170303-08, NPDR


title: Mouse_Ulix_1_5

description: Library name: SIM5111A5


title: 170228-14, NPDR


title: Human_DMSO_5_14

description: Library name: Sample54


title: Mouse_Ulix_1_4

description: Library name: SIM5111A4