title: CD1, E17, nephrogenic zone cell

description:
Library name: HTS_SO86_01_E17-NZC
10x Genomics Chromium GEM-X Single Cell 3' Kit v3

library_source: transcriptomic single cell

data_processing:
UMI collapsing, transcript to gene mapping, and barcode processing were completed using the Kallisto-Bustools workflow (kb-python; Kallisto version 0.50.1 and Bustools version 0.40.0).
Filtered barcode and matrix files were generated by removing likely empty droplets from the raw barcode and matrix files. Empty droplet likelihood was estimated using the emptyDrops function from the DropletUtils Bioconductor package (v1.24.0).
Assembly: GRCm39, release 111
Supplementary files format and content: tab-separated value files and matrix file for unfiltered kb-python output
Supplementary files format and content: tab-separated value files and matrix file for barcodes filtered to remove likely empty droplets. This dataset was used for the downstream analyses.

extract_protocol:
Nephrogenic zone cells (NZC) were isolated from pooled E17 wild-type CD1 kidneys following a 15 minute incubation at 37oC with a solution containing 0.25% pancreatin and 0.1% collagenase in DPBS. NZCs were quenched with FBS at 10% volume following digestion. NZCs were resuspended to 106 cells/mL in DPBS and kept on ice prior to mRNA capture. The Chromium GEM-X Single Cell 3' Kit v3 (10x Genomics) was used following the manufacturer’s protocol for mRNA capture and cDNA synthesis.
mRNA capture and cDNA synthesis was performed using the Chromium GEM-X Single Cell 3' Kit v3 (10x Genomics) following the manufacturer’s protocol. cDNA was then amplified, fragmented, and subjected to 3’ library construction with unique sample dual-indices. Dual-indexed libraries were diluted, pooled in equal molarity, and sequenced in Illumina NovaSeq6000 on a SP-100 flow cell following 10X Genomics' recommendations for paired-end sequencing.

value: CD1 mouse fetal kidney

value: nephrogenic zone cells

value: wild-type


title: TL2-1

status: Public on Jan 06 2026

type: SRA

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

country: China

institute: Gansu Agricultural University

description: Library name: Sample 7

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads  without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: liver tissues

growth_protocol: Rainbow trout (85 ± 0.5 g) for laboratory evaluation were obtained from a commercial aquaculture farm in Gansu (China) and checked free of pathogenic infections after an autopsy. The fish were raised in 1000 L tanks at water temperatures of 12 ± 1℃. During the experiments, the pH ranged from 7.6 to 7.8, and the dissolved oxygen was about 8.5 mg/L. Feeding with commercial dry feed pellets (Shandong Hanye Biotechnology Co., Ltd, China) was performed twice daily, a rate of 2% of their body weight. Animal care and use protocols were approved by Animal Welfare Committee of Gansu Agricultural University (GSAU-Eth-AST-2021-004), and carried out in accordance with the recommendations of the National Institutes of Health Guide for the Care and Use of Laboratory Animals (No. 2020001).

extract_protocol:
The total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the formal experiment, rainbow trout in control group were intraperitoneally injected with PBS, and two experimental groups were intraperitoneally injected with 150 μL inactivated IHNV vaccine (vaccine group) and 150 μL APS combined inactivated IHNV vaccine (APS+vaccine group), respectively. Each experimental group had 200 fish, 100 of which were used for mortality measurements and the remaining 100 for sampling. At 14 days (D 14) after vaccination, 200 fish per group were injected intraperitoneally with 50 µl IHNV (107 TCID50 ml-1) and monitored for mortality for two weeks. The relative percentage of survival (RPS) was calculated using the formula: 1-(vaccinated group mortality/control group mortality) × 100%. For sampling, the anesthetics and its doses were the same as in the vaccine safety tests. Liver and blood were collected from four fish from each group at D1, D3, D7, D14, D15, D21, D30, D60 and D90 to assay for immune-related gene expression and non-specific enzyme activities. Liver samples from D21 were also used for transcriptomic and metabolomic analyses. In addition, the spleens of three fish for each group were collected at D7, D14, D15, D21, D30, D60 and D90 for histopathological examination.

tag: tissue

value: liver tissues

tag: treatment

value: arc+vaccine group_IHNV challenged

tag: batch


title: Bleomycin_D5_CD64_0227 [NGS2117]

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

country: USA

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCm38.
Assembly: GRCm38
Supplementary files format and content: TSV count matrices.

organism: Mus musculus

source_name: lung

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq RNA Library Prep Kit.

value: lung

tag: cell type

value: CD64+ macrophage

tag: time

value: day 5

value: bleomycin


title: TL1-3

description: Library name: Sample 6

value: control group_IHNV challenged


title: TL1-1

description: Library name: Sample 4


title: Saline_D5_CD64_0223 [NGS2117]

value: saline


title: Bleomycin_D5_CD64_0225 [NGS2117]


title: TL1-2

description: Library name: Sample 5


title: WT_TAID_frozen

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

description: Library name: WT_TAID_frozen

library_source: genomic

data_processing:
Trim_galore removes adapters and low-quality reads
Mapping to the mouse genome(mm10) or human genome(hg38)
Standardized to obtain the bw file
Peak calling by MACS
Assembly: mm10 or hg38
Supplementary files format and content: bw files of tag density

molecule: genomic DNA

source_name: Testis

extract_protocol:
For each sample, 10 µL of Concanavalin A (ConA) beads were washed with 100 µL Wash Buffer, resuspended in 10 µL Binding Buffer, and incubated with 200,000–300,000 cells for 10 min at room temperature (RT). After magnetic separation, the primary antibody diluted in Antibody Buffer was added and incubated overnight at 4 °C. The beads were then washed, incubated with secondary antibody for 1 hours at RT, and washed three times with Dig-Wash Buffer. Subsequently, pA–Tn5 Buffer was added, and samples were incubated for 1 hour at RT, followed by three washes with Dig-400 Buffer. Tagmentation was performed with 40 µL of Tagmentation Buffer at 37 °C for 1 hour. The reaction was stopped with EDTA, SDS, and Proteinase K, followed by incubation at 55 °C for 1 hour and 75 °C for 15 min. DNA was purified using Speed Beads, washed twice with 80% ethanol, and eluted in pre-heated dd-water containing 0.1% Tween-20.
A 10 µL aliquot of eluted DNA was extended with 15 µL 2× Equinox PCR mix, 0.375 µL Bst 3.0 DNA polymerase (8 U/µL), and 5 µL nuclease-free water, incubated at 68 °C for 30 min to fill adapter gaps, followed by 95 °C for 5 min to inactivate the enzyme. Index 5 and Index 7 primers were then added, and PCR amplification was performed as described (Supplementary Table 11.3). The final library was purified using DNA Clean beads (1.2× sample volume) for downstream applications.

value: Testis

tag: cell line

value: Germ cells

value: Spermatocyte

tag: genotype

value: WT


title: BPAF_10_donor1_R4_P4

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: s303

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina Basespace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed December 2024), which manages workflows using snakemake v8.0 (Mölder et al., 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al., 2018), STAR v2.7.8a (Dobin et al., 2013) to perform alignment of raw reads to the reference sequence, and the qCount function of the QuasR R package (v1.30.0; Gaidatzis et al., 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

organism: Homo sapiens

source_name: Mammary

growth_protocol: HMECs from three biological donors were kept at low passage and not allowed to exceed 80% confluency to preserve epithelial subpopulations and maintained in complete media. Cells were cultured in T75 flasks supplemented Mammary Epithelial Cell Growth Medium containing phenol red at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 and 2.1 kits (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells (passage 7) were seeded at 20,000 cells per well in 96-well plates in supplemented MEGM without phenol red (Lonza Bioscience). After 48 h, the media were removed and replaced with supplement-free MEGM without phenol red containing chemicals of interest at eight concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM) and E2 (0.1 and 1 nM). The experiment included at least six plate-matched solvent controls (0.1% DMSO) and four technical replicates from each donor were exposed for 48 h.

value: Mammary

value: Primary

value: Epithelial

value: chemical exposure

tag: chemical

value: bisphenol AF

tag: dose

tag: donor


title: CL-3

description: Library name: Sample 3

value: liver tissues

value: control


title: Bleomycin_D5_Alveolar_0221 [NGS2117]

value: lung

value: alveolar macrophage


title: Bleomycin_D5_CD64_0226 [NGS2117]

value: CD64+ macrophage

value: day 5


title: TAIDseq_repB

description: Library name: TAIDseq_repB


title: BPAF_5_donor1_R4_P4

description: Library name: s302


title: BPAF_1_donor1_R4_P4

description: Library name: s301


title: CL-1

description: Library name: Sample 1


title: CL-2

description: Library name: Sample 2


title: TAID_pool

description: Library name: TAID_pool


title: BPAF_0-5_donor1_R4_P4

description: Library name: s300


title: Bleomycin_D5_Alveolar_0220 [NGS2117]

value: bleomycin


title: TAIDseq_repC

description: Library name: TAIDseq_repC


title: TAIDseq_repA

description: Library name: TAIDseq_repA


title: Bleomycin_D5_Alveolar_0219 [NGS2117]


title: BPAF_0-01_donor1_R4_P4

description: Library name: s298


title: Spo11ko_TAID_frozen_rep3

description: Library name: Spo11ko_TAID_frozen_rep3


title: Bleomycin_D14_CD64_0239 [NGS2117]

value: day 14


title: HCT116-GFP, Triptolide, Rep3 (EnChAMP-seq)

city: Ithaca

first: Abdullah

last: Ozer

state: NY

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

description: Library name: HCT116-GFP_Triptolide_Rep3

data_processing:
Adapter sequences were removed using cutadapt (ver3.7) and mapped to the human hg38 genome using bowtie2 –local (ver2.5.1). The sam file was converted to an indexed bam file with samtools view, sort, and index (ver1.7). Finally, the indexed bam file was converted to a RPKM normalized bigwig file using DeepTools bamCoverage (ver3.5.2).
Assembly: GRCh38/hg38
Supplementary files format and content: RPKM normalized bigwig files with 5bp bins.

growth_protocol: Parental and engineered HCT116 cells were cultured in McCoy’s 5A media (Thermo Fisher Scientific, Cat# 16600-108) supplemented with 10% Fetal Bovine Serum (VWR, Cat# MP1300500H) and 100 U/ml Pen-Strep (Thermo Fisher Scientific, Cat# 15140122) in a humidified cell culture incubator at 37 °C with 5% CO2 atmosphere.

extract_protocol:
Cells were harvested at ~90% confluency (~20 million cells/15cm plate). Cells were washed with DPBS, scraped, and collected by centrifugation at 800g for 5 minutes at 4°C. Supernatants were discarded. Nuclei Isolation: Cell pellets were resuspended in 1 mL of ice-cold Hi-C Buffer A (10 mM HEPES [pH 7.5], 10 mM KCl, 1.5 mM MgCl2, 1 mM CaCl2, 0.1% Digitonin (Millipore Sigma, Cat# 300410), with 1X Phosphatase (Sigma Aldrich, Cat# P2850) and 1X Protease inhibitor cocktails (Thermo Fisher Scientific, Cat# A32965), and 1 mM PMSF (Cell Signalling, Cat# 8553S)) and incubated on ice for 30 minutes to allow cell swelling. After incubation, aliquots were taken for western blot analysis. The remaining lysates were centrifuged at 1000g for 15 minutes at 4°C. Nuclei pellets were washed with 1 mL of cold Hi-C Wash Buffer B (Hi-C Buffer A supplemented with 250 mM sucrose), centrifuged as above, and supernatants containing cytoplasmic fraction was discarded. Chromatin Isolation: Nuclei pellets were resuspended in 500 μL of 1.5% Digitonin Chromatin Isolation Buffer A (10 mM HEPES [pH 7.5], 20 mM KCl, 150 mM NaCl, 1.5 mM MgCl2, 1 mM CaCl2, 15% Glycerol, 1.5% Digitonin, with phosphatase and protease inhibitors, and PMSF) and incubated on ice for 30 minutes. Samples were centrifuged at 1000g for 30 minutes at 4°C, and supernatants containing nucleoplasmic fraction were discarded. The pellets were resuspended in 500 μL of fresh Buffer A, and 3 μL of 250 U/μL Benzonase® Nuclease (Millipore Sigma, Cat# E1014) was added for chromatin shearing. The samples were rotated at 4°C for 1 hour, followed by centrifugation at 1000g for 30 minutes at 4°C. Soluble chromatin proteins were collected as supernatants, while the insoluble chromatin fractions were discarded. Affinity purification with anti-GFP nanobody: During Benzonase digestion of chromatin, per sample 10 μL of GFP-Trap® M-270 magnetic particles (ChromoTek, Cat#gtd) were washed three times with Chromatin Isolation Buffer B (10 mM HEPES [pH 7.5], 20 mM KCl, 150 mM NaCl, 1.5 mM MgCl2, 1 mM CaCl2, 15% Glycerol) and resuspend in 50 μL of Buffer B. Soluble chromatin proteins (~500 μL) were incubated with 50 μL of pre-washed magnetic particles per sample overnight at 4°C. Beads were washed sequentially with Chromatin Isolation Buffer B: a 5-minute rotation wash, followed by two stationary washes, and a final transfer to a clean tube. Beads were eluted with 200 μL of 100 mM HEPES (pH 7.5) containing 1% SDS at 65°C for 15 minutes. The supernatants (eluted chromatin) were collected for downstream analysis.
Eluates  of ~5M cell equivalent from EnChAMP experiments were brought to 300ul with 1X TE buffer (10 mM Tris-Cl pH 8.0, 0.1 mM EDTA), extracted once with equal volume Phenol:Chloroform mix pH 8.0 (Thermo Fisher Scientific, Cat# 17909), extracted with equal volume Chloroform, EtOH precipitated (1/10th volume 3M NaAcetate pH 5.2, 2 μl GlycoBlue  co-precipitant (Thermo Fisher Scientific, Cat# AM9516), and 3 volumes 100% EtOH, washed with 70% EtOH, and air dried pellet was resuspended in MilliQ-H2O. DNA amount was quantitated by Qubit dsDNA HS Assay (Thermo Fisher Scientific, Cat# Q32851). 2-40 ng DNA was end-repaired in the presence of a 250 μM dNTP mix (each), 1x T4 DNA Ligase Buffer (NEB), 6 units T4 DNA Polymerase (NEB, Cat# M0203L), 20 units T4 PNK (NEB, Cat# M0201L), and 2.5 units Klenow Polymerase (NEB, Cat# M0210L) at RT for 30 min on a Thermomixer at 600 rpm. End-repaired DNA was purified using MinElute Reaction Clean-up Kit (Qiagen, Cat# 28204) and A-tailed in the presence of 1x Buffer #2 (NEB), 200 uM dATP, and 10 units Klenow exo- polymerase (NEB, Cat# M0212L) at 37C for 30 min on a Thermomixer at 600 rpm. A-tailed DNA was purified using MinElute Reaction Clean-up Kit (Qiagen, Cat# 28204) and ligated to Illumina TRUseq adapters in the presence of 12-120 nM TRUseq Index adapter, 1x T4 DNA Ligase buffer (NEB), 1,200 units T4 DNA Ligase (NEB, Cat# M0202L) at 18 ºC O/N. TRUseq adapter ligated DNA was purified using MinElute Reaction Clean-up Kit (Qiagen) and subjected to a pilot PCR using P5 and P7 oligos to determine appropriate number of PCR cycles to generate a library. Final PCR reactions were carried 11-15 cycles and purified using MinElute PCR Clean-up Kit (Qiagen, Cat# 28004). After quality check with BioAnalyzer analysis, if deemed necessary the libraries were gel purified (150-350 bp region) using 8% native PAGE to get rid of the adapter dimer (~130 bp). Equal amounts of 8-12 samples were pooled and sequenced either by 2x150nt on an Illumina NovaSeq 6000 instrument (NovaGene) or by 2x80nt on an Element Biosciences AVITI instrument (EGC Core Facility).

treatment_protocol: 500 nM of NVP-2 (MedchemExpress, Cat# HY-12214A) for 1 hours, 1 µM of Triptolide (Millipore Sigma, Cat# T3652) for 20 minutes, or left untreated.

value: GFP (control)

value: GFP

value: 1uM Triptolide for 20min


title: Spo11ko_TAID_frozen_rep2

description: Library name: Spo11ko_TAID_frozen_rep2

value: Testis

value: Germ cells

value: Spermatocyte


title: HCT116-GFP, Triptolide, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP_Triptolide_Rep2


title: BPAF_0-001_donor1_R4_P4

description: Library name: s297

value: Mammary

value: Primary

value: Epithelial

value: WT


title: Bleomycin_D14_CD64_0238 [NGS2117]


title: BPA_50_donor1_R4_P4

description: Library name: s296

value: chemical exposure

value: bisphenol A


title: Spo11ko_TAID_frozen_rep1

description: Library name: Spo11ko_TAID_frozen_rep1


title: Bleomycin_D14_CD64_0237 [NGS2117]

value: lung


title: HCT116-GFP-RPB1, Triptolide, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_Triptolide_Rep2


title: BPA_10_donor1_R4_P4

description: Library name: s295


title: Bleomycin_D14_Alveolar_0233 [NGS2117]

value: alveolar macrophage


title: HCT116-GFP-RPB1, Triptolide, Rep3 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_Triptolide_Rep3


title: Prdm9ko_TAID_rep3

description: Library name: Prdm9ko_TAID_rep3


title: BPA_5_donor1_R4_P4

description: Library name: s294


title: BPAF_0-1_donor1_R4_P4

description: Library name: s299

value: bisphenol AF


title: Bleomycin_D14_Alveolar_0231 [NGS2117]

value: bleomycin


title: Bleomycin_D14_Alveolar_0232 [NGS2117]

value: day 14


title: BPA_1_donor1_R4_P4

description: Library name: s293


title: Prdm9wt_TAID_rep1

description: Library name: Prdm9wt_TAID_rep1


title: HCT116-GFP-RPB1, NoTriptolide, Rep3 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NoTriptolide_Rep3


title: HCT116-GFP-RPB1, NoTriptolide, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NoTriptolide_Rep2


title: Prdm9ko_TAID_rep2

description: Library name: Prdm9ko_TAID_rep2


title: HCT116-GFP, NoTriptolide, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP_NoTriptolide_Rep2

value: GFP (control)


title: BPA_0-1_donor1_R4_P4

description: Library name: s291


title: HCT116-GFP, NoTriptolide, Rep3 (EnChAMP-seq)

description: Library name: HCT116-GFP_NoTriptolide_Rep3

value: GFP


title: BPA_0-01_donor1_R4_P4

description: Library name: s290


title: WT_Hippocampus_Input

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

description: Library name: WT_InputSox9.fastq.gz

data_processing:
Quality control was assessed using fastQC
Samples were aligned to the mm10 reference genome using bowtie2
The HOMER (v4.10) software suite was used to generate tag directories, call peaks, and annotate called peaks. The findPeaks command was used with --factor to find Sox9 transcription factor peaks
samtools and deeTools packages were used to produce bigwig files
Assembly: mm10
Supplementary files format and content: bigwig alignment data

source_name: Brain

extract_protocol:
Tissue was dissociated and crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen at -80C. After thawing, cells were lysed to release nuclei, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor to ~200-300bp.
Illumina ChIP-Seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Ilumina, IP-202-1012) with 10 ng of DNA starting material for Input and IP samples. Libraries ranging from 250-350 bp were gel extracted and PCR amplified for 18 cycles. Libraries were purified using AMPure XP beads and library quality was validated using a Tape Station bioanalyzer.

value: Brain

tag: sample group

value: Hippocampus


title: lZ_TAID_rep3

description: Library name: lZ_TAID_rep3

value: Testis

value: Germ cells


title: WT_Hippocampus_Sox9_ChIP

description: Library name: WT_Sox9.fastq.gz


title: Prdm9ko_TAID_rep1

description: Library name: Prdm9ko_TAID_rep1

value: Spermatocyte


title: lZ_TAID_rep2

description: Library name: lZ_TAID_rep2


title: Prdm9wt_TAID_rep2

description: Library name: Prdm9wt_TAID_rep2


title: BPA_0-001_donor1_R4_P4

description: Library name: s289

value: Mammary

value: Primary


title: Alzheimers_Disease_Hippocampus_Input

description: Library name: AD_InputSox9.fastq.gz

value: C57/BL6; APPNLGF; Aldh1l1-GFP


title: HCT116-GFP-RPB1, Triptolide, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_Triptolide_Rep1

value: 1uM Triptolide for 20min


title: HCT116-GFP, Triptolide, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP_Triptolide_Rep1


title: lZ_TAID_rep1

description: Library name: lZ_TAID_rep1

value: WT


title: DMSO_0-1_donor3_R18_P3

description: Library name: s286

value: Epithelial

value: vehicle control

value: dimethyl sulfoxide


title: Aged_18month_Hippocampus_Input

description: Library name: Old_Input.fastq.gz


title: lZ_noAb

description: Library name: lZ_noAb


title: HCT116-GFP, NoTriptolide, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP_NoTriptolide_Rep1


title: lP_TAID_rep3

description: Library name: lP_TAID_rep3


title: Aged_18month_Hippocampus_Sox9_ChIP

description: Library name: Old_Sox9.fastq.gz


title: DMSO_0-1_donor2_R18_P3

description: Library name: s284


title: HCT116-GFP-RPB1, NoTriptolide, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NoTriptolide_Rep1


title: AD_Sox9-Overexpression_Hippocampal_Astrocytes_4

description: Library name: DJ20

data_processing:
Quality control was performed using fastQC
Reads were mapped to the mm10 reference genome using STAR (v2.5.0a) and counts per million were determined using GenomicAlignments and DESeq2 in Rstudio.
Assembly: mm10
Supplementary files format and content: comma seperated values file with normalized CPM values for each sample

molecule: polyA RNA

source_name: brain-hippocampus

extract_protocol:
GFP positive astrocytes were sorted from the hippocampus directly into buffer RLT lysis buffer and RNA was extracted using Qiagen Rneasy micro kit
Illumina sequencing libraries were constructed from total RNA with 8-bp indices using Nugen Trio RNASeq System

value: brain-hippocampus

value: AAV-Sox9 OverExpression virus :AAV-GFAP-Sox9-Flag


title: DMSO_0-1_donor2_R17_P3

description: Library name: s283


title: Alzheimers_Disease_Hippocampus_Sox9_ChIP

description: Library name: AD_Sox9.fastq.gz


title: SFSN-Adipo_3

city: Shanghai

first: Rong

last: Bao

state: shanghai

address: 600 YISHAN ROAD

institute: Department of Orthopaedics Shanghai Jiao Tong University Affiliated Sixth People

description: Library name: PPAR1_3

data_processing:
Data filtering
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Structure variation detection
The clean reads were mapped to the reference genome using HISAT2 [2]. After that, Ericscript (v0.5.5) [3] and rMATS (V4.1.2) [4] were used to detect fusion genes and differential splicing genes (DSGs), respectively
RNA identification
Bowtie2[5] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis
Expression level of gene was calculated by RSEM (v1.3.1) [6]. The heatmap was drawn by pheatmap (v1.0.12) [7] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) [8] (or DEGseq （v1.48.0）[9] or PoissonDis[10])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [11].
For more details, see the data_processing_readme.txt
Assembly: NCBI_GCF_000001895.5_Rnor_6.0
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Rattus norvegicus

source_name: rat bone marrow mesenchymal stem cells

extract_protocol:
1. Introduction This protocol allows to extract both high-quality genomic DNA and total RNA from the same sample. The purified DNA and RNA can be used directly for library preparation. 2.Experimental Procedures 2.1 Sample Lysis 2.1.1 Transfer 30mg of tissue into a 2mL tube with beads. 2.2.1 Add 600µL Buffer RLT Plus. If using snap-frozen cells (no more than 1 × 10⁷ cells), simply add 600µL Buffer RLT Plus directly into the same tube. Homogenize at 65Hz for 60s, then stay at room temperature for 5min. 2.2.3 Centrifuge at 12,000g for 3min. Transfer the supernatant to an AllPrep DNA spin column in a collection tube. Centrifuge at 10,000g for 30s in room temperature. 2.2.4 Collect the flow-through for RNA purification. 2.2 RNA Purification 2.2.1 Add one volume of 70% ethanol to the flow-through. Mix by pipetting at least 5 times. 2.2.2 Transfer 700µL of the mixture into an RNeasy spin column in a collection tube. Centrifuge at 10,000g for 30s; discard the flow-through. Repeat until all mixture has passed through the column. 2.2.3 Add 700μL Buffer RW1 to RNeasy spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.2.4 Add 500μL Buffer RPE to RNeasy spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.2.5 Add 500μL Buffer RPE to RNeasy spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.2.6 Centrifuge at 16,000g for 2min to dry the purification column. Transfer the RNeasy spin column to a 1.5mL tube. 2.2.7 Add 30µL RNase-free water to the RNeasy spin column. Stay at room temperature for 1min, then centrifuge at 16,000g for 2min to elute RNA. 2.2.8 Check RNA quality as required. 2.3 DNA Purification 2.3.1 Add 500μL Buffer AW1 to AlIPrep DNA spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.3.2 Add 500μL Buffer AW2 to AlIPrep DNA spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.3.3 Centrifuge at 16,000g for 2min to dry the purification column. Transfer the AllPrep DNA spin column to a 1.5mL tube. 2.3.4 Add 30µL Buffer EB to theAllPrep DNA spin column. Stay at room temperature for 1min, then centrifuge at 16,000g for 2min to elute DNA. 2.3.5 Check DNA quality as required.
1. Introduction RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts. Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. 2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: rat bone marrow mesenchymal stem cells

value: SFSN

value: SFSN-Adipo


title: SFSN-Ot_1

description: Library name: RUNX21_1

value: SFSN-Ot


title: BPA_0-5_donor1_R4_P4

description: Library name: s292

value: chemical exposure

value: bisphenol A


title: AD_Sox9-Overexpression_Hippocampal_Astrocytes_3

description: Library name: DJ19


title: DMSO_0-1_donor3_R17_P3

description: Library name: s285


title: DMSO_0-1_donor1_R18_P3

description: Library name: s282


title: lP_noAb

description: Library name: lP_noAb

value: Testis

value: Germ cells

value: Spermatocyte


title: lP_TAID_rep2

description: Library name: lP_TAID_rep2


title: AD_Sox9-Overexpression_Hippocampal_Astrocytes_1

description: Library name: DJ9

value: C57/BL6; APPNLGF; Aldh1l1-GFP


title: DMSO_0-1_donor1_R17_P3

description: Library name: s281

value: Mammary

value: Primary


title: SFSN-Adipo_2

description: Library name: PPAR1_2

value: WT


title: SFSN-Adipo_1

description: Library name: PPAR1_1


title: DMSO_0-1_donor3_R16_P3

description: Library name: s278

value: Epithelial

value: vehicle control


title: SFSN-Neu_3

description: Library name: MAP21_3

value: SFSN-Neu


title: SFSN-Ot_2

description: Library name: RUNX21_2


title: AD_control_Hippocampal_Astrocytes_3

description: Library name: DJ181

value: brain-hippocampus


title: L_TAID_rep2

description: Library name: L_TAID_rep2


title: L_TAID_rep1

description: Library name: L_TAID_rep1


title: AD_Sox9-Overexpression_Hippocampal_Astrocytes_2

description: Library name: DJ10

value: AAV-Sox9 OverExpression virus :AAV-GFAP-Sox9-Flag


title: AD_control_Hippocampal_Astrocytes_2

description: Library name: DJ8


title: lP_TAID_rep1

description: Library name: lP_TAID_rep1


title: DMSO_0-1_donor2_R15_P3

description: Library name: s275

value: dimethyl sulfoxide


title: SFSN-Neu_1

description: Library name: MAP21_1

value: rat bone marrow mesenchymal stem cells

value: SFSN


title: Sox9-KO_aged_18month_Hippocampal_Sox9flox_Astrocytes_3

description: Library name: DJ24

value: Tamoxifin


title: DMSO_0-1_donor1_R16_P3

description: Library name: s274


title: eP_TAID_rep3

description: Library name: eP_TAID_rep3


title: AD_control_Hippocampal_Astrocytes_1

description: Library name: DJ7


title: DMSO_0-1_donor3_R15_P3

description: Library name: s277


title: SFSN-FB_3

description: Library name: FSP1_3

value: SFSN-FB


title: L_noAb

description: Library name: L_noAb

value: Testis


title: SFSN-Neu_2

description: Library name: MAP21_2


title: eP_TAID_rep2

description: Library name: eP_TAID_rep2

value: Germ cells


title: Sox9-KO_aged_18month_Hippocampal_Sox9flox_Astrocytes_2

description: Library name: DJ23


title: TABS_8

first: Jiren

last: Yan

state: Shanghai

address: 600 Yishan Road, Xuhui District, Shanghai

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: RAW_H4

data_processing:
Raw reads were filtered using fastp for quality control and adapter removal. Clean reads were aligned to the mouse reference genome (GRCm38) using STAR.
Differential gene expression analysis was performed with DESeq2, applying a threshold of fold change >2 and adjusted p < 0.05.
Heatmaps were generated to visualize global transcriptomic shifts.
Gene set enrichment analysis (GSEA) was conducted using the MSigDB database to identify significantly enriched pathways.
Assembly: GRCm38
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
Raw264.7 cells were cultured with HA/Mg scaffolds or TABS for 3 days under standard conditions, with four replicates per group. Total RNA was extracted using TRIzol, and RNA integrity was assessed with an Agilent 2100 Bioanalyzer (RIN > 7).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit and sequenced on an Illumina NovaSeq platform to generate 150-bp paired-end reads.


title: Sox9-KO_aged_18month_Hippocampal_Sox9flox_Astrocytes_1

description: Library name: DJ22


title: SFSN-FB_2

description: Library name: FSP1_2


title: DMSO_0-1_donor2_R16_P3

description: Library name: s276


title: E2_10_donor3_R3_P3

description: Library name: s270

value: chemical exposure


title: eP_TAID_rep1

description: Library name: eP_TAID_rep1

value: Spermatocyte


title: L_TAID_rep3

description: Library name: L_TAID_rep3


title: DMSO_0-1_donor1_R15_P3

description: Library name: s273

value: Mammary


title: Sox9-KO_young_4month_Hippocampal_Sox9flox_Astrocytes_2

description: Library name: PH10


title: SFSN-FB_1

description: Library name: FSP1_1


title: Control_3

description: Library name: CTRL1_3

value: Control


title: Sox9-KO_young_4month_Hippocampal_Sox9flox_Astrocytes_3

description: Library name: PH12


title: Dmc1wt_TAID_fresh_rep2

description: Library name: Dmc1wt_TAID_fresh_rep2

value: WT


title: Control_2

description: Library name: CTRL1_2


title: E2_10_donor2_R3_P3

description: Library name: s268

value: Primary

value: Epithelial


title: E2_1_donor3_R3_P3

description: Library name: s269


title: Control_1

description: Library name: CTRL1_1


title: E2_1_donor2_R3_P3

description: Library name: s267


title: SFSN-EC_3

description: Library name: CD311_3

value: SFSN-EC


title: eP_noAb

description: Library name: eP_noAb


title: WT_young_4month_Hippocampal_Sox9flox_Astrocytes_3

description: Library name: PH20

value: brain-hippocampus


title: Sox9-KO_young_4month_Hippocampal_Sox9flox_Astrocytes_1

description: Library name: PH9


title: Dmc1ko_TAID_frozen_rep2

description: Library name: Dmc1ko_TAID_frozen_rep2


title: Dmc1wt_TAID_fresh_rep1

description: Library name: Dmc1wt_TAID_fresh_rep1


title: E2_10_donor1_R3_P3

description: Library name: s266


title: DMSO_0-1_donor3_R14_P3

description: Library name: s264

value: vehicle control


title: SFSN-EC_1

description: Library name: CD311_1


title: Dmc1ko_TAID_fresh_rep2

description: Library name: Dmc1ko_TAID_fresh_rep2


title: Dmc1ko_TAID_frozen_rep1

description: Library name: Dmc1ko_TAID_frozen_rep1


title: WT_young_4month_Hippocampal_Sox9flox_Astrocytes_2

description: Library name: PH19


title: WT_young_4month_Hippocampal_Sox9flox_Astrocytes_1

description: Library name: PH18


title: TMBPF_5_donor3_R3_P3

description: Library name: s261

value: tetramethyl bisphenol F


title: WT_aged_18month_Hippocampal_Astrocyte_2

description: Library name: DJ17


title: SFSN-EC_2

description: Library name: CD311_2

value: rat bone marrow mesenchymal stem cells


title: TMBPF_10_donor3_R3_P3

description: Library name: s262


title: Dmc1ko_TAID_fresh_rep1

description: Library name: Dmc1ko_TAID_fresh_rep1


title: WT_aged_18month_Hippocampal_Astrocyte_3

description: Library name: DJ18


title: Spatial transcriptomes of maize embryonic leaves_DQ07

city: Taipei

first: Chi-Chih

last: Wu

address: 128 Academia Road, Section 2, Nankang

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

description: Library name: XGE22_DQ07

data_processing:
The sequencing and data output to the step of basecalling and subsequent library barcode demultiplexing: HiSeq2500: bcl2fastq 2.1.8; NextSeq2000: DRAGEN 3.7.4 & bcl2fastq_2.20
UMI reads were mapped and counts by Spaceranger 1.3 with Zea_mays.Zm-B73-REFERENCE-NAM-5.0.51
Assembly: Genome_build: Zea_mays.Zm-B73-REFERENCE-NAM-5.0.51
Supplementary files format and content: XGE22_image.tar.gz
Library strategy: Spatial Transcriptomics

organism: Zea mays

source_name: shoot

growth_protocol: Seeds of Zea mays cv. White Crystal were germinated on wet filter paper on Petri dishes in a growth chamber at 30 °C in the daytime and at 26 °C at night under the light period of 14 hours a day (6 am to 8 pm).

extract_protocol:
Visium Spatial Gene Expression Slide & Reagent Kit, 16 rxns PN-1000184
10X Visium Gene Expression

treatment_protocol: Post 72 hour imbibition, dissected shoots were fresh frozen and sectioning.

value: shoot


title: 200K_TAID_rep2

description: Library name: 200K_TAID_rep2


title: Spatial transcriptomes of maize embryonic leaves_DQ06

description: Library name: XGE22_DQ06


title: Spatial transcriptomes of maize embryonic leaves_DQ08

description: Library name: XGE22_DQ08


title: Spatial transcriptomes of maize embryonic leaves_DQ05

description: Library name: XGE22_DQ05


title: WT_aged_18month_Hippocampal_Astrocyte_1

description: Library name: DJ16


title: TMBPF_0-1_donor3_R3_P3

description: Library name: s258


title: WT_young_4month_Hippocampal_Astrocyte_3

description: Library name: YC114V2


title: 200K_TAID_rep1

description: Library name: 200K_TAID_rep1


title: TMBPF_1_donor3_R3_P3

description: Library name: s260


title: TMBPF_0-5_donor3_R3_P3

description: Library name: s259


title: TMBPF_50_donor3_R3_P3

description: Library name: s263


title: WT_young_4month_Hippocampal_Astrocyte_2

description: Library name: YC116V2


title: SiNC_4

first: Hongfeng

last: Chang

address: jixi road number 218

institute: The First Affiliated Hospital of Anhui Medical University

description:
Library name: Sample8
siRNA-control

data_processing:
Illumina HiSeq 4000 software was used for basecaling.
After acquiring raw sequencing data, quality control procedures were implemented, including removal of low-quality reads and adapter sequences. Filtered clean reads were aligned to reference genome sequences. Principal component analysis was performed using R software (v.3.2.0) to evaluate biological replicates. Transcript assembly and quantification were executed, with read counts per gene/transcript reflecting expression levels. Transcript expression was quantified in fragments per kilobase of exon per million mapped fragments. Reads were mapped to the transcriptome for quantification of transcript-overlapping reads, and this was followed by differential gene expression analysis.
Assembly: hg38
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: epidermis cell culture

growth_protocol: Human immortalized keratinocytes were maintained in RPMI-1640 suppledmented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using SparkZol RNA Extraction Reagent (AC0101, SparkJade Science, Shandong, China). One microgram of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing standard.

treatment_protocol: Human immortalized keratinocytes were cultured in high-glucose RPMI-1640 medium for 4 days.

value: epidermis cell culture

value: human immortalized keratinocytes

value: epithelial cells

value: siRNA-control


title: 100K_TAID_rep2

description: Library name: 100K_TAID_rep2

value: Testis

value: Germ cells


title: 100K_TAID_rep1

description: Library name: 100K_TAID_rep1

value: Spermatocyte


title: 500K_TAID_rep1

description: Library name: 500K_TAID_rep1


title: SiNC_3

description:
Library name: Sample7
siRNA-control

value: Control


title: Spatial transcriptomes of maize embryonic leaves_DQ03

description: Library name: XGE22_DQ03

value: WT


title: BPAF_10_donor3_R3_P3

description: Library name: s255

value: Mammary

value: Primary

value: chemical exposure

value: bisphenol AF


title: WT_young_4month_Hippocampal_Astrocyte_1

description: Library name: YC112V2

value: brain-hippocampus


title: TMBPF_0-01_donor3_R3_P3

description: Library name: s257

value: Epithelial

value: tetramethyl bisphenol F


title: Spatial transcriptomes of maize embryonic leaves_DQ01

description: Library name: XGE22_DQ01

value: shoot


title: SiNC_2

description:
Library name: Sample6
siRNA-control

value: epidermis cell culture


title: DMSO_0-1_donor3_R13_P3

description: Library name: s256

value: vehicle control

value: dimethyl sulfoxide


title: BPAF_5_donor3_R3_P3

description: Library name: s254


title: Spatial transcriptomes of maize embryonic leaves_DQ02

description: Library name: XGE22_DQ02


title: 50K_TAID_rep1

description: Library name: 50K_TAID_rep1


title: BPAF_1_donor3_R3_P3

description: Library name: s253


title: Spatial transcriptomes of maize embryonic leaves_DQ04

description: Library name: XGE22_DQ04


title: 10K_TAID_rep2

description: Library name: 10K_TAID_rep2


title: 50K_TAID_rep2

description: Library name: 50K_TAID_rep2


title: SiNC_1

description:
Library name: Sample5
siRNA-control

value: human immortalized keratinocytes

value: epithelial cells

value: siRNA-control


title: XGE20-UL04-Spatial Transcriptomcis- embryonic leaf-S1_S5_S9

description: Reads were produced on either HiSeq 2000 or HiSeq 2500 instruments

data_processing:
Library strategy: 10X Visium Gene Expression
The sequencing and data output to the step of basecalling and subsequent library barcode demultiplexing: HiSeq2500: bcl2fastq 2.1.8; NextSeq2000: DRAGEN 3.7.4 & bcl2fastq_2.20
UMI reads were mapped and counts by Spaceranger 1.3 with Zea_mays.Zm-B73-REFERENCE-NAM-5.0.51
Genome_build: Zea_mays.Zm-B73-REFERENCE-NAM-5.0.51
Supplementary_files_format_and_content: Images_capture_area.tar (high resolution of images for spaceranger pipeline)
Supplementary_files_format_and_content: Layout_of_datasets.png (diagram showing section sampling)
Supplementary_files_format_and_content: tar archive with h5, json, png, csv, cloupe, html

source_name: maize shoot post 72 hour imbibition

extract_protocol: Visium Spatial Gene Expression Slide & Reagent Kit, 16 rxns PN-1000184

tag: cultivar

value: White Crystal

tag: tissues

value: shoot apical meristem and serial embyonic leaves

tag: amount of section

tag: depth of coverage


title: SiETV4_4

description:
Library name: Sample4
siRNA ETV4

value: ETV4 knockdown

value: siRNA ETV4


title: 10K_TAID_rep1

description: Library name: 10K_TAID_rep1

value: Testis

value: Germ cells

value: Spermatocyte

value: WT


title: BPAF_0-5_donor3_R3_P3

description: Library name: s252

value: Mammary

value: Primary

value: Epithelial

value: chemical exposure

value: bisphenol AF


title: KASseq_Rep3

description: Library name: KASseq_Rep3

data_processing:
Trim_galore removes adapters and low-quality reads
Mapping to the mouse genome(mm10)
Standardized to obtain the bw file
Peak calling by MACS2
Assembly: mm10
Supplementary files format and content: bw files of tag density

extract_protocol:
two frozen testes from each mouse were dissected in cold 1×PBS and minced into small pieces after removing the tunica albuginea. The tiny tissue chunks were then homogenized into single cell suspension with a A-type Dounce glass homogenizer. After centrifugation for 3 min at 4°C, discarded the supernatant and suspended the cell pellet in 200 µL of labeling medium (5 mM N3-kethoxal in prewarmed 1×PBS) for 10 min at 37°C with gentle shaking (300 rpm), then harvest the cell pellet by centrifugation at 1200 g for 3 min. The total genomic DNA (gDNA) was isolated and finally eluted in 50 µL of 25 mM K3BO3 (pH 7.0) for each sample. For biotinylation, 2~3 µg of gDNA from each sample were mixed with 1 mM of DBCO-PEG4-biotin in 21 mM of K3BO3 (pH 7.0) in final 100 µL of 1×PBS buffer. The mixture was incubated at 37 °C for 1.5 h with shaking at 500 rpm to facilitate the click cycloaddition reaction, followed by RNA removal using RNase A digestion. The final DNA was purified by DNA Clean & Concentrator kit (Zymo) following the manufacturer’s protocol and eluted in 50 µL of 25 mM K3BO3 (pH 7.0). Next, 1 μg of biotinylated DNA into 100 µL of 25 mM K3BO3 (pH 7.0) was sonicated to 150–350 bp sizes using Bioruptor Pico Sonicator (30s on/30s off setting for 22 cycles at 4 ℃). 5 µL of the fragmented DNA was saved as an input control. Subsequently, 10 µL of Dynabeads MyOne streptavidin C1 were washed three times with 50 µL of 1× B&W buffer (5 mM Tris-HCl (pH 7.4), 0.5 mM EDTA, 1 M NaCl and 0.05% Tween-20), using a magnetic rack to separate the beads after wash. Next, resuspended prewashed beads in 95 µL of 2× B&W buffer (10 mM Tris-HCl (pH 7.4), 1 mM EDTA, 2 M NaCl and 0.1% Tween-20) with the 95 µL of fragmented DNA and incubated at room temperature for 20 min. To remove kethoxal, resuspended the beads in 15 µL of nuclease-free water and heated at 95 °C for 10 min to elute enriched ssDNA.
The eluted DNA can be stored at −20 °C for subsequent ssDNA library construction following the manufacturer’s protocol (Accel-NGS ssDNA library kit). The barcoded PCR was carried out for 12-14 cycles for each sample, and the library was subsequently size-selected for DNA ranging between 200 bp ~ 500 bp prior to PE150 sequencing.

value: Extracting the cell nuclei from the frozen testicular tissue


title: XGE20-UL01-Spatial Transcriptomcis- embryonic leaf-S1_S2_S3_S4


title: SiETV4_2

description:
Library name: Sample2
siRNA ETV4

value: epidermis cell culture

value: human immortalized keratinocytes


title: XGE21-VR01-Spatial Transcriptomcis- embryonic leaf-S1_S2_S3_S4


title: SiETV4_3

description:
Library name: Sample3
siRNA ETV4

value: epithelial cells


title: KASseq_Rep2

description: Library name: KASseq_Rep2


title: SiETV4_1

description:
Library name: Sample1
siRNA ETV4


title: XGE21-VR02-Spatial Transcriptomcis- embryonic leaf-S1_S2_S3_S4

value: White Crystal


title: BPAF_0-01_donor3_R3_P3

description: Library name: s250


title: KASseq_Rep1

description: Library name: KASseq_Rep1


title: BPAF_0-001_donor3_R3_P3

description: Library name: s249


title: XGE21-VR03-Spatial Transcriptomcis- embryonic leaf-S1_S2_S3_S4

value: shoot apical meristem and serial embyonic leaves


title: KASseq_Input_Rep2

description: Library name: KASseq_Input_Rep2


title: XGE21-VR04-Spatial Transcriptomcis- embryonic leaf-S1_S2_S3_S5


title: Unstimulated_7801 [NGS5340]

description:
Source: Lonza
SAM24437801

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCh38.
Assembly: GRCh38
Supplementary files format and content: TSV count matrices.

source_name: small airway epithelial cells

growth_protocol: Cells were grown (up to passage 4) and plated in the manufacturer's recommended media.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Cells were treated either with PBS or with OSM (10ng/mL) for 24h. Cells were washed with PBS then lysed with RLT buffer.

value: small airway epithelial cells

tag: subject id

value: unstimulated


title: BPA_50_donor3_R3_P3

description: Library name: s248

value: bisphenol A


title: Unstimulated_7800 [NGS5340]

description:
Source: Lonza
SAM24437800


title: XGE20-UL02-Spatial Transcriptomcis- embryonic leaf-S1_S3_S5


title: CML Dx-99

type: genomic

city: Toronto

first: Sagi

last: Abelson

state: ON

address: 661 University Avenue

institute: Ontario Institute for Cancer Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader(HiScan) and standard recommended Illumina scanner settings

data_processing:
Raw IDAT files were preprocessed and normalized using preprocessNoob from the minfi package in R (v4.2.2)
Beta values

label: Cy3 and Cy5

source_name: Peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Peripheral blood

tag: disease

value: CML

tag: Stage

value: Diagnosis

tag: age

tag: Sex

value: Male


title: BPA_10_donor3_R3_P3

description: Library name: s247

tag: tissue

value: Mammary

value: Primary

tag: cell type

value: WT

tag: treatment

tag: batch


title: Unstimulated_7799 [NGS5340]

description:
Source: Lonza
SAM24437799


title: KASseq_Input_Rep1

description: Library name: KASseq_Input_Rep1

value: Testis

tag: cell line

value: Germ cells

value: Spermatocyte

tag: genotype


title: RPA2_HEPES

description: Library name: RPA2_HEPES

data_processing:
Trim_galore removes adapters and low-quality reads
Mapping to the mouse genome(mm10) or human genome(hg38)
Standardized to obtain the bw file
Peak calling by MACS2
Assembly: mm10 or hg38
Supplementary files format and content: bw files of tag density
Library strategy: CUT&Tag

extract_protocol:
For each sample, 10 µL of Concanavalin A (ConA) beads were washed with 100 µL Wash Buffer, resuspended in 10 µL Binding Buffer, and incubated with 200,000–300,000 cells for 10 min at room temperature (RT). After magnetic separation, the primary antibody diluted in Antibody Buffer was added and incubated overnight at 4 °C. The beads were then washed, incubated with secondary antibody for 1 hours at RT, and washed three times with Dig-Wash Buffer. Subsequently, pA–Tn5 Buffer was added, and samples were incubated for 1 hour at RT, followed by three washes with Dig-400 Buffer. Tagmentation was performed with 40 µL of Tagmentation Buffer at 37 °C for 1 hour. The reaction was stopped with EDTA, SDS, and Proteinase K, followed by incubation at 55 °C for 1 hour and 75 °C for 15 min. DNA was purified using Speed Beads, washed twice with 80% ethanol, and eluted in pre-heated dd-water containing 0.1% Tween-20.
Index 5 and Index 7 primers were then added, and PCR amplification was performed as described (Supplementary Table 11.3). The final library was purified using DNA Clean beads (1.2× sample volume) for downstream applications.

value: Extracting the cell nuclei from the frozen testicular tissue


title: BPAF_0-1_donor3_R3_P3

description: Library name: s251

value: Epithelial

value: chemical exposure

tag: chemical

value: bisphenol AF

tag: dose

tag: donor


title: BPA_1_donor3_R3_P3

description: Library name: s245


title: BPA_5_donor3_R3_P3

description: Library name: s246


title: CML Dx-97

source_name: Bone marrow

value: Bone marrow


title: OSM_7805 [NGS5340]

description:
Source: Lonza
SAM24437805

value: small airway epithelial cells

value: recombinant human OSM at 10ng/mL


title: Unstimulated_7798 [NGS5340]

description:
Source: Lonza
SAM24437798

value: unstimulated


title: Spo11ko_H3K4me3

description: Library name: Spo11ko_H3K4me3_CUTTag


title: CML Dx-96

value: CML


title: RPA2_TAPS

description: Library name: RPA2_TAPS


title: CML Dx-95

value: Diagnosis


title: BPA_0-5_donor3_R3_P3

description: Library name: s244

value: bisphenol A


title: Prdm9ko_H3K4me3

description: Library name: Prdm9ko_H3K4me3


title: OSM_7804 [NGS5340]

description:
Source: Lonza
SAM24437804


title: CML Dx-93

value: Male


title: OSM_7802 [NGS5340]

description:
Source: Lonza
SAM24437802


title: Prdm9wt_H3K4me3

description: Library name: Prdm9wt_H3K4me3


title: MRE11_Ctrl_rep3

description: Library name: MRE11_Ctrl_rep3

value: The cells from the testes used two-step digestion method.


title: noAb_400

description: Library name: noAb_400

value: WT


title: Unstimulated_9126 [NGS4630]

description:
Source: Promocell
SAM24419126

source_name: pulmonary microvascular endothelial cells

growth_protocol: Cells were grown (up to passage 4) and plated in each manufacturer's recommended media.

treatment_protocol: Where appropriate, cells were blocked for 2h with antibodies (8-20ug/mL), after which OSM (10ng/mL) was added for a total of 24h incubation. Cells were washed in PBS and lysed in RLT buffer.

value: Unstimulated


title: MRE11_Ctrl_rep2

description: Library name: MRE11_Ctrl_rep2

value: Testis

value: Germ cells


title: CML Dx-98

value: Female


title: OSM_7803 [NGS5340]

description:
Source: Lonza
SAM24437803


title: CML Dx-90


title: MRE11_Ctrl_rep1

description: Library name: MRE11_Ctrl_rep1

value: Spermatocyte


title: BPA_0-1_donor3_R3_P3

description: Library name: s243

value: Mammary

value: Primary

value: Epithelial

value: chemical exposure


title: CML Dx-91

value: Bone marrow


title: Unstimulated_9120 [NGS4630]

description:
Source: Lonza
SAM24419120

value: pulmonary microvascular endothelial cells


title: BPA_0-01_donor3_R3_P3

description: Library name: s242


title: DMSO_0-1_donor2_R14_P3

description: Library name: s240

value: vehicle control

value: dimethyl sulfoxide


title: Unstimulated_9114 [NGS4630]

description:
Source: Promocell
SAM24419114


title: TMBPF_50_donor2_R3_P3

description: Library name: s239

value: tetramethyl bisphenol F


title: TMBPF_10_donor2_R3_P3

description: Library name: s238


title: MRE11_6mM_rep3

description: Library name: MRE11_6mM_rep3


title: CML Dx-88

value: CML

value: Diagnosis


title: Unstimulated_9108 [NGS4630]

description:
Source: Promocell
SAM24419108


title: CML Dx-84

value: Male


title: TMBPF_5_donor2_R3_P3

description: Library name: s237

value: WT


title: MRE11_6mM_rep1

description: Library name: MRE11_6mM_rep1

value: Testis

value: The cells from the testes used two-step digestion method.


title: MRE11_6mM_rep2

description: Library name: MRE11_6mM_rep2

value: Germ cells


title: OSM_aOSMR_GNE_9131 [NGS4630]

description:
Source: Promocell
SAM24419131

value: OSM + anti-OSMR#2


title: TMBPF_1_donor2_R3_P3

description: Library name: s236

value: Mammary


title: BPA_0-001_donor3_R3_P3

description: Library name: s241

value: Primary

value: bisphenol A


title: CML Dx-89


title: TMBPF_0-5_donor2_R3_P3

description: Library name: s235

value: Epithelial

value: chemical exposure


title: lZ_H3K27ac

description: Library name: lZ_H3K27ac_CUTTag

value: Spermatocyte

value: Extracting the cell nuclei from the frozen testicular tissue


title: CML Dx-83

value: Bone marrow


title: lZ_H3K4me3

description: Library name: lZ_H3K4me3_CUTTag


title: lZ_H3K9me3

description: Library name: lZ_H3K9me3_CUTTag


title: CML Dx-80


title: OSM_aOSMR_GNE_9119 [NGS4630]

description:
Source: Promocell
SAM24419119

value: pulmonary microvascular endothelial cells


title: TMBPF_0-1_donor2_R3_P3

description: Library name: s234

value: tetramethyl bisphenol F


title: OSM_aOSMR_GNE_9113 [NGS4630]

description:
Source: Promocell
SAM24419113


title: lP_H3K27ac

description: Library name: lP_H3K27ac_CUTTag


title: TMBPF_0-01_donor2_R3_P3

description: Library name: s233


title: CML Dx-81

value: Peripheral blood

value: CML

value: Diagnosis


title: OSM_aOSMR_9128 [NGS4630]

description:
Source: Promocell
SAM24419128

value: OSM + anti-OSMR#1


title: CML Dx-78

value: Female


title: DMSO_0-1_donor2_R13_P3

description: Library name: s232

value: WT

value: vehicle control

value: dimethyl sulfoxide


title: OSM_aOSMR_GNE_9125 [NGS4630]

description:
Source: Lonza
SAM24419125

value: OSM + anti-OSMR#2


title: lP_H3K9me3

description: Library name: lP_H3K9me3_CUTTag

value: Testis

value: Germ cells


title: CML Dx-77

value: Male


title: OSM_aOSMR_9122 [NGS4630]

description:
Source: Lonza
SAM24419122


title: BPAF_10_donor2_R3_P3

description: Library name: s231

value: Mammary

value: Primary

value: Epithelial

value: chemical exposure

value: bisphenol AF


title: lP_H3K4me3

description: Library name: lP_H3K4me3_CUTTag

value: Spermatocyte

value: Extracting the cell nuclei from the frozen testicular tissue


title: CML Dx-82

value: Bone marrow

value: CML

value: Diagnosis


title: OSM_aOSMR_9116 [NGS4630]

description:
Source: Promocell
SAM24419116

value: pulmonary microvascular endothelial cells

value: OSM + anti-OSMR#1


title: CML Dx-76

value: Female


title: BPAF_5_donor2_R3_P3

description: Library name: s230

value: WT


title: BPAF_1_donor2_R3_P3

description: Library name: s229


title: L_H3K27ac

description: Library name: L_H3K27ac_CUTTag

value: Testis


title: CML Dx-75


title: OSM_aOSM_9129 [NGS4630]

description:
Source: Promocell
SAM24419129

value: OSM + anti-OSM


title: BPAF_0-5_donor2_R3_P3

description: Library name: s228


title: CML Dx-74

value: Male


title: L_H3K4me3

description: Library name: L_H3K4me3_CUTTag

value: Germ cells


title: OSM_aOSM_9123 [NGS4630]

description:
Source: Lonza
SAM24419123


title: CML Dx-68


title: BPAF_0-01_donor2_R3_P3

description: Library name: s226

value: Mammary

value: Primary


title: IgG_no_16HD

description: Library name: IgG_no_16HD

value: The cells from the testes used two-step digestion method.


title: BPAF_0-1_donor2_R3_P3

description: Library name: s227

value: Epithelial

value: chemical exposure

value: bisphenol AF


title: CML Dx-67

value: Bone marrow


title: OSM_aOSM_9117 [NGS4630]

description:
Source: Promocell
SAM24419117


title: OSM_aOSMR_9110 [NGS4630]

description:
Source: Promocell
SAM24419110


title: CML Dx-72

value: CML


title: IgG_400

description: Library name: IgG_400

value: Spermatocyte


title: BPAF_0-001_donor2_R3_P3

description: Library name: s225


title: OSM_aOSM_9111 [NGS4630]

description:
Source: Promocell
SAM24419111

value: pulmonary microvascular endothelial cells


title: IgG_300

description: Library name: IgG_300


title: OSM_9127 [NGS4630]

description:
Source: Promocell
SAM24419127

value: OSM + isotype control


title: BPA_50_donor2_R3_P3

description: Library name: s224

value: bisphenol A


title: CML Dx-65

value: Diagnosis


title: OSM_9115 [NGS4630]

description:
Source: Promocell
SAM24419115


title: BPA_10_donor2_R3_P3

description: Library name: s223

value: WT


title: IgG_5_16HD

description: Library name: IgG_5_16HD

value: Testis


title: OSM_9121 [NGS4630]

description:
Source: Lonza
SAM24419121


title: CML Dx-64

value: Male


title: L_H3K9me3

description: Library name: L_H3K9me3_CUTTag

value: Germ cells

value: Extracting the cell nuclei from the frozen testicular tissue


title: CML Dx-62

value: Female


title: BPA_5_donor2_R3_P3

description: Library name: s222

value: Mammary

value: Primary


title: BPA_1_donor2_R3_P3

description: Library name: s221

value: Epithelial

value: chemical exposure


title: OSM_9109 [NGS4630]

description:
Source: Promocell
SAM24419109


title: BPA_0-5_donor2_R3_P3

description: Library name: s220


title: H3K27ac_no_16HD

description: Library name: H3K27ac_no_16HD

value: The cells from the testes used two-step digestion method.


title: H3K27ac_400

description: Library name: H3K27ac_400_CUTTag


title: CML Dx-60

value: Bone marrow

value: CML


title: aOSM_OSMR_9130 [NGS4630]

description:
Source: Promocell
SAM24419130

value: pulmonary microvascular endothelial cells

value: OSM + anti-OSM + anti-OSMR#1


title: BPA_0-1_donor2_R3_P3

description: Library name: s219

value: bisphenol A


title: aOSM_OSMR_9124 [NGS4630]

description:
Source: Lonza
SAM24419124


title: aOSM_OSMR_9118 [NGS4630]

description:
Source: Promocell
SAM24419118


title: CML Dx-59

value: Diagnosis


title: H3K27ac_300

description: Library name: H3K27ac_300_CUTTag

value: Spermatocyte

value: WT


title: BPA_0-01_donor2_R3_P3

description: Library name: s218


title: H3K27ac_10_16HD

description: Library name: H3K27ac_10_16HD

value: Testis


title: H3K27ac_5_16HD

description: Library name: H3K27ac_5_16HD

value: Germ cells


title: IgG_10_16HD

description: Library name: IgG_10_16HD


title: CML Dx-58

value: Male


title: CML Dx-55


title: BPA_0-001_donor2_R3_P3

description: Library name: s217


title: CML Dx-54

value: Female


title: DMSO_0-1_donor1_R14_P3

description: Library name: s216

value: Mammary

value: vehicle control

value: dimethyl sulfoxide


title: CML Dx-53


title: H3K9me3_400

description: Library name: H3K9me3_400_CUTTag


title: Unstimulated_8304 [NGS4564]

description:
Source: Lonza
SAM24418304

source_name: normal human lung fibroblast

treatment_protocol: Where appropriate, cells were blocked for 2h with antibodies (8-20ug/mL), after which OSM (10ng/mL) was added for a total of 24h incubation.

value: normal human lung fibroblast

value: Unstimulated


title: H3K9me3_300

description: Library name: H3K9me3_300_CUTTag

value: The cells from the testes used two-step digestion method.


title: CML Dx-61

value: Bone marrow

value: CML


title: Unstimulated_8298 [NGS4564]

description:
Source: Lonza
SAM24418298


title: Unstimulated_8292 [NGS4564]

description:
Source: Lonza
SAM24418292


title: aOSM_OSMR_9112 [NGS4630]

description:
Source: Promocell
SAM24419112

value: pulmonary microvascular endothelial cells

value: OSM + anti-OSM + anti-OSMR#1


title: CML Dx-52

value: Diagnosis


title: TMBPF_50_donor1_R3_P3

description: Library name: s215

value: Primary

value: Epithelial

value: chemical exposure

value: tetramethyl bisphenol F


title: TMBPF_10_donor1_R3_P3

description: Library name: s214

value: WT


title: Unstimulated_8280 [NGS4564]

description:
Source: Lonza
SAM24418280


title: eP_H3K27ac

description: Library name: eP_H3K27ac_CUTTag

value: Testis

value: Germ cells

value: Spermatocyte

value: Extracting the cell nuclei from the frozen testicular tissue


title: CML Dx-51

value: Male


title: TMBPF_5_donor1_R3_P3

description: Library name: s213

value: Mammary


title: eP_H3K9me3

description: Library name: eP_H3K9me3_CUTTag


title: CML Dx-50


title: Unstimulated_8286 [NGS4564]

description:
Source: Lonza
SAM24418286

value: normal human lung fibroblast

value: Unstimulated


title: TMBPF_1_donor1_R3_P3

description: Library name: s212


title: eP_H3K4me3

description: Library name: eP_H3K4me3_CUTTag


title: OSM_aOSMR_GNE_8309 [NGS4564]

description:
Source: Lonza
SAM24418309

value: OSM + anti-OSMR GNE


title: CML Dx-49

value: Bone marrow

value: CML

value: Female


title: Dmc1ko_H3K4me3

description: Library name: Dmc1ko_H3K4me3_CUTTag


title: TMBPF_0-5_donor1_R3_P3

description: Library name: s211

value: Primary


title: OSM_aOSMR_GNE_8303 [NGS4564]

description:
Source: Lonza
SAM24418303


title: CML Dx-45

value: Diagnosis


title: OSM_aOSMR_GNE_8297 [NGS4564]

description:
Source: Lonza
SAM24418297


title: Vehicle R2

city: La Jolla

first: Dwayne

middle: G

last: Stupack

address: 3855 Health Sciences

department: Obstetrics and Gynecology

institute: UC San Diego Moores Cancer Center

description: Library name: Vehicle Injected FAKwt 2

data_processing:
RNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (mm10)
RNA-Seq: Cell Ranger v.7 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
Expression matrix consists of sample specific  barcodes/features/matrix  tsv files
Assembly: mm10
Supplementary files format and content: tsv (barcodes, features and gene matrix)

source_name: ascites

growth_protocol: Prior to injection:  KMF cells are grown in DMEM supplemented with 10% fetal bovine serum (FBS, Omega Scientific), 1 mM non-essential amino acids, 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
RNA-Seq: 10X Genomics Chromium Prep (10X Genomics, PN-1000120). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
RNA-Seq: The cDNA libraries were constructed using the Chromium Next GEM Single Cell 3′ HT Kit (10X Genomics), per the manufacturer’s original protocol.

treatment_protocol: 5 million KMF cells were injected IP into C57bl/6 mice.  Mice were treated with cisplatin (2.5mg/kg) and docetaxol (5mg/kg), twice weekly, VS 4718 FAK inhibitor group  (Verastem) BID 100mg/kg, and docetaxol group (0.15mg/kg biweekly).

value: ascites

value: KMF

value: all cells

tag: strain


title: TMBPF_0-01_donor1_R3_P3

description: Library name: s209

value: Epithelial

value: WT

value: chemical exposure

value: tetramethyl bisphenol F


title: TMBPF_0-1_donor1_R3_P3

description: Library name: s210


title: CML Dx-44

value: Male


title: Vehicle R1

description: Library name: Vehicle Injected FAKwt 1


title: DMSO_0-1_donor1_R13_P3

description: Library name: s208

value: Mammary

value: vehicle control

value: dimethyl sulfoxide


title: OSM_aOSMR_GNE_8291 [NGS4564]

description:
Source: Lonza
SAM24418291

value: normal human lung fibroblast

value: OSM + anti-OSMR GNE


title: FAKiDoxil R2

description: Library name: PLD_FAKi treated FAKwt 2


title: BPAF_10_donor1_R3_P3

description: Library name: s207

value: bisphenol AF


title: CML Dx-43

value: Bone marrow

value: CML


title: CML Dx-42

value: Diagnosis


title: FAKiDoxil R1

description: Library name: PLD_FAKi treated FAKwt 1

value: ascites


title: OSM_aOSMR_8300 [NGS4564]

description:
Source: Lonza
SAM24418300

value: OSM 10ng/mL + anti-OSMR


title: OSM_aOSMR_8306 [NGS4564]

description:
Source: Lonza
SAM24418306


title: FAKi R1

description: Library name: FAK Inhibitor treated FAKwt 1

value: KMF

value: all cells


title: OSM_aOSMR_8294 [NGS4564]

description:
Source: Lonza
SAM24418294


title: CML Dx-38

value: Female


title: FAKi R2

description: Library name: FAK Inhibitor treated FAKwt 2


title: Doxil R2

description: Library name: PLD treated FAKwt 2


title: OSM_aOSMR_GNE_8285 [NGS4564]

description:
Source: Lonza
SAM24418285


title: CML Dx-40


title: CML Dx-39


title: CML Dx-36


title: BPAF_0-1_donor1_R3_P3

description: Library name: s203

value: Primary

value: Epithelial

value: WT

value: chemical exposure


title: BPAF_1_donor1_R3_P3

description: Library name: s205

value: Mammary


title: Doxil R1

description: Library name: PLD treated FAKwt 1


title: Chemo (platinum taxane) R2

description: Library name: P/T treated FAKwt 2


title: OSM_aOSMR_8282 [NGS4564]

description:
Source: Lonza
SAM24418282


title: BPAF_0-5_donor1_R3_P3

description: Library name: s204


title: BPAF_0-01_donor1_R3_P3

description: Library name: s202


title: CML Dx-35

value: Male


title: CML Dx-34


title: BPAF_0-001_donor1_R3_P3

description: Library name: s201


title: OSM_aOSMR_8288 [NGS4564]

description:
Source: Lonza
SAM24418288

value: normal human lung fibroblast


title: Chemo (platinum taxane) R1

description: Library name: P/T treated FAKwt 1


title: OSM_aOSM_8295 [NGS4564]

description:
Source: Lonza
SAM24418295

value: OSM 10ng/mL + anti-OSM


title: BPAF_5_donor1_R3_P3

description: Library name: s206

value: bisphenol AF


title: FAK KD R2

description: Library name: Untreated FAK Kinase Dead 2


title: CML Dx-33

value: Bone marrow


title: OSM_aOSM_8301 [NGS4564]

description:
Source: Lonza
SAM24418301


title: CML Dx-31

value: CML


title: BPA_50_donor1_R3_P3

description: Library name: s200

value: bisphenol A


title: OSM_aOSM_8289 [NGS4564]

description:
Source: Lonza
SAM24418289


title: CML Dx-30

value: Diagnosis


title: FAK KD R1

description: Library name: Untreated FAK Kinase Dead 1

value: ascites


title: FAK KO R1

description: Library name: Untreated FAK deleted KT13 1

value: KMF


title: FAK KO R2

description: Library name: Untreated FAK deleted KT13 2

value: all cells


title: BPA_1_donor1_R3_P3

description: Library name: s197


title: BPA_10_donor1_R3_P3

description: Library name: s199


title: CML Dx-29

value: Female


title: OSM_aOSM_8283 [NGS4564]

description:
Source: Lonza
SAM24418283


title: OSM_8305 [NGS4564]

description:
Source: Lonza
SAM24418305

value: OSM 10ng/mL + isotype control


title: OSM_aOSM_8307 [NGS4564]

description:
Source: Lonza
SAM24418307


title: OSM_8299 [NGS4564]

description:
Source: Lonza
SAM24418299


title: BPA_0-5_donor1_R3_P3

description: Library name: s196

value: Primary

value: Epithelial


title: Control R1

description: Library name: Untreated FAKwt 1


title: Control R2

description: Library name: Untreated FAKwt 2


title: BPA_5_donor1_R3_P3

description: Library name: s198

value: WT

value: chemical exposure


title: OSM_8287 [NGS4564]

description:
Source: Lonza
SAM24418287


title: CML Dx-24

value: Male


title: BPA_0-01_donor1_R3_P3

description: Library name: s194

value: Mammary


title: OSM_8293 [NGS4564]

description:
Source: Lonza
SAM24418293

value: normal human lung fibroblast


title: CML Dx-23


title: BPA_0-001_donor1_R3_P3

description: Library name: s193


title: WT AD Skin anti Ly6G 2

city: Inchon

first: YunJae

last: Jung

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Microbiology

country: South Korea

institute: College of Medicine, Gachon University

description: Library name: AD-Anti Ly6G -2

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to rn6 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -e
The reads were prepared for analysis using the Trimmomatic version 0.38 to remove adapter sequences and trim the low-quality bases. Subsequently, the processed reads were aligned to the Rattus norvegicus reference genome (rn6) using HISAT version 2.1.0 by incorporating both HISAT and Bowtie2 for alignment.83 Reference genome sequences and gene annotation data were sourced from the NCBI Genome Assembly and NCBI RefSeq databases. Following alignment, data formatted in SAM was sorted and indexed using SAMtools version 1.9. Then, the StringTie version 2.1.3b tool was used to assemble and quantify the transcripts.84,85 Differential gene expression analysis was performed using edgeR version 3.40.2 with raw count data input.86 The exactTest function within edgeR was used to determine the statistical significance of the differentially expressed genes (DEGs) after adjusting the p-values using the Benjamini–Hochberg method to control the false discovery rate. The DEGs were identified based on the criteria: |fold change| ≥ 2 and p < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM, TPM values for each Sample

source_name: Ear skin tissue

growth_protocol: C57BL/6 mice purchased from Orient Bio (Gyeonggi-do, Korea) were maintained at standard temperature and humidity in a specific pathogen-free environment. All procedures were reviewed and approved by the Center of Animal Care and Use at the Lee Gil Ya Cancer and Diabetes Institute, Gachon University (LCDI-2023-0038, LCDI-2023-0028).

extract_protocol:
RNA from the skin and small intestines of the mice was extracted using QIAzol and purified using an RNeasy mini kit. The purified RNA was processed with DNase I  to remove genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce AD-like inflammation, bilateral ear skin was topically treated with 50 µM MC903 (Tocris Biochemicals, Bristol, UK) in 20 µL of 100% ethanol daily for 10 days. For OSM neutralization, mice received intradermal injections of anti-OSM antibody (20 μg/mouse; R&D Systems) every other day during the 10-day MC903 treatment period, and for neutrophil depletion, mice received intraperitoneal injections of anti-Ly6G antibody (200 μg/mouse; Bio X Cell) administered 2 days prior to and 1 and 4 days after MC903 application.

value: Ear skin tissue


title: WT AD Skin anti Ly6G 3

description: Library name: AD-Anti Ly6G -3


title: OSM_8281 [NGS4564]

description:
Source: Lonza
SAM24418281


title: CML Dx-20

value: Bone marrow


title: CML Dx-28

value: CML


title: BPA_0-1_donor1_R3_P3

description: Library name: s195

value: bisphenol A


title: DMSO_0-1_donor3_R11_P2

description: Library name: s189

value: vehicle control

value: dimethyl sulfoxide


title: CML Dx-19

value: Peripheral blood

value: Diagnosis


title: WT AD Skin anti Ly6G 1

description: Library name: AD-Anti Ly6G -1


title: aOSM_OSMR_8302 [NGS4564]

description:
Source: Lonza
SAM24418302

value: OSM + anti-OSM & OSMR


title: DMSO_0-1_donor2_R12_P2

description: Library name: s188


title: aOSM_OSMR_8296 [NGS4564]

description:
Source: Lonza
SAM24418296


title: WT AD Skin anti OSM 1

description: Library name: AD-Anti OSM -1


title: WT AD Skin anti OSM 2

description: Library name: AD-Anti OSM -2


title: DMSO_0-1_donor2_R11_P2

description: Library name: s187


title: CML Dx-14

value: Female


title: aOSM_OSMR_8290 [NGS4564]

description:
Source: Lonza
SAM24418290


title: DMSO_0-1_donor3_R12_P2

description: Library name: s190

value: Primary


title: WT AD Skin anti OSM 3

description: Library name: AD-Anti OSM -3


title: CML Dx-13


title: Spp1-EGFP KI reporter mice, PBS day 7, Spp1-EGFP+CD11b- SiglecF+ macrophages_2

city: Tokyo

first: Kohsuke

last: Shirakawa

address: 35 Shinanomachi, Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

description: Library name: C7_SPP1GFP_posAMs_2

data_processing:
Raw paired-end reads were quality-checked with FastQC (v0.11.5), and low-quality bases and adapters were trimmed using Trimmomatic (v0.38) with parameters: ILLUMINACLIP:path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were aligned to the mouse reference genome (GRCm38) using HISAT2 (v2.1.0). SAM files were converted to BAM format using samtools, and gene-level read counts were obtained using featureCounts (v1.6.3). Normalization was performed in TPM.
Assembly: Mouse reference genome GRCm38 (GENCODE M25)
Supplementary files format and content: Processed data files include gene expression count tables in tab-delimited format (raw counts and TPM), and lists of differentially expressed genes with associated statistical values (log2 fold change, adjusted p-value).

extract_protocol:
Total RNA was extracted from tissue samples using a standard phenol-chloroform method or an RNA purification kit according to the manufacturer's protocol. RNA quality was assessed using a Bioanalyzer or Nanodrop spectrophotometer.
RNA-seq libraries were prepared from high-quality total RNA samples using a poly(A) selection method, followed by cDNA synthesis and library construction.

value: lung

value: lung macrophages


title: Spp1-EGFP KI reporter mice, PBS day 7, Spp1-EGFP+CD11b- SiglecF+ macrophages_3

description: Library name: C7_SPP1GFP_posAMs_3


title: DMSO_0-1_donor1_R12_P2

description: Library name: s186

value: Epithelial

value: WT


title: PositiveControl_UniversalHuman_R3_P7

description: Library name: s672

organism: synthetic construct

value: Mammary

value: technical control

value: universal human RNA


title: CML Dx-27

value: Bone marrow

value: Male


title: aOSM_OSMR_8284 [NGS4564]

description:
Source: Lonza
SAM24418284

value: normal human lung fibroblast


title: aOSM_OSMR_8308 [NGS4564]

description:
Source: Lonza
SAM24418308


title: DMSO_0-1_donor1_R11_P2

description: Library name: s185

value: vehicle control


title: CML Dx-11

value: CML


title: CML Dx-08


title: Spp1-EGFP KI reporter mice, PBS day 7, Spp1-EGFP+CD11b- SiglecF+ macrophages_1

description: Library name: C7_SPP1GFP_posAMs_1


title: DMSO_0-1_donor3_R10_P2

description: Library name: s182

value: dimethyl sulfoxide


title: DMSO_0-1_donor3_R9_P2

description: Library name: s181


title: PositiveControl_Brain_R3_P7

description: Library name: s671

value: brain RNA


title: Spp1-EGFP KI reporter mice, Bleomycin day 30, Spp1-EGFP+CD11b- SiglecF+ macrophages_3

description: Library name: B30_SPP1GFP_posAMs_3


title: Spp1-EGFP KI reporter mice, Bleomycin day 30, Spp1-EGFP+CD11b- SiglecF+ macrophages_2

description: Library name: B30_SPP1GFP_posAMs_2


title: CML Dx-07

value: Peripheral blood

value: Diagnosis


title: CML Dx-06


title: DMSO_0-1_donor2_R10_P2

description: Library name: s180

value: Primary


title: DMSO_0-1_donor1_R10_P2

description: Library name: s178


title: Spp1-EGFP KI reporter mice, Bleomycin day 14, Spp1-EGFP+CD11b- SiglecF+ macrophages_3

description: Library name: B14_SPP1GFP_posAMs_3

value: lung


title: DMSO_0-1_donor2_R9_P2

description: Library name: s179


title: Spp1-EGFP KI reporter mice, Bleomycin day 30, Spp1-EGFP+CD11b- SiglecF+ macrophages_1

description: Library name: B30_SPP1GFP_posAMs_1

value: lung macrophages


title: NegativeControl_R6_P7

description: Library name: s656

value: Epithelial

value: lysis buffer


title: PositiveControl_UniversalHuman_R2_P6

description: Library name: s568

value: Mammary


title: PositiveControl_Brain_R2_P6

description: Library name: s567

value: technical control


title: CML Dx-05


title: NegativeControl_R4_P6

description: Library name: s560


title: CML Dx-09

value: Female


title: CML Dx-04

value: Bone marrow


title: DMSO_0-1_donor1_R9_P2

description: Library name: s177

value: WT


title: E2_10_donor3_R2_P2

description: Library name: s174

value: chemical exposure


title: CML Dx-03

value: Male


title: NegativeControl_R5_P7

description: Library name: s655


title: Spp1-EGFP KI reporter mice, Bleomycin day 14, Spp1-EGFP+CD11b+ SiglecF- macrophages_3

description: Library name: B14_SPP1GFP_posIMs_3


title: CML Dx-02

value: CML


title: Spp1-EGFP KI reporter mice, Bleomycin day 14, Spp1-EGFP+CD11b+ SiglecF- macrophages_2

description: Library name: B14_SPP1GFP_posIMs_2


title: PositiveControl_UniversalHuman_R1_P5

description: Library name: s480

value: universal human RNA


title: Spp1-EGFP KI reporter mice, Bleomycin day 14, Spp1-EGFP+CD11b- SiglecF+ macrophages_2

description: Library name: B14_SPP1GFP_posAMs_2


title: MDS-Dx-92

value: MDS


title: E2_1_donor2_R2_P2

description: Library name: s171


title: E2_10_donor2_R2_P2

description: Library name: s172


title: MDS-Dx-90


title: CML Dx-18


title: Spp1-EGFP KI reporter mice, Bleomycin day 14, Spp1-EGFP+CD11b- SiglecF+ macrophages_1

description: Library name: B14_SPP1GFP_posAMs_1


title: NegativeControl_R1_P5

description: Library name: s471


title: DMSO_0-1_donor3_R8_P2

description: Library name: s168

value: vehicle control

value: dimethyl sulfoxide


title: E2_1_donor1_R2_P2

description: Library name: s169

value: Primary


title: Spp1-EGFP KI reporter mice, Bleomycin day 14, Spp1-EGFP+CD11b+ SiglecF- macrophages_1

description: Library name: B14_SPP1GFP_posIMs_1

value: lung


title: Spp1-EGFP KI reporter mice, Bleomycin day 7, Spp1-EGFP+CD11b+ SiglecF- macrophages_3

description: Library name: B7_SPP1GFP_posIMs_3

value: lung macrophages


title: E2_1_donor3_R2_P2

description: Library name: s173

value: Epithelial


title: NegativeControl_R2_P5

description: Library name: s472

value: lysis buffer


title: MDS-Dx-88

value: Diagnosis


title: Spp1-EGFP KI reporter mice, Bleomycin day 7, Spp1-EGFP+CD11b+ SiglecF- macrophages_2

description: Library name: B7_SPP1GFP_posIMs_2


title: MDS-Dx-89


title: PositiveControl_UniversalHuman_R4_P4

description: Library name: s384

value: Mammary

value: technical control


title: MDS-Dx-87

value: Bone marrow


title: PositiveControl_Brain_R1_P5

description: Library name: s479

value: brain RNA


title: Spp1-EGFP KI reporter mice, Bleomycin day 7, Spp1-EGFP+CD11b+ SiglecF- macrophages_1

description: Library name: B7_SPP1GFP_posIMs_1


title: NegativeControl_R3_P6

description: Library name: s559


title: TMBPF_50_donor3_R2_P2

description: Library name: s167

value: WT

value: chemical exposure

value: tetramethyl bisphenol F


title: Spp1-EGFP KI reporter mice, Bleomycin day 7, Spp1-EGFP-CD11b+ SiglecF- macrophages_3

description: Library name: B7_SPP1GFP_negIMs_3


title: MDS-Dx-85

value: Male


title: TMBPF_10_donor3_R2_P2

description: Library name: s166


title: MDS-Dx-80

value: MDS

value: Female


title: Spp1-EGFP KI reporter mice, Bleomycin day 7, Spp1-EGFP-CD11b+ SiglecF- macrophages_2

description: Library name: B7_SPP1GFP_negIMs_2


title: NegativeControl_R16_P4

description: Library name: s376


title: PositiveControl_Brain_R4_P4

description: Library name: s383


title: TMBPF_1_donor3_R2_P2

description: Library name: s164


title: TMBPF_5_donor3_R2_P2

description: Library name: s165


title: NegativeControl_R14_P4

description: Library name: s368


title: MDS-Dx-75


title: MDS-Dx-74


title: WT C57BL/6J, Bleomycin day 7, CD11b+ SiglecF- macrophages_3

description: Library name: WT_Bleo_IMs_3


title: TMBPF_0-5_donor3_R2_P2

description: Library name: s163


title: TMBPF_0-1_donor3_R2_P2

description: Library name: s162


title: WT C57BL/6J, Bleomycin day 7, CD11b+ SiglecF- macrophages_2

description: Library name: WT_Bleo_IMs_2


title: WT C57BL/6J, Bleomycin day 7, CD11b+ SiglecF- macrophages_1

description: Library name: WT_Bleo_IMs_1


title: PositiveControl_UniversalHuman_R3_P3

description: Library name: s288

value: universal human RNA


title: NegativeControl_R13_P4

description: Library name: s367

value: Primary


title: MDS-Dx-73


title: MDS-Dx-70


title: WT C57BL/6J, PBS day 7, CD11b+ SiglecF- macrophages_3

description: Library name: WT_PBS_IMs_3

value: lung


title: MDS-Dx-68


title: DMSO_0-1_donor3_R7_P2

description: Library name: s160

value: vehicle control

value: dimethyl sulfoxide


title: NegativeControl_R12_P3

description: Library name: s280

value: Epithelial

value: lysis buffer


title: BPAF_10_donor3_R2_P2

description: Library name: s159

value: Mammary

value: bisphenol AF


title: WT C57BL/6J, PBS day 7, CD11b+ SiglecF- macrophages_2

description: Library name: WT_PBS_IMs_2

value: lung macrophages


title: Spp1-EGFP KI reporter mice, Bleomycin day 7, Spp1-EGFP-CD11b+ SiglecF- macrophages_1

description: Library name: B7_SPP1GFP_negIMs_1


title: NegativeControl_R11_P3

description: Library name: s279

value: technical control


title: WT C57BL/6J, PBS day 7, CD11b+ SiglecF- macrophages_1

description: Library name: WT_PBS_IMs_1


title: NegativeControl_R10_P3

description: Library name: s272


title: MDS-Dx-66

value: Bone marrow

value: Diagnosis


title: PositiveControl_Brain_R3_P3

description: Library name: s287

value: brain RNA


title: mESCs, cKO (tamoxifen) and SCR AMO, R2

city: Irvine

first: Ivan

last: Marazzi

address: 839 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California

description: Library name: mESCs, cKO (tamoxifen) and SCR AMO, rep2

data_processing:
Illumina Short Reads were mapped onto the WT and Exosc3 cKO mESCs and EpiLCs novel transcriptome using STAR using the following parameters: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100. Gene- and TE-level quantification was performed with TEcount using the RepeatMasker gtf file generated from the mm10 genome. Isoform-level quantification was performed with RSEM. Differential expression was calculated using DESeq2 with default parameters.
Assembly: Novel transcriptome generated with the WT and Exosc3 cKO mESCs and EpiLCs long and short-read RNA-seq (GEO:GSE205211) based on mm10.
Supplementary files format and content: tab-deliminated TEcount gene and TE expression counts. Column titles are numbered by the sample id, i.e. 1 is 'mESCs, EtOH and U1 AMO, rep1', 2 is 'mESCs, EtOH and U6atac AMO, rep1', etc.

source_name: mESCs

growth_protocol: mESCs were cultured in 2i/Lif media.

extract_protocol:
On the day of collection, cells were collected in TRIzol and RNA was isolated following the manufacturer’s recommendations.
RNA libraries were prepared using either the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) or TruSeq kit (Illumina) following the manufacturer’s recommendations.

treatment_protocol: Exosc3 cKO was induced by the addition of 100 nM tamoxifen (4-OHT). Control wells were treated with ethanol (EtOH) alone. ASOs was transfected with Lipofectamine RNAiMAX (Thermofisher scientific) at a final concentration of 100nM. AMOs were added to the cell suspensions at a final concentration of 15μM and electroporated into cells using the Biorad Gene Pulser XCell electroporation system.

value: mESCs


title: MDS-Dx-65

value: MDS


title: BPAF_5_donor3_R2_P2

description: Library name: s158

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina Basespace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed December 2024), which manages workflows using snakemake v8.0 (Mölder et al., 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al., 2018), STAR v2.7.8a (Dobin et al., 2013) to perform alignment of raw reads to the reference sequence, and the qCount function of the QuasR R package (v1.30.0; Gaidatzis et al., 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 and 2.1 kits (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

value: WT

value: chemical exposure


title: NegativeControl_R9_P3

description: Library name: s271

value: Primary


title: BPAF_1_donor3_R2_P2

description: Library name: s157


title: MDS-Dx-60

value: Male


title: mESCs, cKO (tamoxifen) and U6atac AMO, R2

description: Library name: mESCs, cKO (tamoxifen) and U6atac AMO, rep2


title: NegativeControl_R15_P4

description: Library name: s375


title: BPAF_0-5_donor3_R2_P2

description: Library name: s156


title: TMBPF_0-01_donor3_R2_P2

description: Library name: s161

value: tetramethyl bisphenol F


title: PositiveControl_UniversalHuman_R2_P2

description: Library name: s192

value: universal human RNA


title: MDS-Dx-59

value: Female


title: BPAF_0-1_donor3_R2_P2

description: Library name: s155

value: Epithelial


title: mESCs, cKO (tamoxifen) and U1 AMO, R2

description: Library name: mESCs, cKO (tamoxifen) and U1 AMO, rep2


title: mESCs, EtOH and SCR AMO, R2

description: Library name: mESCs, EtOH and SCR AMO, rep2


title: PositiveControl_Brain_R2_P2

description: Library name: s191

value: Mammary


title: MDS-Dx-64


title: mESCs, EtOH and U6atac AMO, R2

description: Library name: mESCs, EtOH and U6atac AMO, rep2


title: BPAF_0-01_donor3_R2_P2

description: Library name: s154

value: bisphenol AF


title: NegativeControl_R8_P2

description: Library name: s184

value: lysis buffer


title: BPAF_0-001_donor3_R2_P2

description: Library name: s153


title: MDS-Dx-57


title: mESCs, EtOH and U1 AMO, R2

description: Library name: mESCs, EtOH and U1 AMO, rep2


title: MDS-Dx-55


title: NegativeControl_R7_P2

description: Library name: s183

value: technical control


title: NegativeControl_R6_P2

description: Library name: s176


title: BPA_50_donor3_R2_P2

description: Library name: s152

value: bisphenol A


title: PositiveControl_UniversalHuman_R1_P1

description: Library name: s96


title: MDS-Dx-51

value: Bone marrow

value: Diagnosis


title: MDS-Dx-50


title: mESCs, cKO (tamoxifen) and SCR AMO, R1

description: Library name: mESCs, cKO (tamoxifen) and SCR AMO, rep1

value: mESCs


title: BPA_10_donor3_R2_P2

description: Library name: s151


title: MDS-Dx-49

value: MDS


title: NegativeControl_R5_P2

description: Library name: s175


title: MDS-Dx-46


title: mESCs, cKO (tamoxifen) and U1 AMO, R1

description: Library name: mESCs, cKO (tamoxifen) and U1 AMO, rep1


title: PositiveControl_Brain_R1_P1

description: Library name: s95

value: brain RNA


title: mESCs, cKO (tamoxifen) and U6atac AMO, R1

description: Library name: mESCs, cKO (tamoxifen) and U6atac AMO, rep1


title: BPA_1_donor3_R2_P2

description: Library name: s149

value: WT

value: chemical exposure


title: MDS-Dx-58


title: mESCs, EtOH and U6atac AMO, R1

description: Library name: mESCs, EtOH and U6atac AMO, rep1


title: MDS-Dx-45

value: Male


title: mESCs, EtOH and SCR AMO, R1

description: Library name: mESCs, EtOH and SCR AMO, rep1


title: NegativeControl_R3_P1

description: Library name: s87

value: Primary


title: BPA_0-5_donor3_R2_P2

description: Library name: s148


title: BPA_5_donor3_R2_P2

description: Library name: s150


title: MDS-Dx-44


title: mESCs, EtOH and U1 AMO, R1

description: Library name: mESCs, EtOH and U1 AMO, rep1


title: BPA_0-01_donor3_R2_P2

description: Library name: s146


title: NegativeControl_R2_P1

description: Library name: s80


title: BPA_0-001_donor3_R2_P2

description: Library name: s145


title: BPA_0-1_donor3_R2_P2

description: Library name: s147


title: MDS-Dx-42


title: Mouse retina, Opa1V291D_S2

city: New York

first: Eugene Yu-Chuan

last: Kang

address: 701 W. 168 St, HHSC 2nd floor, 210

institute: Columbia University Irving Medical Center

description:
Library name: Sample3
10x Genomics

data_processing:
The data was aggregated using the Cell Ranger aggr program. The integrated dataset was first imported into the Rosalind platform (https://www.rosalind.bio/) for dimension reduction and unsupervised clustering using Cell Ranger Graph Based Clustering (10 Genomics). The dataset was then loaded into R (v4.2) and the Seurat package (v5.0).(105) Cell types were annotated using SC-type (v1.0)(106) with cell markers for major retinal cells
Assembly: Mouse  mm9
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: nuclear RNA

source_name: Retina

extract_protocol:
Mouse retinas were harvested and nucleus extraction was performed using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec) according to the manufacturer’s guidelines. Upon isolation, the nuclei were counted using trypan blue and a Countess III Automated Cell Counter (Thermo Fisher Scientific, Waltham, MA, USA).
SnRNA libraries were prepared using the Chromium Single Cell 3' kit (10X Genomics) and sequenced on an Illumina platform using standard protocols. After obtaining the sequencing data, we used Cell Ranger (v8.0) with default parameters to generate a filtered_feature_bc_matrix.h5 file containing cell barcodes and transcript counts for each sample.

value: Retina

value: Retinal cells

value: 360 days


title: DMSO_0-1_donor2_R8_P2

description: Library name: s144

value: Mammary

value: Epithelial

value: vehicle control

value: dimethyl sulfoxide


title: Mouse retina, Opa1V291D_S1

description:
Library name: Sample2
10x Genomics


title: WT Skin MC903 5

description: Library name: WT-MC903-5

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to rn6 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -e
The reads were prepared for analysis using the Trimmomatic version 0.38 to remove adapter sequences and trim the low-quality bases. Subsequently, the processed reads were aligned to the Rattus norvegicus reference genome (rn6) using HISAT version 2.1.0 by incorporating both HISAT and Bowtie2 for alignment.83 Reference genome sequences and gene annotation data were sourced from the NCBI Genome Assembly and NCBI RefSeq databases. Following alignment, data formatted in SAM was sorted and indexed using SAMtools version 1.9. Then, the StringTie version 2.1.3b tool was used to assemble and quantify the transcripts.84,85 Differential gene expression analysis was performed using edgeR version 3.40.2 with raw count data input.86 The exactTest function within edgeR was used to determine the statistical significance of the differentially expressed genes (DEGs) after adjusting the p-values using the Benjamini–Hochberg method to control the false discovery rate. The DEGs were identified based on the criteria: |fold change| ≥ 2 and p < 0.05.
Assembly: mm10
Supplementary files format and content: FPKM, TPM values for each Sample

treatment_protocol: To induce AD-like inflammation, bilateral ear skin was topically treated with 50 µM of MC903 (calcipotriol; Tocris Biochemicals, Bristol, UK) in 20 µL of 100% ethanol and with 10 µL of 10 mg/mL ovalbumin (OVA; Sigma-Aldrich, St. Louis, MO, USA) in phosphate-buffered saline (PBS) daily for 10 days. Control mice were treated with 20 µL of 100% ethanol followed by 10 µL of 10 mg/mL OVA in PBS. To induce itch flares associated with atopic dermatitis, mice were administered an intradermal injection of 20 µL of 2.5 mg/mL OVA on day 10. Scratching behavior was recorded for 5 min prior to the injection and for 30 min following the challenge.

value: Ear skin tissue

value: 50 µM of MC903


title: NegativeControl_R4_P1

description: Library name: s88

value: technical control

value: lysis buffer


title: TMBPF_50_donor2_R2_P2

description: Library name: s143

value: tetramethyl bisphenol F


title: MDS-Dx-38

value: Bone marrow

value: MDS

value: Diagnosis


title: MDS-Dx-40

value: Female