title: OSW-1-resistant HeLa cells_2

city: Kamigori-cho, Ako-gun

first: Kanae

last: Sasaki

state: Hyogo

address: 3-2-1 Kouto

department: Department of Molecular Biochemistry, Graduate School of Sciences

institute: University of Hyogo

library_source: other

data_processing:
Torrent Suite software v5.4.0 (Thermo Fisher Scientific) is used for basecalling.
The raw reads were aligned to the sgRNA library (Human library A/B gRNA sequences) using TMAP implemented in SgRNA Screening custom plugin V1.1 in Torrent Suite software v5.4.0.
The raw read counts were calculated by HTSeq-0.5.3p9 implemented in SgRNAScreening custom plugin V1.1.
Normalization of read count data was performed by DESeq_1.30.0 inplemented in SgRNAScreening custom plugin V1.1.
Assembly: sgRNA library (Human library A/B gRNA sequences)
Supplementary files format and content: Tab-delimited text files include gene symbol and gene expression (normalized) for each sample.

molecule: other

source_name: HeLa

extract_protocol:
gDNA was prepared with the conventional phenol-chloroform method. DNA fragments including sgRNA sequences were amplified by PCR using the gDNA as templates.
DNA libraries for GeCKO screening were prepared using Ion Plus Fragment Library Kit following manufacture's protocols.
GeCKO screening

tag: cell line

value: HeLa

value: Malignant epithelial cells derived from cervical cancer

value: Inhibition of the exchange transport of cholesterol and PI4P between the ER and the Golgi by OSW-1


title: NZB_W heart, biological rep2

status: Public on Feb 16 2024

type: RNA

city: Erlangen

first: Christoph

last: Daniel

address: Krankenhausstr. 8-10

department: Nephropathology

country: Germany

institute: FAU Erlangen-Nürnberg

description: Gene expression data from female mouse hearts with moderate kidney injury.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneScan 3000 7G.

data_processing: Data were normalized using the Robust Multi-array Average (GC-RMA) algorithm, and analyzed with the Partek Genomics Suite

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: hearts from NZB_W female mice with moderate kidney injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse hearts were collected from mice after bleeding and perfusion with 0,9% NaCl

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturers instructions

treatment_protocol: Mice were not treated, but female mice with two different genotype were used NZB_W as nephritic and NZW as healthy control mice.

tag: kidney disease

value: Lupus nephritis

tag: kidney injury

value: moderate kidney injury

tag: tissue

value: heart


title: Rat lens, 2ME2-2

city: Fukui

first: Masaru

last: Takashima

address: 3-9-1 Bunkyo

country: Japan

institute: University of Fukui

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
RaGene-2_0-st.pgf
RaGene-2_0-st.mps
Generated log2 values using robust multi-array average (RMA) method with R statistical software

organism: Rattus norvegicus

source_name: Rat lens, 30mM galactose, 6days, 40µM 2ME2 added, replicate2

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: The lens removed from the culture medium was ground with a biosmasher until it fell apart. Then treat the sample with TRIZOL, cDNA synthesis and amplification was performed

tag: strain

value: Sprague Dawley

value: lens

tag: condition

value: galactose-induced cataract

tag: treatment

value: Galactose, 2ME2

tag: time


title: Rat lens, Control_Day4

source_name: Rat lens, without galactose, 4 days

value: no cataract

value: without galactose


title: Rat lens, 2ME2

source_name: Rat lens, 30mM galactose, 6days, 40µM 2ME2 added, replicate1


title: Rat lens, Control_Day6

source_name: Rat lens, without galactose, 6 days


title: Rat lens, Galactose-1

source_name: Rat lens, 30mM galactose, 6days, replicate1

value: Galactose


title: BCCL2 R1_02

city: Chicago

first: Kyle

last: Schachtschneider

state: IL

address: 2201 West Campbell Park Drive

country: USA

institute: Sus Clinicals Inc

description:
expression results for Oncopig bladder cancer cell lines with and without gemcitabine treatment
Oncopig BCCL cells were cultured in DMEM medium (Vitrocell Embriolife, Campinas, Brazil)

hyb_protocol: The RNeasy Mini Kit was used to purify the amplified cRNA samples, according to the manufacturer instructions (Agilent). Then we Used the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1 (or higher) to quantify the cRNA. Next Prepared the 10× Blocking Agent, Prepared hybridization samples, Prepared the hybridization assembly and then Hybridized, all following the steps of the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual). For the Wash, we Added Triton X-102 to Gene Expression wash buffers, Prewarm Gene Expression Wash Buffer 2, Prepare the equipment and Wash the microarray slides, also following the steps of the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual). Microarray slides “HD Human GE 4 × 44K v2 Microarray” (1 slide, part number: G2519F-026652) and “Porcine (V2) Gene Expression Microarray, 4 × 44K” (1 slide, part number: G2519F-026440) were used for hybridization.

scan_protocol: The Scaned of the slides was performed in a SureScan/Agilent C microarray scanner and Agilent Scan Control software v7.0.03. Then we Extracted data using Agilent Feature Extraction Software. All steps were performed according to the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual)

data_processing:
Microarray slide analysis was performed in the software GeneSpring GX (Agilent Technologies Inc, Santa Clara, CA, USA). The software uses lowess normalization to adjust for internal differences between channels.
Untreated and treated groups of each cell line were first compared to each other using p (<0,05) and fold change to identify differentially expressed genes (DEGs) (2). DEGs were then compared between the human and Oncopig samples to identify common transcriptional changes in response to gemcitabine exposure.

organism: Sus scrofa

source_name: Gemcitabine Treated Oncopig Bladder Cancer Cell Line

label_protocol: We used the Low Input Quick Amp Labeling Kit, according to the manufacturer instructions (Agilent). Two-Color generates fluorescent cRNA (complimentary RNA) with a sample input RNA range between 10 ng and 200 ng of total RNA or a minimum of 5 ng of poly A+ RNA for two-color processing. The method uses T7 RNA Polymerase Blend (red cap), which simultaneously amplifies target material and incorporates Cyanine 3-CTP or Cyanine 5-CTP. Amplification is typically at least a 100-fold from total RNA to cRNA with the use of this kit. The steps were performed  following the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual).

growth_protocol: Oncopig BCCL cells were cultured in DMEM medium (Vitrocell Embriolife, Campinas, Brazil) and 5637 cells were cultured in RPMI medium. Both mediums were supplemented with 10% fetal bovine serum. The cells grew in a controlled atmosphere at 37ºC, 95% humidity and 5% CO2. The experiments were performed after cells reached the sub-confluence stage (<90%). Cells were then seeded in 6-well plates at a density of 2x10^5 cells

extract_protocol: After the treatment period of 48h, cells were washed with PBS and total RNA from the samples was extracted using TRIzol reagent, following manufacturer instructions (Invitrogen). Then, Qiagen RNeasy Kits (QIAGEN GmbH, Hilden, Germany) were used to isolate and purify the RNA according to manufacturer's recommendations. The quality and integrity of total RNA was verified by Nanovue Spectrophotometer (GE Healthcare) and Agilent 2100 bioanalyzer kit (Agilent Technologies, Santa Clara, CA, USA). cDNA synthesis was performed using 10 µl of total RNA at 100 ng/µl added to 10 µl of the High Capacity cDNA Reverse Transcription kit (Applied Biosystems ™, UK). The reaction condition was 25oC for 10 minutes, 37oC for two hours, 85 o C for 5 minutes and 4 o C to finish the reaction, followed by storage of the samples at –20 o C.

treatment_protocol: RNA extractions of human and Oncopig cells were performed in 6-well plates at a density of 2x10^5 cells per well after exposure to the chemotherapeutic gemcitabine at 1 µM for 48h. The control group consisted of cells exposed to medium only for 48h as well.

source_name: Untreated Oncopig Bladder Cancer Cell Line

value: untreated


title: NZB_W heart, biological rep1


title: BCCL2 R3_07

value: exposure to the chemotherapeutic gemcitabine at 1 µM for 48h


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-93]

type: SRA

city: Lyon

first: Anne-Pierre

last: Morel

state: Rhone-Alpes

address: 28, rue Laennec, Cheney D 2nd floor

country: France

institute: Cancer Research Center of Lyon

library_source: transcriptomic

data_processing:
Raw reads were aligned on the human genome with STAR.
Gene expression was quantified with STAR gene count, following the annotations of gencode v29.
Samples with less than 50000 reads were excluded.
Assembly: GRCh38
Supplementary files format and content: STAR gene count

organism: Homo sapiens

source_name: HME-RASi

extract_protocol:
Briefly, freshly harvested single cells were sorted into 96-well plates containing the lysis buffer (0.2% Triton X-100, 1U/  l RNase inhibitor, Thermo Fisher Scientific). RT was performed using SuperScript II (Thermo Fisher Scientific) in the presence of 1   M oligo-dT30VN (IDT), 1   M Template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Full-length scRNAseq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Roche) and IS PCR primer (IDT), with 23 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end reads of 75 bp length (PE75) with library indexes corresponding to cell barcodes.

value: HME-RASi

tag: cell type

value: mammary epithelial cells RAS inductible

tag: sequencing plate

tag: nbcells


title: IP_H2AK9ac_W833R_siTIP60_sip300_Vehicle

city: TianJin

first: Kaiwen

last: Bao

country: China

institute: Tianjin Medical University

library_source: genomic

data_processing:
ChIP-seq reads were first processed using TrimGalore (v0.6.4_dev) to trim adaptor and low-quality reads.
The quality of each trimmed file was verified by FastQC (v0.11.9)
The trimmed reads were then aligned to the human genome hg38 using Bowtie2 (v2.4.5)
Signal tracks for each sample were generated using bamCoverage (deepTools v3.4.3) tool and were normalized to Reads per kilo per million mapped reads (RPKM).
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Approximately 10 million cells were then cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with glycine for 5 min. The fixed cells were resuspended in SDS lysis buffer in the presence of protease inhibitors and subjected to 30 cycles of sonication in ice-cold water to generate chromatin fragments of 300 bp in length.
The purified DNA (5 ng of average size 300 bp) was used for library preparation with a VAHTS Universal DNA Library Prep Kit for Illumina V3 and sequenced with PE150 (paired-end, 50 bp reads) on Novogene’s NovaSeq high-throughput sequencing platform.

value: HeLa

tag: genotype

tag: chip antibody


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-10]


title: IP_H2AK5ac_W833R_siTIP60_sip300_Vehicle


title: BCCL2 R2_05


title: Ctrl HeLa cells_2

value: Malignant epithelial cells derived from cervical cancer

value: WT


title: IP_H2AK9ac_W833R_siTIP60_sip300_AcK


title: MSC GEX

city: Indianapolis

first: Yue

last: Wang

address: 975 W. Walnut street

department: Medical Genetics

institute: Indiana University

description:
cDNA library for 28bp and 91bp paired-end sequencing
filtered_feature_bc_matrix.h5
per_barcode_metadata.tsv

library_source: transcriptomic single cell

data_processing:
CellRanger (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
These RNA+ATAC multiome data were firstly demultiplexed using genotype-free pipeline from souporcell to separate the cell barcodes from different individuals.
The 10x Genomics multiome RNA+ATAC data was processed using Seurat and Signac following the standard workflow
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mesenchymal stem cells

growth_protocol: MSCBMT™ Basal Media (PT-3238) and MSCGM™ SingleQuots Supplement Kit (PT-4105) were purchased from Lonza to ensure the cells' health in culture. The media were changed every 3 days.

extract_protocol:
Cells were then lysed with 0.1X lysis buffer for 4 minutes to isolate nuclei, based on the protocol of Demonstrated Protocol Nuclei Isolation Complex Sample ATAC GEX Se-quencing, CG000375 RevB (10X Genomics, Inc).
Following the Chromium NextGEM Multiome ATAC GEX User Guide, CG000338_RevB (10X Genomics, Inc), tagmentation of nuclei preparation was first performed. Thereafter, briefly, along with the single cell multiome gel beads and partition oil, the single nuclei master mixture containing tagmented single nuclei suspension was transferred onto a Next GEM Chip J, and the chip loaded to the Chromium Controller for GEM generation and barcoding, followed by pre-amplification PCR, ATAC library preparation, cDNA synthesis and cDNA library preparation.
single cell multiome

treatment_protocol: After the cell monolayer reached 70-80% confluency, the MSC from each of the four do-nors were collected and combined in equal numbers to create a mixed cell preparation.

tag: individual

value: Donors 1-4

value: mesenchymal stem cells


title: IP_H2AK5ac_W833R_siTIP60_sip300_AcK


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-69]


title: OSW-1-resistant HeLa cells_1

value: Inhibition of the exchange transport of cholesterol and PI4P between the ER and the Golgi by OSW-1


title: Ctrl HeLa cells_1


title: IP_FLAG_H2AK5UAGK9UAG_AcK

value: Wt

value: FLAG


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-81]


title: HeLa cells treated with OSW-1_3

data_processing:
Torrent Suite software v5.4.0 (Thermo Fisher Scientific) is used for basecalling.
The raw reads were aligned to the human reference genome (hg19) using  Torrent Suite software v5.4.0, AmpliSeq RNA plugin.
The raw read counts were calculated by Torrent Suite software v5.4.0, AmpliSeq RNA plugin.
Calculation of RPM was performed by Torrent Suite software v5.4.0, AmpliSeq RNA plugin.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include gene symbol and gene expression (RPM) for each sample.

extract_protocol:
Total RNA was prepared with Sepasol Super G (Nacalai Tesque). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ion AmpliSeq Library Kit Plus following manufacture's protocols.

treatment_protocol: HeLa cells were treated with 5 nM OSW-1 or DMSO for 18 h.


title: Input_W833R_siTIP60_sip300_Vehicle


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-57]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-45]


title: Input_FLAG_H2AK5UAGK9UAG_Vehicle


title: Input_W833R_siTIP60_sip300_AcK


title: IP_H2AK9ac_W833R_Scr_Vehicle


title: HeLa cells treated with OSW-1_2


title: Input_W833R_Scr_Vehicle


title: HeLa cells treated with DMSO_2

value: control


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-33]


title: HeLa cells treated with DMSO_3


title: Input_FLAG_H2AK5UAGK9UAG_AcK


title: spatial transcriptomics ROI11

city: Seoul

first: Minji

last: Kang

address: 103 daehak-ro

department: biomedical sciences

country: South Korea

institute: Seoul National University graduate school

description: FFPE spatial transcriptome analysis

data_processing:
Fastq files were converted into DCC files by GeoMxNGSPipeline software
GeoMx DSP Analysis Suite (GEOMX-0094, v2.4.2.2) was utilized to analyze the spatial transcriptomic data. Target genes with 5% of the segment above the threshold were retained in the datasets and gene expressions with lower than the limit of quantitation were initially excluded.
Assembly: hg18
Supplementary files format and content: dcc

source_name: Kidney biopsy tissue

extract_protocol:
5-um thickness kidney biopsy sections were mounted on charged slides
Add PCR master mix and primer to transcripts samples, followed by PCR amplification. Combine each PCR product into a single microtube. Perform purification using AMPure magnetic beads and 80% ethanol. Obtain the libraries by elution in elution buffer.

value: Kidney biopsy tissue


title: spatial transcriptomics ROI12

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics ROI10

description: FFPE spatial transcriptome analysis


title: IP_H2AK5ac_W833R_Scr_Vehicle


title: HeLa cells treated with OSW-1_1


title: IP_FLAG_H2AK5UAGK9UAG_Vehicle


title: spatial transcriptomics ROI8

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics ROI9

description: FFPE spatial transcriptome analysis


title: HeLa cells treated with DMSO_1


title: spatial transcriptomics ROI7

description: FFPE spatial transcriptome analysis


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-92]


title: spatial transcriptomics ROI5

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics ROI6

description: FFPE spatial transcriptome analysis


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-80]


title: spatial transcriptomics ROI4

description: FFPE spatial transcriptome analysis


title: A.m.-A.m._2

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
Aligned to the reference with STAR (version 2.7.5c) following best practices (2 pass mode)
Pre-processing and manipulation of BAM files with samtools (version 1.9) and STAR (version 2.7.5c)
Read counts using FeatureCounts (version 2.0.3) from the SubRead package
Assembly: mm10
Supplementary files format and content: featurecounts default read counts file where S_01=UU_1, S_02=UU_2, S_03=UU_3, S_37=U-Am_1, S_38=U-Am_2, S_39=U-Am_3, S_41=Am-Am_1, S_42=Am-Am_2 and S_43=Am-Am_3

source_name: Mouse bone marrow-derived macrophage

growth_protocol: DMEM supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Macherey-Nagel™ NucleoSpin™ RNA extraction kit
TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031058 Rev. E), using “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA Single Indexes (Illumina Inc. Cat. # 20020492 and 20020493)

treatment_protocol: In vitro stimulation with Akkermansia muciniphila at a multiplicity of infection of 10

value: Mouse bone marrow-derived macrophage

value: stimulated and restimulated


title: spatial transcriptomics ROI3

description: FFPE spatial transcriptome analysis


title: spatial transcriptomics ROI2

description: FFPE spatial transcriptome analysis


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-68]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-56]


title: spatial transcriptomics ROI1

description: FFPE spatial transcriptome analysis


title: U-A.m._3

value: acutely stimulated


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-217]


title: P4_BCa_seq

city: Guangzhou

first: Changhao

last: Chen

state: Guangdong

address: 107 Yanjiangxi Road, Yuexiu District, Guangzhou, Guangdong Province, P. R. China

department: Urology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: paraffin section spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to Ensembl_release96 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantified using Space Ranger's default settings
Assembly: Ensembl_release96
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrixmtx.gz: gene expression count data in Matrix Market Exchange Format
Library strategy: spatial transcriptomics

source_name: bladder cancer tissues

extract_protocol:
The paraffin sections of bladder cancer were obtained from Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University. Then, the tissue sections were subjected to the Visium Spatial Tissue Optimization Slide kit to fit the time for permeabilization by generating fluorescently labeled cDNA tissue prints.
spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides and Reagent kit according to the manufactures’ construction.

value: bladder cancer tissues

value: surgery


title: A.m.-A.m._1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-44]

value: HME-RASi


title: P2_BCa_seq


title: P3_BCa_seq


title: P1_BCa_seq


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-21]

value: mammary epithelial cells RAS inductible


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-32]


title: U-A.m._2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-9]


title: U-A.m._1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-20]


title: P8_BCa_scRNAseq

description: 10x Genomics

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Assembly: Ensembl_release96
Supplementary files format and content: expression files and matrix files

extract_protocol:
Fresh bladder cancer tissues were obtained from patients and washed with ice-cold PBS. Then, the tissues were subjected to prepare single cell suspensions with tumor dissociation kit. Subsequently, the cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction.
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produced Illumina-ready sequencing libraries. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.

tag: Sex

value: Female

tag: age

tag: tumor stage


title: A.m.-A.m._3


title: P7_BCa_scRNAseq

description: 10x Genomics

value: Male


title: P6_BCa_scRNAseq

description: 10x Genomics


title: U_2

value: unstimulated


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-8]

tag: cell line


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-91]


title: chip_10A_2

city: London

first: Julia

last: Perea Paizal

address: Imperial College London, Department of Bioengineering

country: United Kingdom

institute: Imperial College London

description:
MCF-10A cells that have transited the constriction. replicate 2
CONST_10AvsCONTROL_10A_deg_all
CONST_10AvsCONTROL_10A.all_GOenrich_significant

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. ClusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: CONST_231vsCONTROL_231_deg_all: excel file with the differential deglist results from comparing the group of MDA-MB-231 cells that have transited the constriction (CONST) to MDA-MB-231 cells untransited (CONTROL).
Supplementary files format and content: CONST_LM2vsCONTROL_LM2_deg_all: excel file with the differential deglist results from comparing LM2 cells that have transited the constriction (CONST) to LM2 cells untransited (CONTROL)
Supplementary files format and content: CONST_10AvsCONTROL_10A_deg_all: excel file with the differential deglist results from comparing MCF-10A cells that have transited the constriction (CONST) to MCF-10A cells untransited (CONTROL)
Supplementary files format and content: CONST_231vsCONTROL_231.all_GOenrich_significant: significant GO enrichment between MDA-MB-231 cells that have transited the constriction (CONST) and MDA-MB-231 cells untransited (CONTROL)
Supplementary files format and content: CONST_LM2vsCONTROL_LM2.all_GOenrich_significant: significant GO enrichment between LM2 cells that have transited the constriction (CONST) and LM2 cells untransited (CONTROL)
Supplementary files format and content: CONST_10AvsCONTROL_10A.all_GOenrich_significant: significant GO enrichment between MCF-10A cells that have transited the constriction (CONST) and MCF-10A cells untransited (CONTROL)

growth_protocol: MDA-MB-231 and LM2 were cultured in cell culture medium StableCell™ DMEM - high glucose (Sigma-Aldrich) (4.5g/L glucose,stable glutamine, and sodium bicarbonate, (Sigma-Aldrich)), 10% heat-inactivated Fetal Bovine Serum (FBS) (Gibco) and 1% Penicillin/Streptomycin (Invitrogen). MCF-10A cells were cultured in DMEM/F12 (31331, Gibco) supplemented with 5% horse serum (16050, Gibco), 10μg/ml insulin (I-1882, Sigma), 20 ng/ml epidermal growth factor (E-9644, Sigma), 100ng/ml cholera toxin (C-8052, Sigma), 500ng/ml hydrocortisone (H-0888, Sigma), and 100mg/ml penicillin/streptomycin (15070, Gibco). Cells cultures were maintained at 37 °C/5% CO2/4% O2 incubators.

extract_protocol:
RNA was extracted using a All prep DNA/RNA Mini Kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Cells transited microfludic constriction channels of 5x5x150µm3 (width by height by length) dimensions under physiological hydrostatic pressures.  Cells were collected after transit, followed by RNA extraction.

value: breast

value: transit through 5x5x150µm3 constrictions


title: contrl_10A_1

description:
MCF-10A cells that have not transited the constriction (control). replicate 1
CONST_10AvsCONTROL_10A_deg_all
CONST_10AvsCONTROL_10A.all_GOenrich_significant

value: control (untransited cells)


title: chip_10A_1

description:
MCF-10A cells that have transited the constriction. replicate 1
CONST_10AvsCONTROL_10A_deg_all
CONST_10AvsCONTROL_10A.all_GOenrich_significant


title: contrl_10A_2

description:
MCF-10A cells that have not transited the constriction (control). replicate 2
CONST_10AvsCONTROL_10A_deg_all
CONST_10AvsCONTROL_10A.all_GOenrich_significant


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-79]


title: Sham_3

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

description: RNA-seq

data_processing:
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19. The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Supplementary_files_format_and_content: FPKM

source_name: Kidney

extract_protocol:
Total RNA was isolated from the kidneys using TRIzol (Life Technologies, Inc., Carlsbad, CA) and Direct-zol RNA MiniPrep (Zymo Research Corporation., Irvine, CA) according to the manufacturer's protocol.
The Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer's instructions.
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75 bp single-end mode.

tag: surgery

value: Sham


title: Sham_2

description: RNA-seq


title: contrl_LM2_1

description:
LM2 cells that have not transited the constriction (control). replicate 1
CONST_LM2vsCONTROL_LM2_deg_all
CONST_LM2vsCONTROL_LM2.all_GOenrich_significant

value: breast cancer


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-67]


title: chip_LM2_1

description:
LM2 cells that have transited the constriction. replicate 1
CONST_LM2vsCONTROL_LM2_deg_all
CONST_LM2vsCONTROL_LM2.all_GOenrich_significant


title: P9_BCa_scRNAseq

description: 10x Genomics


title: chip_LM2_2


title: contrl_LM2_2

description:
LM2 cells that have not transited the constriction (control). replicate 2
CONST_LM2vsCONTROL_LM2_deg_all
CONST_LM2vsCONTROL_LM2.all_GOenrich_significant


title: contrl_231_2

description:
MDA-MB-231 cells that have not transited the constriction (control). replicate 2
CONST_231vsCONTROL_231_deg_all
CONST_231vsCONTROL_231.all_GOenrich_significant


title: chip_231_2

description:
MDA-MB-231 cells that have transited the constriction. replicate 2
CONST_231vsCONTROL_231_deg_all
CONST_231vsCONTROL_231.all_GOenrich_significant


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-55]


title: Sham_1

description: RNA-seq


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-43]


title: contrl_231_1

description:
MDA-MB-231 cells that have not transited the constriction (control). replicate 1
CONST_231vsCONTROL_231_deg_all
CONST_231vsCONTROL_231.all_GOenrich_significant


title: U_3


title: chip_231_1

description:
MDA-MB-231 cells that have transited the constriction. replicate 1
CONST_231vsCONTROL_231_deg_all
CONST_231vsCONTROL_231.all_GOenrich_significant


title: IVCC_3

description: RNA-seq

value: IVCC


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-31]


title: IVCC_2

description: RNA-seq


title: AT 4, 1 Gy, 1h

city: Poznan

first: Agnieszka

last: Dzikiewicz-Krawczyk

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

data_processing:
Data was processed using the nf-core/LncPipe pipeline.
Trimmed reads were aligned to the reference genome with HISAT2. GENCODE (version 30 lift 37) and lncpedia LNCipedia version 5.2 were used.
Kallisto was used for transcript quantification and edgeR for differential expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each sample

growth_protocol: Lymphoblastoid (LCL) cell lines were cultured in RPMI1640 supplemented with 15% fetal bovine serum (FBS), L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested 1h and 8h after IR. Total RNA was extracted from the cells using the Quick-RNA Miniprep Kit (Zymo Research).
rRNA removel and strand-specific RNA library was prepared using

treatment_protocol: Cells were X-ray irradiated using a Gammacell 1000 137Cs irradiator with a dose of 1 Gy.

value: EBV-immortalized lymphoblasts

value: ATM mutation

value: 1 Gy

value: 1 h


title: AT 4, 1 Gy, 8h

value: 8 h


title: AT 4, 0 Gy, 1h

value: no treatment

value: 0 h


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-19]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: AT 3, 1 Gy, 8h


title: U_1

value: Mouse bone marrow-derived macrophage


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-7]


title: low DFI 2

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description:
fertility_associated_tsRNAs.xlsx
miRNAs_that_associated_with_daughter_fertility.xlsx

data_processing:
Sperm RNA was exreacted via miRNeasy Mini Kit (QIAGEN, Toronto, ON, Canada, Cat. # 217004)
NEBnext RNA library preparation kit (Catalog#: E7530L) was used for small RNA library construction and illumine sequencing
small rna library was cut then sent for sequencing.
The trimmomatic v0.39(Bolger, 2014) had been used for data trimming of the fastq file, and mapping had been made with the star v2.7.10b(Dobin, 2013).
The index was built with mature miRNA fasta from Mirbase. The differentially expression analysis had been made with the DESeq2 v1.34.0(Love, 2014).tRAX was used for tsRNAs analysis, and for analyzing tRNA-derived small RNAs,tRAX groups the sequencing reads into different tRNA fragment types(Holmes, 2022).
Assembly: miRbase and tsRNA analysis of eXpression(tRAX) was used, briefly, the custom tRNA reference database(built by tRAX) including all trna
Supplementary files format and content: miRNAs that associated with bull fertility(excel format),miRNAs that associated with daughter fertility(excel format);fertility associated tsRNAs(excel format).

organism: Bos taurus

source_name: sperm

treatment_protocol: no extra treatment

value: sperm

tag: associated daughter fertility

value: low


title: AT 3, 1 Gy, 1h


title: AT 3, 0 Gy, 1h


title: low DFI 1

extract_protocol:
Sperm RNA was exreacted via miRNeasy Mini Kit (QIAGEN, Toronto, ON, Canada, Cat. # 217004)
NEBnext RNA library preparation kit (Catalog#: E7530L) was used for small RNA library construction and illumine sequencing

tag: tissue


title: AT 2, 1 Gy, 8h


title: AT 2, 0 Gy, 1h


title: high DFI 2

value: high


title: AT 1, 1 Gy, 1h


title: AT 2, 1 Gy, 1h


title: AT 1, 1 Gy, 8h


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-78]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-90]


title: Control 4, 1 Gy, 8h

value: WT


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-54]


title: IVCC_1

description: RNA-seq

tag: strain


title: AT 1, 0 Gy, 1h


title: Control 4, 1 Gy, 1h


title: Control 4, 0 Gy, 1h


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-42]


title: low BFI 3

description:
fertility_associated_tsRNAs.xlsx
miRNAs_that_associated_with_bull_fertility.xlsx

tag: bull fertility


title: low BFI 2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-66]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-30]


title: Control 3, 1 Gy, 8h

tag: treatment


title: low BFI 1


title: Control 3, 1 Gy, 1h

tag: time


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-18]

tag: cell type


title: Control 3, 0 Gy, 1h


title: Control 2, 1 Gy, 8h


title: Control 2, 0 Gy, 1h


title: Control 1, 0 Gy, 1h


title: mouse neocortex, Smad1, replicate4

city: Basel

first: Peter

last: Scheiffele

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
ChIP-seq reads were aligned to the December 2011 (mm10) mouse genome assembly from UCSC. Alignments were performed in R using the qAlign function from the QuasR package1 (v. 1.14.0) with default settings
This calls the Bowtie aligner with the parameters “ -m 1 –best –strata”, which reports only reads that map to a unique position in the genome2. The reference genome package (“BSgenome.Mmusculus.UCSC.mm10”) was downloaded from Bioconductor (https://www.bioconductor.org).
BigWig files were created using qExportWig from the QuasR package with the bin size set to 50.
Peaks were called for each ChIP replicate against a matched input using the MACS2 callpeak function with the default options.
Peaks were then annotated to the closest gene and to a genomic feature (promoter, 3’ UTR, exon, intron, 5’ UTR or distal intergenic) using the ChIPseeker R package.
The promoter region was defined as -3 kb to + 3kb around the annotated TSS. Transcripts were extracted from the TxDb.Mmusculus.UCSC.mm10.ensGene annotation R package.
Assembly: mm10
Supplementary files format and content: narrowPeak format, list of annotated peaks to the closest gene

source_name: P35-P42 neocortex

extract_protocol:
Cells were fixed with 1.5% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was digested by using MNase for 20 minutes at 37 C.
Libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, #E7645L) according to the manufacturer’s instructions and PCR amplified.

value: P35-P42 neocortex

tag: fraction

value: ChIP


title: high DFI 1


title: mouse neocortex, Smad1, replicate3


title: Control 1, 1 Gy, 1h


title: Vec_Ctrl_Rep2

source_name: HeLa

extract_protocol:
Approximately 10 million cells were then cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with glycine for 5 min. The fixed cells were resuspended in SDS lysis buffer  in the presence of protease inhibitors and subjected to 30 cycles of sonication in ice-cold water to generate chromatin fragments of 300 bp in length.
The purified DNA (5 ng of average size 300 bp) was used for library preparation with a VAHTS Universal DNA Library Prep Kit for Illumina V3  and sequenced with PE150 (paired-end, 50 bp reads) on Novogene’s NovaSeq high-throughput sequencing platform.

value: HeLa

value: Anti-FLAG M2 magnetic beads


title: Vec_Ctrl_Rep1


title: Control 1, 1 Gy, 8h

value: EBV-immortalized lymphoblasts


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-53]

tag: sequencing plate

tag: nbcells


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-89]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-77]


title: mouse neocortex, Smad1, replicate2

tag: genotype

tag: chip antibody


title: Vec_DSB_Rep2


title: Vec_DSB_Rep1


title: LIG4_siMIDEAS_DMSO_DSB_Rep1


title: LIG4_siMIDEAS_DMSO_DSB_Rep2


title: Control 2, 1 Gy, 1h

value: 1 Gy


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-65]


title: high BFI 1


title: LIG4_siMIDEAS_ZXH-3-26_DSB_Rep2


title: LIG4_siMIDEAS_ZXH-3-26_DSB_Rep1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-41]


title: mouse neocortex, Smad1, replicate1


title: high BFI and high DFI 1

description:
fertility_associated_tsRNAs.xlsx
miRNAs_that_associated_with_bull_fertility.xlsx
miRNAs_that_associated_with_daughter_fertility.xlsx


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-6]


title: LIG4_siDNTTIP1_DMSO_DSB_Rep1


title: LIG4_Scr_ZXH-3-26_DSB_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-29]


title: LIG4_siDNTTIP1_ZXH-3-26_DSB_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-76]


title: mouse neocortex, input, replicate4

value: input


title: LIG4_Scr_DMSO_Ctrl_Rep1


title: Input_Scr_DSB_Rep2


title: LIG4_siDNTTIP1_ZXH-3-26_DSB_Rep1


title: high BFI and low DFI 1


title: LIG4_siDNTTIP1_DMSO_DSB_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-17]


title: mouse neocortex, input, replicate3


title: LIG4_Scr_ZXH-3-26_DSB_Rep1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-5]


title: mouse neocortex, input, replicate2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-52]


title: Input_Scr_DSB_Rep1


title: LIG4_Scr_DMSO_DSB_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-88]


title: Input_Scr_Ctrl_Rep1


title: LIG4_Scr_DMSO_DSB_Rep1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-40]


title: intestinal epithelium, B6 dam DOL42, sample 3

city: Pittsburgh

first: Darryl

last: Abbott

state: PA

address: 4401 Penn Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
trimmed high quality reads were aligned to genome  using bowtie2
Raw count values generated with Subread
Gene expression values were nromalized to transcripts per million
Differential peak analysis determined using DESeq2 with cutoffs of 2 fold and p value<0.05
Assembly: mm10
Supplementary files format and content: csv file contains transcripts per million (TPM)

source_name: small intestine

growth_protocol: mice were housed in specific pathogen free conditions.Animals were cohoused when possible to avoid cage dependent microbiome shifts.

extract_protocol:
Digested small intestinal epithelium was stained and sorted for EpCam+ CD45- Ter119- cells. Sorted cells were pelleted and flash frozen. Following the acquisition of all groups, the samples were thawed and RNAextracted using SMART-seq v4 Ultra Low Input RNA kit for sequencing (Clontech).
Nextera XT DNA Library Preparation kit (Illumina)

treatment_protocol: IgA -/+ mice were generated by breeding a C57BL/6 with an IgA-/- mouse. IgA -/+ mice nursed by an IgA -/- dam lacked were compared to IgA -/+ nursed by a C57BL/6 dam, to determine te isolated role of maternal IgA on the developing intestine.

value: small intestine

value: EpCAM+ epithelial cell

value: Igha -/+

tag: group

value: control


title: LIG4_Scr_DMSO_Ctrl_Rep2


title: intestinal epithelium, B6 dam DOL42, sample 2


title: intestinal epithelium, B6 dam DOL24, sample 2


title: H2AK9ac_siMIDEAS_DSB_Rep1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-64]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: intestinal epithelium, B6 dam DOL24, sample 1


title: intestinal epithelium, B6 dam DOL42, sample 1


title: H2AK9ac_siMIDEAS_Ctrl_Rep2


title: mouse neocortex, input, replicate1


title: H2AK9ac_siMIDEAS_DSB_Rep2


title: Input_Scr_Ctrl_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-28]


title: H2AK9ac_siDNTTIP1_DSB_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-4]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-16]


title: intestinal epithelium, B6 dam DOL14, sample 3


title: H2AK9ac_siMIDEAS_Ctrl_Rep1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-87]


title: H2AK9ac_siDNTTIP1_DSB_Rep1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-75]


title: intestinal epithelium, B6 dam DOL14, sample 2


title: M6_spleen_CNS

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

description: BD Rhapsody

data_processing:
The demultiplexing barcoded processing, gene counting using seven Bridges (https://igor.sbgenomics.com)
Assembly: mm10
Supplementary files format and content: Tab-separated file

growth_protocol: EAE induction, tissue collection at peak of disease. FOXP3+ Tregs are sorted as GFP+RFP+ and exFOXP3 T cells as GFP-RFP+. All 4 cell populations were stained with sample tag antibodies.

extract_protocol:
Cells were single-cell capture using the BD Rhapsody Express system. Cells were lysed. Free floating mRNA was allowed to bind to the Cell Capture bead present in the same nanowell, and beads were collected.
Next, DNA library preparation was performed using the BD Rhapsody WTA Amplification Kit.

tag: disease state

value: EAE induction

value: T cells

value: BAC-FOXP3Cre-GFP Rosa26flSTOPflRFP (FOXP3Cre-GFP RosaRFP) fate-mapping mice

tag: age

value: 12-13 weeks old


title: AC8 Overexpressing C57/B6 mice, pooled, cardiac cell suspension

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Cells were sequenced at a target read depth of 75,000 reads/cell using a NovaSeq 6000 sequencer (Illumina). Single-cell counts were generated from unaligned reads by sequence alignment and de-multiplexing using Cell Ranger from 10x Genomics.
Single-cell counts were generated from unaligned reads by sequence alignment and de-multiplexing using Cell Ranger from 10x Genomics. Post-alignment QA/QC performed using single-cell counts suggested that none of the 10,667 cells expressed mitochondrial genes at greater than 5 percent of their total gene expression; cells were not excluded from further analysis.
Normalized cell counts were generated using filter exclude features where value <= 0.0 in at least 99.9 % of the cells, CPM (counts per million), the scale factor of 10000, and log transformation.
Of the 22,441 genes, 13,331 passed these criteria, and the remaining 9,110 were filtered out.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

source_name: Heart

extract_protocol:
A single cell suspension was made from fresh cardiac tissue obtained from AC8 overexpressing mice and littermate controls, An equal number of FACS-sorted CD45+CD31- (leukocytes), CD45-CD31- (resident mesenchymal cells), and CD45-CD31+ (endothelial cells) cells were mixed and processed to generate single-cell cDNA libraries.
Using the 10X Genomics platform Cells were sequenced at a target read depth of 75,000 reads/cell using a Novaseq 6000 sequencer (Illumina). Single-cell counts were generated from unaligned reads by sequence alignment and de-multiplexing using Cell Ranger from 10x Genomics.

value: Heart

value: Cardiac CD45+CD31- (leukocytes), CD45-CD31- (resident mesenchymal cells), and CD45-CD31+ (endothelial cells)

value: AC8 Overexpressing


title: H2AK9ac_siDNTTIP1_Ctrl_Rep2

tag: cell line

value: HeLa


title: intestinal epithelium, IgA -/- dam DOL14, sample 3

value: no maternal IgA


title: intestinal epithelium, B6 dam DOL14, sample 1


title: C57/B6 mice, pooled, cardiac cell suspension

value: Wild Type


title: TPPU_Male_Heart_3791

city: Durham

first: Matthew

middle: Lund

last: Edin

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Adapter sequences were trimmed from reads using Cutadapt (Martin 2011) and low quality reads were removed from analysis using Sickle 1.33 (Joshi et al 2011).
RNA-seq reads were mapped to the mouse reference genome (mm39) using STAR(Dobin et al., 2013) with default parameters.
Gene counts were generated using Salmon (Patro et al 2017) and transformed with log2(1 + x).
Differential expression analysis was performed on aggregated gene pseudocounts using limma-voom 3.42.2 (Law et al 2014).
Assembly: mm39
Supplementary files format and content: Processed data represents Salmon gene pseudocounts in tab-delimited format.

source_name: Heart sample from 10-week-old male mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2, treated with 3 mg/kg TPPU

extract_protocol:
Mouse Lung and Heart were collected into RNA Later and processed to purified mRNA using the RNeasy 96 QIAcube HT Kit according to manufacturer’s instructions.
Total RNA-seq libraries were generated in the NIEHS Epigenomics Core using Ribo-Zero Gold and sequenced on the Illumina NovaSeq 6000 to over 140 million reads per biological replicate.

tag: Sex

value: Male

value: WT

value: TPPU


title: intestinal epithelium, IgA -/- dam DOL14, sample 2

value: small intestine

value: EpCAM+ epithelial cell

value: Igha -/+


title: H2AK9ac_Scr_DSB_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-51]

data_processing:
Raw reads were aligned on the human genome with STAR.
Gene expression was quantified with STAR gene count, following the annotations of gencode v29.
Samples with less than 50000 reads were excluded.
Assembly: GRCh38
Supplementary files format and content: STAR gene count

extract_protocol:
Briefly, freshly harvested single cells were sorted into 96-well plates containing the lysis buffer (0.2% Triton X-100, 1U/  l RNase inhibitor, Thermo Fisher Scientific). RT was performed using SuperScript II (Thermo Fisher Scientific) in the presence of 1   M oligo-dT30VN (IDT), 1   M Template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Full-length scRNAseq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Roche) and IS PCR primer (IDT), with 23 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end reads of 75 bp length (PE75) with library indexes corresponding to cell barcodes.

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: intestinal epithelium, IgA -/- dam DOL14, sample 1


title: H2AK9ac_Scr_Ctrl_Rep2

data_processing:
ChIP-seq reads were first processed using TrimGalore (v0.6.4_dev) to trim adaptor and low-quality reads.
The quality of each trimmed file was verified by FastQC (v0.11.9)
The trimmed reads were then aligned to the human genome hg38 using Bowtie2 (v2.4.5)
Signal tracks for each sample were generated using bamCoverage (deepTools v3.4.3) tool and were normalized to Reads per kilo per million mapped reads (RPKM).
Assembly: hg38
Supplementary files format and content: bigWig


title: H2AK9ac_Scr_DSB_Rep1


title: H2AK9ac_siDNTTIP1_Ctrl_Rep1


title: TPPU_Male_Heart_3735


title: TPPU_Male_Heart_3727


title: H2AK9ac_Scr_Ctrl_Rep1


title: intestinal epithelium, IgA -/- dam DOL24, sample 2


title: intestinal epithelium, IgA -/- dam DOL24, sample 1


title: TPPU_Female_Heart_3666

source_name: Heart sample from 10-week-old female mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2, treated with 3 mg/kg TPPU

value: Female


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-3]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-63]


title: H2AK5ac_siMIDEAS_DSB_Rep1

value: H2AK5ac(PTM BIO,PTM-106)


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-15]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-86]


title: TPPU_Female_Heart_3642


title: intestinal epithelium, IgA -/- dam DOL42, sample 3


title: H2AK5ac_siMIDEAS_Ctrl_Rep2


title: intestinal epithelium, IgA -/- dam DOL24, sample 3


title: TPPU_Male_Heart_3774


title: H2AK5ac_siMIDEAS_Ctrl_Rep1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-74]


title: intestinal epithelium, IgA -/- dam DOL42, sample 2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-39]


title: TPPU_Female_Heart_3602


title: TPPU_Female_Heart_3612


title: TPPU_Male_Heart_3784


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-62]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-27]


title: H2AK5ac_siDNTTIP1_DSB_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-50]


title: H2AK5ac_siMIDEAS_DSB_Rep2


title: TPPU_Female_Heart_2


title: 14 days in vitro cortical cultures, nonstimulated, replicate3

data_processing:
RNA-seq reads were aligned to mm10 using STAR and visualized in IGV genome browser to determine strand protocol.
Reads with quality scores less than 30, and mapping rates below 65 and having contaminations from noncoding RNAs were not considered for further analysis.
If passed QC, QuasR’s qCount function was used to count reads mapping to annotated exons (from Ensembl genome annotations)
Assembly: For each gene, counts were summed for all annotated exons, without double-counting exons present in multiple transcript isoforms (“exon-union model”)
Supplementary files format and content: mm10
Supplementary files format and content: .txt, FPKM values

source_name: E16.5 neocortex

growth_protocol: Neurobasal medium, 1x B-27 supplement, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted with Trizol reagent and phenol-chloroform extraction, and followed by Dnase treatment and column purification with RNeasy micro kit (Qiagen).
Librarries were prepared from 200 ng total RNA by using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA). 15 cycles of PCR were performed

value: E16.5 neocortex

value: neuron

value: no treatment


title: 14 days in vitro cortical cultures, Bmp2 stimulated for 6 hours, replicate3

value: 21 ng/ml BMP2, 6 hour


title: H2AK5ac_siDNTTIP1_DSB_Rep1

value: HeLa


title: H2AK5ac_siDNTTIP1_Ctrl_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-38]


title: Infected_Male_Heart_5

source_name: Heart sample from 10-week-old male mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2

value: Heart

value: Infected


title: 14 days in vitro cortical cultures, Bmp2 stimulated for 1 hour, replicate3

value: 20 ng/ml BMP2, 1 hour


title: H2AK5ac_siDNTTIP1_Ctrl_Rep1


title: Infected_Male_Heart_3734

value: Male

value: WT


title: 14 days in vitro cortical cultures, nonstimulated, replicate2


title: H2AK5ac_Scr_DSB_Rep2


title: intestinal epithelium, IgA -/- dam DOL42, sample 1

value: small intestine

value: no maternal IgA


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-26]


title: 14 days in vitro cortical cultures, Bmp2 stimulated for 6 hours, replicate2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-2]


title: H2AK5ac_Scr_DSB_Rep1


title: Infected_Male_Heart_3730


title: Infected_Male_Heart_3690


title: 14 days in vitro cortical cultures, Bmp2 stimulated for 1 hour, replicate2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-85]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-73]


title: H2AK5ac_Scr_Ctrl_Rep2


title: 14 days in vitro cortical cultures, nonstimulated, replicate1


title: H2AK5ac_Scr_Ctrl_Rep1


title: 14 days in vitro cortical cultures, Bmp2 stimulated for 6 hours, replicate1


title: Infected_Female_Heart_3669

source_name: Heart sample from 10-week-old female mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2


title: Infected_Male_Heart_6


title: Infected_Female_Heart_3682


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-61]


title: H2A_DSB_Rep2


title: 14 days in vitro cortical cultures, Bmp2 stimulated for 1 hour, replicate1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-49]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-14]


title: H2A_DSB_Rep1


title: Infected_Female_Heart_3621


title: H2A_Ctrl_Rep2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-37]


title: Infected_Female_Heart_1


title: 14 days in vitro cortical cultures, untreated, H3K27ac ChIP, replicate3

description: ChIP

data_processing:
ChIP-seq reads were aligned to the December 2011 (mm10) mouse genome assembly from UCSC. Alignments were performed in R using the qAlign function from the QuasR package1 (v. 1.14.0) with default settings
This calls the Bowtie aligner with the parameters “ -m 1 –best –strata”, which reports only reads that map to a unique position in the genome2. The reference genome package (“BSgenome.Mmusculus.UCSC.mm10”) was downloaded from Bioconductor (https://www.bioconductor.org).
BigWig files were created using qExportWig from the QuasR package with the bin size set to 50.
Peaks were called for each ChIP replicate against a matched input using the MACS2 callpeak function with the default options.
Peaks were then annotated to the closest gene and to a genomic feature (promoter, 3’ UTR, exon, intron, 5’ UTR or distal intergenic) using the ChIPseeker R package.
Assembly: The promoter region was defined as -3 kb to + 3kb around the annotated TSS. Transcripts were extracted from the TxDb.Mmusculus.UCSC.mm10.ensGene annotation R package.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak for Smad1/5 and broad peak for H3K27ac (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Covaris sonicator for 20 minutes.
Libraries were generated using the KAPA Hyper Prep (Roche #KK8504) according to the manufacturer’s instructions and PCR amplified.

tag: antibody

value: H3K27ac ChIP


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-25]

value: HME-RASi


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-13]

value: mammary epithelial cells RAS inductible


title: 14 days in vitro cortical cultures, untreated, input, replicate3

description: input

tag: tissue


title: Baseline_Male_Heart_4

source_name: Heart sample from 10-week-old male mouse expressing human ACE2

value: Baseline


title: gH2AX_siMIDEAS_DSB_Rep2


title: 14 days in vitro cortical cultures, Bmp2 stimulated, H3K27ac ChIP, replicate3

description: ChIP

value: 20 ng/ml BMP2


title: gH2AX_siMIDEAS_DSB_Rep1


title: Baseline_Male_Heart_3764


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-1]

source_name: HME-RASi


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-192]


title: Baseline_Male_Heart_3792


title: Infected_Female_Heart_3624

value: Female


title: 14 days in vitro cortical cultures, Bmp2 stimulated, input, replicate3

description: input

value: E16.5 neocortex

value: neuron


title: gH2AX_siMIDEAS_Ctrl_Rep2


title: Baseline_Male_Heart_3716


title: H2A_Ctrl_Rep1


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-180]


title: 14 days in vitro cortical cultures, Bmp2 stimulated, Smad1/5 ChIP, replicate3

description: ChIP

value: Smad1/5 ChIP


title: 14 days in vitro cortical cultures, untreated, H3K27ac ChIP, replicate2

description: ChIP

value: no treatment


title: gH2AX_siDNTTIP1_DSB_Rep2

value: HeLa


title: gH2AX_siMIDEAS_Ctrl_Rep1


title: Baseline_Male_Heart_3715

value: Heart


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-168]


title: 14 days in vitro cortical cultures, untreated, Smad1/5 ChIP, replicate3

description: ChIP


title: Baseline_Female_Heart_3673

source_name: Heart sample from 10-week-old female mouse expressing human ACE2


title: gH2AX_siDNTTIP1_DSB_Rep1


title: 14 days in vitro cortical cultures, untreated, input, replicate2

description: input


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-156]


title: Baseline_Female_Heart_3671


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-144]


title: gH2AX_siDNTTIP1_Ctrl_Rep2


title: Baseline_Female_Heart_3636


title: 14 days in vitro cortical cultures, Bmp2 stimulated, H3K27ac ChIP, replicate2

description: ChIP


title: gH2AX_siDNTTIP1_Ctrl_Rep1


title: Baseline_Female_Heart_3610


title: 14 days in vitro cortical cultures, Bmp2 stimulated, Smad1/5 ChIP, replicate2

description: ChIP


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-132]


title: Baseline_Female_Heart_3605


title: gH2AX_Scr_DSB_Rep1


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-179]


title: 14 days in vitro cortical cultures, Bmp2 stimulated, input, replicate2

description: input


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-108]


title: gH2AX_Scr_DSB_Rep2


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-167]


title: TPPU_Male_Lung_3727

source_name: Lung sample from 10-week-old male mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2, treated with 3 mg/kg TPPU

value: Lung

value: TPPU


title: 14 days in vitro cortical cultures, untreated, Smad1/5 ChIP, replicate2

description: ChIP

value: WT


title: gH2AX_Scr_Ctrl_Rep2


title: 14 days in vitro cortical cultures, untreated, Smad1/5 ChIP, replicate1

description: ChIP


title: 14 days in vitro cortical cultures, untreated, H3K27ac ChIP, replicate1

description: ChIP


title: TPPU_Male_Lung_3784

value: Male


title: 14 days in vitro cortical cultures, untreated, input, replicate1

description: input


title: TPPU_Male_Lung_3735


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-155]


title: FLAG_MIDEAS_DSB_Rep2

value: Anti-FLAG M2 magnetic beads


title: 14 days in vitro cortical cultures, Bmp2 stimulated, H3K27ac ChIP, replicate1

description: ChIP

value: H3K27ac ChIP


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-131]

value: HME-RASi


title: 14 days in vitro cortical cultures, Bmp2 stimulated, Smad1/5 ChIP, replicate1

description: ChIP


title: TPPU_Male_Lung_3774


title: FLAG_MIDEAS_DSB_Rep1


title: FLAG_MIDEAS_Ctrl_Rep2


title: 14 days in vitro cortical cultures, Bmp2 stimulated, input, replicate1

description: input


title: TPPU_Female_Lung_2

source_name: Lung sample from 10-week-old female mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2, treated with 3 mg/kg TPPU


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-119]

value: mammary epithelial cells RAS inductible


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-178]


title: FLAG_MIDEAS_Ctrl_Rep1


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-107]


title: gH2AX_Scr_Ctrl_Rep1


title: FLAG_DNTTIP1_DSB_Rep2


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-143]


title: FLAG_DNTTIP1_DSB_Rep1


title: TPPU_Female_Lung_3666


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-190]


title: L4_infected_lung_cells_bcg_C57Bl6_rep3

first: Hannah

last: Painter

address: Keppel Street

institute: LSHTM

description:
hp1902strandset.Rmatrix.txt
matrix column name: L4B3

data_processing:
The BBDuk tool from the BBTools suite (v38.79) was used to trim adaptor sequences and the final 5% of 3’ bases.
STAR (v2.7.3a) was used to generate a genome index and subsequently map the trimmed reads to the Mus musculus index.
Read counting was performing using the default settings of featureCounts to count meta-features, specifying a stranded dataset.
Quality control steps were performed using FastQC (v0.11.9) and CollectRnaSeqMetrics from the Picard Tools suite
Assembly: GRCm38
Supplementary files format and content: hp1902strandset.Rmatrix.txt (featureCounts count matrix  cleaned using Vim and saved as an Rmatrix.txt file )

source_name: lung

growth_protocol: Female C57BL/6 mice (5–7 weeks old) received 1x10^6 CFU BCG Aeras Pasteur or no treatment. Six weeks post vaccination, mice were humanely culled, and lung was removed and processed to generate single cell suspensions. Lung cells (individual mice) were uninfected/infected overnight for gene expression analysis. Specifically, 1 x 10^6 lung cells per mouse were seeded in duplicate (uninfected/infected) in 24-well plates and cultured overnight at 37°C (5% CO2) in the presence or absence of 1 x 10^6 CFU mycobacteria (N0072, N0052 or N1283). The following day, plates were centrifuged at 500 x g to pellet eukaryotic cells, supernatants were removed and 600 µL RNAprotect cell reagent was added to stabilise transcription and prevent RNA degradation. Samples were stored at –70°C until RNA extraction.

extract_protocol:
For RNA extraction, samples in RNAprotect were thawed fully and centrifuged at 5,000 x g. Total RNA purification was performed using the RNeasy Mini Kit and an on-column DNase digestion according to the manufacturer’s instructions. RNA integrity was assessed, and concentration determined, using the TapeStation system. All samples submitted for sequencing had an RNA integrity number equivalent value ≥8.2.
Library preparation and sequencing was performed at UCL Genomics (University College London, UK). The NEBNext Ultra II Unidirectional RNA library prep kit and Poly(A) mRNA Magnetic Isolation Module (both New England Biolabs, UK) were used to process 200 ng total RNA per sample according to the manufacturer’s instructions. Limited cycle PCR was performed with 100 ng for 14 cycles. Libraries to be multiplexed in the same run were pooled in equimolar quantities, calculated from Qubit (Invitrogen, UK) and Bioanalyser (Agilent) fragment analysis. Samples were sequenced on the NextSeq 500 (Illumina, UK) instrument using a 75-bp single read run with a corresponding 8-bp UMI read.

value: lung

value: primary

tag: ex vivo infection


title: L4_infected_lung_cells_bcg_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: L4B2


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-166]


title: TPPU_Female_Lung_3612

value: Female


title: L4_infected_lung_cells_control_C57Bl6_rep3

description:
hp1902strandset.Rmatrix.txt
matrix column name: L4C3

value: unvaccinated


title: TPPU_Female_Lung_3602


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-154]


title: FLAG_DNTTIP1_Ctrl_Rep1


title: TPPU_Female_Lung_3642


title: FLAG_DNTTIP1_Ctrl_Rep2


title: TPPU_Male_Lung_3791


title: L4_infected_lung_cells_control_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: L4C2


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-142]


title: Infected_Male_Lung_3690

source_name: Lung sample from 10-week-old male mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2

value: Infected


title: Infected_Male_Lung_5


title: L4_infected_lung_cells_control_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: L4C1


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-130]


title: L4_infected_lung_cells_bcg_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: L4B1


title: L2_infected_lung_cells_bcg_C57Bl6_rep3

description:
hp1902strandset.Rmatrix.txt
matrix column name: L2B3


title: S112-P007-C-120m

city: Melbourne

first: Rochelle

last: Davis

state: VIC

address: 264 Ferntree Gully Rd, Notting Hill

country: Australia

institute: Monash University

data_processing:
fastq files were processed by Cutadapt (V1.9.1) to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and bases of a quality lower than 20.
Filtered data were aligned to the reference genome, GRCh37, using Hisat2(v2.0.1)
Assembly: GRCh37
Supplementary files format and content: Count table includes raw read counts and FPKM values for each Sample

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA was isolated from PBMC samples using the RNeasy Plus Mini Kit (QIAGEN GmbH, Hilden, Germany) and eluted in 60µL RNase-Free water
1μg total RNA was used for library preparation. Poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module. The mRNA fragmentation and priming were performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, before PCR amplification and validation of PCR products by Qsep100 (Bioptic, Taiwan, China) and quantification by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA)

value: Peripheral Blood Mononuclear Cells

tag: condition

value: abdominal obesity

tag: subject id

value: Control

tag: timepoint

value: 120 minutes


title: Infected_Male_Lung_6

value: Lung

tag: treatment


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-118]

first: Anne-Pierre

last: Morel

tag: cell type

tag: time


title: S111-P007-C-0m

value: 0 minutes (fasting)


title: L2_infected_lung_cells_bcg_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: L2B2


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-189]

tag: sequencing plate

tag: nbcells


title: S110-P007-I-240m

value: Intervention

value: 240 minutes


title: Infected_Male_Lung_3734

value: Male

tag: genotype

value: WT


title: L2_infected_lung_cells_bcg_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: L2B1


title: S109-P007-I-120m


title: Infected_Male_Lung_3730


title: Infected_Female_Lung_3621

source_name: Lung sample from 10-week-old female mouse expressing human ACE2, infected with 1000 PFU SARS-CoV-2


title: S108-P007-I-0m


title: L2_infected_lung_cells_control_C57Bl6_rep3

description:
hp1902strandset.Rmatrix.txt
matrix column name: L2C3


title: S113-P007-C-240m


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-165]

value: HME-RASi


title: L2_infected_lung_cells_control_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: L2C2


title: Infected_Female_Lung_3624


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-153]

value: mammary epithelial cells RAS inductible


title: L2_infected_lung_cells_control_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: L2C1

value: lung


title: Infected_Female_Lung_3682


title: S107-P008-C-240m


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-141]


title: S106-P008-C-120m


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-129]


title: L1_infected_lung_cells_bcg_C57Bl6_rep3

description:
hp1902strandset.Rmatrix.txt
matrix column name: L1B3

value: primary


title: Infected_Female_Lung_3669

value: Female


title: L1_infected_lung_cells_bcg_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: L1B2


title: Infected_Female_Lung_1


title: S104-P008-I-240m


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-177]


title: L1_infected_lung_cells_bcg_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: L1B1


title: S103-P008-I-120m


title: Baseline_Male_Lung_3792

source_name: Lung sample from 10-week-old male mouse expressing human ACE2

value: Baseline


title: Baseline_Male_Lung_3716


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-105]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-188]


title: L1_infected_lung_cells_control_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: L1C2

value: unvaccinated


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-176]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-164]


title: Baseline_Male_Lung_3715


title: L1_infected_lung_cells_control_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: L1C1


title: S100-P011-C-120m

value: Peripheral Blood Mononuclear Cells


title: S101-P011-C-240m

value: abdominal obesity


title: S105-P008-C-0m

value: Control


title: Baseline_Male_Lung_3764


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-152]


title: uninfected_lung_cells_bcg_C57Bl6_rep3

description:
hp1902strandset.Rmatrix.txt
matrix column name: UB3

value: uninfected


title: Baseline_Male_Lung_4

value: Lung


title: Baseline_Female_Lung_3636

source_name: Lung sample from 10-week-old female mouse expressing human ACE2


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-140]


title: S99-P011-C-0m

value: 0 minutes (fasting)


title: S98-P011-I-240m

value: Intervention


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-117]


title: Baseline_Female_Lung_3610


title: uninfected_lung_cells_bcg_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: UB2


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-128]


title: L1_infected_lung_cells_control_C57Bl6_rep3

description:
hp1902strandset.Rmatrix.txt
matrix column name: L1C3


title: S97-P011-I-120m

value: 120 minutes


title: uninfected_lung_cells_bcg_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: UB1


title: uninfected_lung_cells_control_C57Bl6_rep3

description:
hp1902strandset.Rmatrix.txt
matrix column name: UC3


title: S102-P008-I-0m


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-116]


title: Baseline_Female_Lung_3671


title: uninfected_lung_cells_control_C57Bl6_rep2

description:
hp1902strandset.Rmatrix.txt
matrix column name: UC2


title: Baseline_Female_Lung_3655


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-104]


title: S96-P011-I-0m


title: S95-P005-C-240m

value: 240 minutes


title: Baseline_Female_Lung_3605

value: WT


title: S94-P005-C-120m


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-143]

value: HME-RASi


title: 14 days in vitro cKO cortical cultures, nonstimulated, replicate4

source_name: P0 neocortex

growth_protocol: Neurobasal medium, 1x B-27 supplement, 2mM glutamine, 1x penicillin/streptomycin. Cells were isolated from P0 Smad1fl/fl pups and cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted with Trizol reagent and phenol-chloroform extraction, and followed by Dnase treatment and column purification with RNeasy micro kit (Qiagen).
Librarries were prepared from 100 ng total RNA by using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA). 15 cycles of PCR were performed

treatment_protocol: At days in vitro 9, cells were infected either with syn-eGFP or syn-icre viruses. At day 14, cells were treated with either vehicle (solvent of BMP2) or 20 ng/ml BMP2 for 1 hour or 6 hours and harvested.

value: P0 neocortex

value: neuron

value: cKO

value: no treatment


title: uninfected_lung_cells_control_C57Bl6_rep1

description:
hp1902strandset.Rmatrix.txt
matrix column name: UC1

value: lung

value: primary


title: S93-P005-C-0m

value: Peripheral Blood Mononuclear Cells


title: uninfected_lung_cells_bcgin_C57Bl6_3

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U3-4_S8

data_processing:
The BBDuk tool from the BBTools suite (v38.79) was used to trim adaptor sequences and the final 5% of 3’ bases.
STAR (v2.7.3a) was used to generate a genome index and subsequently map the trimmed reads to the Mus musculus index.
Read counting was performing using the default settings of featureCounts to count meta-features, specifying a stranded dataset.
Quality control steps were performed using FastQC (v0.11.9) and CollectRnaSeqMetrics from the Picard Tools suite
Assembly: GRCm38
Supplementary files format and content: hp1802newcounts_edit.Rmatrix.txt (featureCounts count matrix  cleaned using Vim and saved as an Rmatrix.txt file )

growth_protocol: Female C57BL/6 mice (5–7 weeks old) received 1x10^6 CFU BCG Aeras Pasteur via the subcutaneous route, 0.5x10^6 CFU BCG Aeras Pasteur via the intranasal route or no treatment. Six weeks post vaccination, mice were humanely culled, and lungs were removed and processed to generate single cell suspensions. RNA was extracted from 1 x 10^6 lung cells per mouse were seeded in duplicate. Specifically, cells were centrifuged at 500 x g to pellet eukaryotic cells, supernatants, removed and 600 µL RNAprotect cell reagent added to stabilise transcription and prevent RNA degradation. Samples were stored at –70°C until RNA extraction.

tag: strain


title: uninfected_lung_cells_bcgin_C57Bl6_2

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U3-3_S17


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 6 hours, replicate4

value: 20 ng/ml BMP2, 6 hour


title: S92-P005-I-240m

value: abdominal obesity


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-131]

value: mammary epithelial cells RAS inductible


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-119]


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 1 hour, replicate4

value: 20 ng/ml BMP2, 1 hour


title: S91-P005-I-120m


title: uninfected_lung_cells_bcgsc_C57Bl6_3

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U2-6_S6


title: 14 days in vitro cKO cortical cultures, nonstimulated, replicate3


title: S90-P005-I-0m

value: 0 minutes (fasting)


title: S89-P009-C-240m

value: Control


title: uninfected_lung_cells_bcgsc_C57Bl6_2

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U2-5_S5


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-107]


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 6 hours, replicate3


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-178]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-155]


title: 14 days in vitro cKO cortical cultures, nonstimulated, replicate2


title: S87-P009-C-0m


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 1 hour, replicate3


title: S88-P009-C-120m

value: 120 minutes


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 6 hours, replicate2


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-190]


title: uninfected_lung_cells_bcgsc_C57Bl6_1

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U2-4_S4


title: S86-P009-I-240m

value: Intervention

value: 240 minutes


title: uninfected_lung_cells_control_C57Bl6_1

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U1-1_S1

value: unvaccinated


title: uninfected_lung_cells_bcgin_C57Bl6_1

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U3-1_S7


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 1 hour, replicate2

value: P0 neocortex


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-130]

value: HME-RASi


title: 14 days in vitro cKO cortical cultures, nonstimulated, replicate1

value: neuron

value: cKO


title: S85-P009-I-120m


title: G4-DOX(+), PINCH(+), IACS(+)-Ex5

first: Yonghui

last: Jin

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Institute for Life and Medical Sciences

institute: Kyoto University

data_processing:
Adapter sequences and low-quality bases were trimmed from the raw reads using Cutadapt v3.4.
The trimmed reads were mapped to mm10 mouse reference genome sequences using STAR ver 2.7.9a with the GENCODE v23 gtf file.
The number of reads mapped to each gene (the raw read counts) were calculated using htseq-count ver 0.13.5 with the GENCODE gtf file.
Gene expression levels were determined as Transcripts Per Kilobase Million (TPM) values with DESeq2 v1.30.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted with  RNeasy mini kit (Qiagen) following the manufacturer`s instruction. RNA-seq libraries were generated from 200ng~300 ng of total RNA.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep following the manufacturer's instructions.

value: skeletal muscle

value: FOP-ACVR1 on

value: pinch and IACS


title: S84-P009-I-0m

value: Peripheral Blood Mononuclear Cells


title: G4-DOX(+), PINCH(+), IACS(+)-Ex4


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 6 hours, replicate1

value: 20 ng/ml BMP2, 6 hour


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-118]

address: 28, rue Laennec, Cheney D 2nd floor

institute: Cancer Research Center of Lyon

value: mammary epithelial cells RAS inductible


title: S83-P017-C-240m

value: abdominal obesity


title: uninfected_lung_cells_control_C57Bl6_3

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U1-4_S3

value: lung

value: primary


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-177]


title: S82-P017-C-120m

value: Control

value: 120 minutes


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 6 hours, replicate4

value: WT


title: 14 days in vitro cKO cortical cultures, Bmp2 stimulated for 1 hour, replicate1

value: 20 ng/ml BMP2, 1 hour


title: G3-DOX(+), PINCH(+)-Ex5

value: pinch


title: S81-P017-C-0m

value: 0 minutes (fasting)


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-106]

value: HME-RASi


title: 14 days in vitro WT cortical cultures, nonstimulated, replicate4

value: P0 neocortex

value: neuron

value: no treatment


title: G4-DOX(+), PINCH(+), IACS(+)-Ex1

value: skeletal muscle

value: FOP-ACVR1 on

value: pinch and IACS


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-154]

value: mammary epithelial cells RAS inductible


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-165]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-189]


title: uninfected_lung_cells_control_C57Bl6_2

description:
hp1802newcounts_edit.Rmatrix.txt
matrix column names: U1-3_S2

value: unvaccinated


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-166]


title: G4-DOX(+), PINCH(+), IACS(+)-Ex3


title: G4-DOX(+), PINCH(+), IACS(+)-Ex2


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-129]


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 1 hour, replicate4


title: S79-P017-I-120m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: Intervention


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-153]


title: 14 days in vitro WT cortical cultures, nonstimulated, replicate3


title: S78-P017-I-0m


title: G3-DOX(+), PINCH(+)-Ex4


title: G3-DOX(+), PINCH(+)-Ex3


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 6 hours, replicate3

value: 20 ng/ml BMP2, 6 hour


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-142]


title: S80-P017-I-240m

value: 240 minutes


title: G3-DOX(+), PINCH(+)-Ex2


title: S77-P019-C-240m

value: Control


title: G3-DOX(+), PINCH(+)-Ex1

value: pinch


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-105]


title: S75-P019-C-0m

value: 0 minutes (fasting)


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-188]

value: HME-RASi


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-176]


title: S74-P019-I-240m


title: G2-DOX(-), PINCH(+)-Ex4

value: FOP-ACVR1 off


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 1 hour, replicate3

value: P0 neocortex

value: neuron

value: WT

value: 20 ng/ml BMP2, 1 hour


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 6 hours, replicate2


title: G2-DOX(-), PINCH(+)-Ex2

value: skeletal muscle


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-152]

value: mammary epithelial cells RAS inductible


title: G2-DOX(-), PINCH(+)-Ex3


title: G2-DOX(-), PINCH(+)-Ex5


title: G2-DOX(-), PINCH(+)-Ex1


title: 14 days in vitro WT cortical cultures, nonstimulated, replicate1

value: no treatment


title: 14 days in vitro WT cortical cultures, nonstimulated, replicate2


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 1 hour, replicate2


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-164]


title: S72-P019-I-0m

value: Peripheral Blood Mononuclear Cells


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-140]


title: S76-P019-C-120m

value: abdominal obesity

value: 120 minutes


title: S73-P019-I-120m

value: Intervention


title: S70-P013-C-120m


title: G1-DOX(-), PINCH(-)-Ex6

value: sham


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-116]


title: S69-P013-C-0m

value: Control


title: S71-P013-C-240m

value: 240 minutes


title: G1-DOX(-), PINCH(-)-Ex4


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-104]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-187]


title: sWAT_i88_HFD_Ime

city: Tokyo

first: Motoharu

last: Awazawa

address: 1-21-1 Toyama, Shinjuku

institute: National Institute for Global Health and Medicine

data_processing:
QC and adopter trimming were done by fastq.Raw sequencing reads were aligned to mouse reference genome(GRCm39) by STAR, and gene-level read counts were calculated by RSEM.
The raw read counts were normalized with transcripts per million (TPM).
Assembly: GRCm39
Supplementary files format and content: xlsx

source_name: sWAT

extract_protocol:
RNA extrantion by FavorPrep Tissue Total RNA Mini Kit
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module for PolyA selection and NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina for strand specific library follwing manufacturer's protocols.

value: sWAT

value: HFD+Ime


title: G1-DOX(-), PINCH(-)-Ex3

value: FOP-ACVR1 off


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-128]

city: Lyon

value: HME-RASi


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 6 hours, replicate1

value: P0 neocortex

value: neuron

value: 20 ng/ml BMP2, 6 hour


title: G1-DOX(-), PINCH(-)-Ex5

value: skeletal muscle


title: sWAT_i89_HFD_Ime


title: sWAT_i91HFD_Ime


title: sWAT_i94_HFD_Ime


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-163]

value: mammary epithelial cells RAS inductible


title: S67-P013-I-120m


title: sWAT_i86_HFD_Ime


title: 14 days in vitro WT cortical cultures, Bmp2 stimulated for 1 hour, replicate1

value: WT

value: 20 ng/ml BMP2, 1 hour


title: S64-P014-C-120m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity


title: S65-P014-C-240m


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-151]


title: sWAT_i83_HFD_Control

value: HFD


title: G1-DOX(-), PINCH(-)-Ex1

value: sham


title: S22-0435

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: S22-0435_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment and FeatureCount for expression count.The reads were aligned to CanFam3  reference genome and mapping to the canine transcriptome  annotations. We then normalized the RNA-seq read counts for genes, applied a variance stabilizing transformation, and identified differentially expressed genes using the DESeq2 package. Differential gene expression determined by a false discovery rate cutoff of 0.05.
Assembly: canFam3
Supplementary files format and content: raw expression count matrix

organism: Canis lupus familiaris

source_name: Meningioma

extract_protocol:
Tissue samples from canines with spontaneous meningioma were acquired as surgical biopsies or from immediate post-mortem necropsies and archived as formalin-fixed, paraffin-embedded (FFPE) samples at Texas A&M University between 2011 and 2022. Following histopathological diagnosis, 5-10 25um thickness scrolls were collected from each meningioma for RNA sequencing. Scrolls were deparaffinized with xylene at room temperature, re-hydrated with an ethanol series, and subject to total RNA extraction using TRIzol reagent (Thermofisher, manufacturer’s instructions). RNA quantity and quality was evaluated on a TapeStation and all samples with a concentration of 10 ng/µl between 200-1,000nts were used for library preparation (n=62). Illumina library preparation was performed to manufacturer’s specification and 150 nt paired-end sequencing was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols.Paired-end RNA sequencing was performed.

tag: library name

tag: survival

value: Sx (lost to follow-up)

tag: breed

value: Labrador Retriever

value: Female

value: Neutered


title: sWAT_i80_HFD_Control

value: sWAT


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-139]

tag: cell line

value: HME-RASi


title: S68-P013-I-240m

value: Intervention

value: 240 minutes


title: S63-P014-C-0m

value: Control

value: 0 minutes (fasting)


title: S22-0358

description: S22-0358_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx

value: Australian Shepherd

tag: Sex


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-175]

value: mammary epithelial cells RAS inductible


title: G1-DOX(-), PINCH(-)-Ex2

tag: tissue

value: skeletal muscle

value: FOP-ACVR1 off


title: sWAT_i79_HFD_Control

value: HFD


title: S66-P013-I-0m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-127]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-115]


title: S22-0086

description: S22-0086_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx + RT (lost to follow-up)

value: Mixed

value: Male


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-103]


title: S60-P014-I-0m


title: S21-0542

description: S21-0542_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx (lost to follow-up)

value: Boxer

value: Intact


title: sWAT_i75_HFD_Control

value: sWAT


title: Liver_i94_HFD_Ime

source_name: Liver

value: Liver

value: HFD+Ime


title: S59-P006-C-240m

value: Control

value: 240 minutes


title: S61-P014-I-120m

value: Intervention

value: 120 minutes


title: S21-0582

description: S21-0582_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Australian Shepherd

value: Neutered


title: Liver_i91HFD_Ime


title: S19-0785

description: S19-0785_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Shetland Sheepdog

value: Female


title: S58-P006-C-120m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity


title: Liver_i89_HFD_Ime


title: S21-0082

description: S21-0082_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx + RT (lost to follow-up)

value: Silken Windhound

value: Male


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-174]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: S57-P006-C-0m

value: 0 minutes (fasting)


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-162]


title: S19-0707

description: S19-0707_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx

value: Shih Tzu


title: S62-P014-I-240m

value: 240 minutes


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-150]


title: S56-P006-I-240m

value: Intervention


title: Liver_i86_HFD_Ime

value: Liver

value: HFD+Ime


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-138]


title: S55-P006-I-120m

value: 120 minutes


title: Liver_i88_HFD_Ime


title: S18-0370

description: S18-0370_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Labrador Retriever

value: Neutered


title: S18-0049

description: S18-0049_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx + RT

value: Intact


title: sWAT_i76_HFD_Control

value: sWAT

value: HFD


title: Liver_i83_HFD_Control


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-126]


title: S17-0386

description: S17-0386_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx + RT (lost to follow-up)

value: Chihuahua

value: Female


title: S54-P006-I-0m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: 0 minutes (fasting)


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-114]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: Liver_i80_HFD_Control

value: Liver


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-186]


title: S17-0036

description: S17-0036_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx (lost to follow-up)


title: S16-0779

description: S16-0779_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Rat Terrier

value: Male


title: S52-P002-C-120m

value: Control

value: 120 minutes


title: Liver_i76_HFD_Control


title: S53-P002-C-240m

value: 240 minutes


title: Liver_i79_HFD_Control


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-185]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-102]


title: S50-P002-I-240m

value: Intervention


title: S51-P002-C-0m


title: Liver_i75_HFD_Control

value: HFD


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-173]


title: S15-0779

description: S15-0779_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx

value: Golden Retriever

value: Neutered


title: BAT_i94_HFD_Ime

source_name: BAT

value: BAT

value: HFD+Ime


title: S49-P002-I-120m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-149]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: S48-P002-I-0m

value: 0 minutes (fasting)


title: S15-0621

description: S15-0621_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx (lost to follow-up)

value: Australian Shepherd


title: BAT_i91HFD_Ime


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-161]


title: BAT_i89_HFD_Ime


title: S14-0380

description: S14-0380_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx + RT (lost to follow-up)

value: Mixed

value: Female


title: S47-P018-C-240m

value: Control

value: 240 minutes


title: BAT_i88_HFD_Ime


title: S13-0156

description: S13-0156_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx

value: German Shepherd


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-137]


title: S16-0318

description: S16-0318_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Golden Retriever

value: Male

value: Neutered


title: S46-P018-C-120m

value: Peripheral Blood Mononuclear Cells

value: 120 minutes


title: S12-0277

description: S12-0277_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx + RT

value: Weimaraner


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-125]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-101]


title: BAT_i86_HFD_Ime

value: BAT

value: HFD+Ime


title: S11-0307

description: S11-0307_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx (lost to follow-up)

value: Australian Shepherd


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-113]


title: BAT_i83_HFD_Control

value: HFD


title: S11-0485

description: S11-0485_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Doberman Pinscher


title: S44-P018-I-240m

value: abdominal obesity

value: Intervention

value: 240 minutes


title: BAT_i80_HFD_Control


title: S42-P018-I-0m

value: 0 minutes (fasting)


title: S41-P015-C-240m

value: Control


title: BAT_i79_HFD_Control


title: N21-0027

description: N21-0027_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Sx

value: Fox Terrier

value: Male

value: Neutered