title: 1023, Macaca fascicularis, OccipitalCortex,OccipitalCortex

description: Library name: itox001023

source_name: OccipitalCortex,OccipitalCortex

value: OccipitalCortex,OccipitalCortex


title: 1206, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

status: Public on Mar 25 2026

type: SRA

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

country: USA

institute: Pfizer

description: Library name: itox001206

library_source: transcriptomic

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

molecule: total RNA

organism: Macaca fascicularis

source_name: SubstantiaNigra,SubstantiaNigra

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

tag: tissue

value: SubstantiaNigra,SubstantiaNigra

tag: batch


title: 1408, Mus musculus, Cecum,Cecum

description: Library name: itox001408

organism: Mus musculus

source_name: Cecum,Cecum

value: Cecum,Cecum


title: 1207, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

description: Library name: itox001207


title: D-gal-LPS1

city: Beijing

first: yanlin

last: wang

address: Dongzhimen Hospital

country: China

institute: Beijing University of Chinese Medicine

description: Library name: D-1

data_processing:
Normalized and logarithmic converted expression of mouse genes (FPKM) by using the limma relative log expression normalization method. Then, principal component analyses (PCA) analysis was performed to demonstrate a large degree of differentiation between each group for further analysis. Normalized RNA-seq data was used for a heatmap of gene expression (https://www.omicstudio.cn/home). Furthermore, normalized and logarithmic converted RNA-seq data was used for PCA analysis and others. Software R (version 4.1.2) and the limma R package were used for differential gene expression analysis. The results of differential expression were used as the input for gene set enrichment analysis (GSEA) with the ClusterProfiler package. The gene expression heatmap was generated using the tool in Lianchuan Biological website (https://www.omicstudio.cn/tool). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the clusterProfiler R package. Additionally, the enrichment analysis bubble charts of upregulated and downregulated genes were generated by clusterProfiler.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: CSV file including gene count for each sample.

source_name: liver

growth_protocol: Laboratory animals: 6–8-week-old male C57BL/6 mice purchased from Shanghai Slake Co., Ltd. The use of all mice in this study was approved by the Animal Ethics Committee of the Shanghai Institute of Materia Medica, and all procedures were conducted in accordance with its ethical standards and animal welfare principles. Animal experiments were conducted at the Animal Center of the Shanghai Institute of Materia Medica. The mice were SPF grade. During housing, no more than 5 mice were kept per cage, and the Animal Center provided specialized commercial mouse maintenance feed. Unless otherwise specified, the housing temperature was 22°C. Mice had free access to food and water and were maintained under a 12-hour light-dark cycle (light from 7:00 to 19:00, dark from 19:00 to 7:00).

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Following Illumina's (San Diego, California, USA) experimental protocol, purified total RNA underwent mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3'-end A-addition, adapter ligation, and enrichment to complete sequencing library preparation.

value: liver


title: Ctrl3

description: Library name: V-3

treatment_protocol: Laboratory animals: 6–8-week-old male C57BL/6 mice purchased from Shanghai Slake Co., Ltd. The use of all mice in this study was approved by the Animal Ethics Committee of the Shanghai Institute of Materia Medica, and all procedures were conducted in accordance with its ethical standards and animal welfare principles. Animal experiments were conducted at the Animal Center of the Shanghai Institute of Materia Medica. The mice were SPF grade. During housing, no more than 5 mice were kept per cage, and the Animal Center provided specialized commercial mouse maintenance feed. Unless otherwise specified, the housing temperature was 22°C. Mice had free access to food and water and were maintained under a 12-hour light-dark cycle (light from 7:00 to 19:00, dark from 19:00 to 7:00).


city: Oxford

first: Naveed

last: Akbar

state: England

address: Division of Cardiovascular Medicine, Radcliffe Department of Medicine, HS04

country: United Kingdom

institute: University of Oxford

description:
Library name: OxAMI01_00440_13082018_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis

data_processing:
Quality of raw sequence reads was assessed using FastQC (v0.11.8). Adapter sequences and low-quality bases were trimmed using CLC Genomics Workbench v11.0.1 (Quality limit = 0.05). Trimmed reads were mapped to the Homo sapiens GRCh38 (hg38) reference genome using Salmon v0.99.0 in mapping-based mode with the following parameters: --libType ISR --gcBias --validateMappings. Gene-level counts and normalized TPM/FPKM values were derived from Salmon quantification outputs.
Assembly: Homo sapiens GRCh38 (hg38)

organism: Homo sapiens

source_name: Peripheral blood monocyte

growth_protocol: Peripheral venous blood was collected from healthy male volunteers in EDTA tubes or from leukapheresis cones obtained from the NHS Blood Bank. PBMCs were isolated by density gradient centrifugation. Peripheral venous blood from MI patients was collected into EDTA tubes and diluted 1:1 with PBS. Monocytes were isolated by negative selection using the EasySep™ Human Monocyte Enrichment Kit (without CD16 depletion) (StemCell Technologies, Grenoble, France) following the manufacturer’s instructions. Enriched monocytes were cultured in complete DMEM (5 mmol/L glucose) supplemented with 10% FBS, 2% penicillin–streptomycin, and 2 mM L-glutamine, under control or M1-proinflammatory conditions (100 ng/mL LPS + 10 ng/mL IFN-γ) for 6 h at 37 °C and 5% CO₂.

extract_protocol:
Following stimulation, cells were washed with PBS, centrifuged, and lysed using the lysis buffer from the miRvana miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Lysates were snap-frozen and stored at −80 °C until RNA extraction.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol, including poly-A selection, RNA fragmentation, first- and second-strand cDNA synthesis, end repair/A-tailing, adapter ligation, and PCR enrichment. Libraries were quantified, pooled in equimolar amounts, and sequenced on Illumina HiSeq 3000/4000 instruments.

treatment_protocol: PBMCs were exposed to plasma extracellular vesicles (EVs) isolated from STEMI or control (NSTEMI) patients for 6 or 18 hours in siolation or followed by M1-type stimulation with 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) and 10 ng/mL recombinant human interferon-γ (IFN-γ; Invitrogen/R&D Systems) for 6 hours at 37 °C and 5% CO₂. Following stimulation, cells were washed with PBS, pelleted, and lysed for RNA extraction. Peripheral blood monocytes from NSTEMI and STMI patients were treated and activated using the same stimulants.

tag: cell type

value: Peripheral blood monocyte

tag: genotype

value: wild-type

tag: treatment

value: LPSplusIFN


title: 1413, Mus musculus, Cecum,Cecum

description: Library name: itox001413


title: 1208, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

description: Library name: itox001208


title: 1022, Macaca fascicularis, Neutrophils,Neutrophils

description: Library name: itox001022

source_name: Neutrophils,Neutrophils

value: Neutrophils,Neutrophils


title: Ctrl2

description: Library name: V-2


title: 3.Control.0.0.0

description: Library name: 3.Control.0.0.0

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells

value: Control


title: 1209, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

description: Library name: itox001209


title: OxAMI01_00440_13082018_Control_Monocyte

description:
Library name: OxAMI01_00440_13082018_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1416, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox001416

source_name: Colon (mid),Colon (mid)

value: Colon (mid),Colon (mid)


title: 1414, Mus musculus, Cecum,Cecum

description: Library name: itox001414


title: D-gal-LPS2

description: Library name: D-2


title: 2.Control.0.0.0

description: Library name: 2.Control.0.0.0


description:
Library name: OxAMI01_00440_10102018_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: Ctrl1

description: Library name: V-1


title: 1409, Mus musculus, Cecum,Cecum

description: Library name: itox001409


title: EBV+Burkitt, arginine free media rep3

city: Boston

first: Shaowen

last: White

state: MA

address: 181 Longwood Ave, Channing Labs Room 861

department: Medicine

institute: Brigham and Women's Hospital

description: Library name: A6

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped to the human GRCh38, hg19 genome assembly using STAR v2.7.10a
genes were filtered based on having at least 10 reads in at least 3 samples
DESeq2 v1.48.2 was used to evaluate gene differential expression (DE)
Assembly: GRCh38.p14 (GCF_000001405.40 ), Akata EBV genom (GCA_900004315.1)
Supplementary files format and content: csv files counting read counts

molecule: polyA RNA

source_name: Burkitt lymphoma

growth_protocol: P3HR-1 cells were maintained in RPMI media with 10% fetal bovine serum (FBS) and antibiotics in humidified chamber with 5% CO2 at 37C

extract_protocol:
Snap-frozen cell pellets were submitted to Quintara Biosciences, Cambridge, MA.
Snap-frozen cell pellets were submitted to Quintara Biosciences, Cambridge, MA.

treatment_protocol: P3HR-1 were washed with PBS three times to remove old media, and seeded in SILAC RPMI 1640 media (Thermo Fisher A33823) supplied with 0.22mM L-lysine hydrochloride (Thermo Fisher A16249.18), with or without 1.15mM L-arginine (Thermo Fisher A15738.22), at 5e5 cells/ml. Cells were cultured for 5 days, and media was refreshed on day3. On day 5, cells were washed once with PBS and snap frozen.

value: Burkitt lymphoma

tag: cell line

value: cancerous lymphocyte

value: WT

value: arginine restriction


title: 1634, Mus musculus, Brain- Hippocampus,Brain- Hippocampus

description: Library name: itox001634

source_name: Brain- Hippocampus,Brain- Hippocampus

value: Brain- Hippocampus,Brain- Hippocampus


title: 1211, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

description: Library name: itox001211


title: OxAMI01_00440_10102018_Control_Monocyte

description:
Library name: OxAMI01_00440_10102018_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1.Control.0.0.0

description: Library name: 1.Control.0.0.0


title: 1210, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

description: Library name: itox001210


title: EBV+Burkitt, arginine free media rep2

description: Library name: A5


title: 1417, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox001417


title: 1418, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox001418


title: 1212, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

description: Library name: itox001212


description:
Library name: OxAMI01_00438_25072018_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1419, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox001419


title: EBV+Burkitt, arginine free media rep1

description: Library name: A4


title: OxAMI01_00438_25072018_Control_Monocyte

description:
Library name: OxAMI01_00438_25072018_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1420, Mus musculus, Colon (mid),Colon (mid)

description: Library name: itox001420


title: EBV+Burkitt, replete media, rep3

description: Library name: A3

value: control


title: 1214, Macaca fascicularis, TLymphocytesCD4,TLymphocytesCD4

description: Library name: itox001214


title: 1421, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001421

source_name: Esophagus (mid),Esophagus (mid)

value: Esophagus (mid),Esophagus (mid)


title: EBV+Burkitt, replete media, rep2

description: Library name: A2


title: EBV+Burkitt, replete media, rep1

description: Library name: A1


description:
Library name: OxAMI01_00438_17092018_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: OxAMI01_00438_17092018_Control_Monocyte

description:
Library name: OxAMI01_00438_17092018_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


description:
Library name: OxAMI002_00069_29012019_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1423, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001423


title: 1215, Macaca fascicularis, TLymphocytesCD4,TLymphocytesCD4

description: Library name: itox001215


title: 197, Rattus norvegicus, Brown Fat (intrascapular)

description: Library name: itox000197

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read counts mapped to human

organism: Rattus norvegicus

source_name: Brown Fat (intrascapular)

value: Brown Fat (intrascapular)


title: 1218, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001218

source_name: TemporalCortex,TemporalCortex

value: TemporalCortex,TemporalCortex


title: 196, Rattus norvegicus, Artery- Aorta (abdominal descending)

description: Library name: itox000196

source_name: Artery- Aorta (abdominal descending)

value: Artery- Aorta (abdominal descending)


description:
Library name: OxAMI002_00069_05032019_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis

value: Peripheral blood monocyte


title: 1422, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001422


title: 1219, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001219


title: 198, Rattus norvegicus, Kidney (left to include cortex and medulla)

description: Library name: itox000198


title: 1425, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001425


title: 1424, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001424


title: 1217, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001217


title: 1213, Macaca fascicularis, SubstantiaNigra,SubstantiaNigra

description: Library name: itox001213

value: SubstantiaNigra,SubstantiaNigra


description:
Library name: OxAMI002_00069_05032019_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis

value: wild-type


title: 1220, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001220


description:
Library name: OxAMI002_00053_03102018_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis

value: LPSplusIFN


title: 1426, Mus musculus, Esophagus (mid),Esophagus (mid)

description: Library name: itox001426


title: 199, Rattus norvegicus, Mammary Gland/Tissue (female only)

description: Library name: itox000199

source_name: Mammary Gland/Tissue (female only)

value: Mammary Gland/Tissue (female only)


title: 1221, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001221


title: 200, Rattus norvegicus, Brain - Spinal cord (cervical)

description: Library name: itox000200

source_name: Brain - Spinal cord (cervical)

value: Brain - Spinal cord (cervical)


title: 1469, Mus musculus, Tongue,Tongue

description: Library name: itox001469

source_name: Tongue,Tongue

value: Tongue,Tongue


description:
Library name: OxAMI002_00069_29012019_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis

value: Control


description:
Library name: OxAMI002_00053_03102018_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 201, Rattus norvegicus, Skin (inguinal)

description: Library name: itox000201

source_name: Skin (inguinal)

value: Skin (inguinal)


title: 1222, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001222


description:
Library name: OxAMI002_00053_03092018_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1470, Mus musculus, Tongue,Tongue

description: Library name: itox001470


title: 202, Rattus norvegicus, Urinary Bladder

description: Library name: itox000202

source_name: Urinary Bladder

value: Urinary Bladder


title: 1223, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001223


title: 1228, Macaca fascicularis, Testis,Testis

description: Library name: itox001228

source_name: Testis,Testis

value: Testis,Testis


title: 203, Rattus norvegicus, DRG-L4

description: Library name: itox000203


title: 1472, Mus musculus, Tongue,Tongue

description: Library name: itox001472


description:
Library name: OxAMI002_00053_03092018_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1473, Mus musculus, Tongue,Tongue

description: Library name: itox001473


description:
Library name: OXAMI_100455_05032019_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: OXAMI_100455_05032019_Control_Monocyte

description:
Library name: OXAMI_100455_05032019_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1224, Macaca fascicularis, TemporalCortex,TemporalCortex

description: Library name: itox001224


title: 1272, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001272


title: 1474, Mus musculus, Tongue,Tongue

description: Library name: itox001474


title: 205, Rattus norvegicus, Brain- Hippocampus

description: Library name: itox000205

source_name: Brain- Hippocampus

value: Brain- Hippocampus


description:
Library name: OXAMI_100455_04022019_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis

source_name: Peripheral blood monocyte


title: 1273, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001273


title: 206, Rattus norvegicus, Pituitary

description: Library name: itox000206

source_name: Pituitary

value: Pituitary


title: 204, Rattus norvegicus, Brain-Striatum

description: Library name: itox000204

source_name: Brain-Striatum

value: Brain-Striatum


title: 1475, Mus musculus, Tongue,Tongue

description: Library name: itox001475


title: OXAMI_100455_04022019_Control_Monocyte

description:
Library name: OXAMI_100455_04022019_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 1471, Mus musculus, Tongue,Tongue

description: Library name: itox001471


title: 207, Rattus norvegicus, Small intestine- Jejunum (mid)

description: Library name: itox000207

source_name: Small intestine- Jejunum (mid)

value: Small intestine- Jejunum (mid)


title: 1274, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001274


title: 1477, Mus musculus, Tongue,Tongue

description: Library name: itox001477


title: 983, Macaca fascicularis, MammaryGland,MammaryGland

description: Library name: itox000983

source_name: MammaryGland,MammaryGland

value: MammaryGland,MammaryGland


description:
Library name: OXAMI_0200072_05032019_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis


title: 208, Rattus norvegicus, Spleen

description: Library name: itox000208

source_name: Spleen

value: Spleen


title: 1480, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001480

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 1276, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001276


description:
Library name: OXAMI_0200072_04022019_LPSplusIFN_Monocyte
csv files include individual or mean grouped expression for the described analysis

value: Peripheral blood monocyte


title: 210, Rattus norvegicus, Cecum

description: Library name: itox000210

source_name: Cecum

value: Cecum


title: OXAMI_0200072_04022019_Control_Monocyte

description:
Library name: OXAMI_0200072_04022019_Control_Monocyte
csv files include individual or mean grouped expression for the described analysis

value: wild-type


title: 1277, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001277


title: 1479, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001479


title: 1275, Macaca fascicularis, Tongue,Tongue

description: Library name: itox001275


title: 1282, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001282

source_name: Trachea,Trachea

value: Trachea,Trachea


title: mia.paca_2_g12ci_3

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

description: Library name: Sample-30

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: MIA Paca-2

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using PureInk TM RNA Mini kit (Ref#12183025, Thermo Fisher Scientific). mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MIA Paca-2

value: Pancreatic cancer

value: MIA Paca-2 (KRASG12C)

value: YES


title: 254, Rattus norvegicus, Ileum

description: Library name: itox000254

source_name: Ileum

value: Ileum


title: 1481, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001481


title: 1482, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001482


title: 255, Rattus norvegicus, Adipose - Visceral (Omentum)

description: Library name: itox000255

source_name: Adipose - Visceral (Omentum)

value: Adipose - Visceral (Omentum)


title: OXAMI_0200072_05032019_Contro_Monocyte

description:
Library name: OXAMI_0200072_05032019_Contro_Monocyte
csv files include individual or mean grouped expression for the described analysis

value: Control


title: 256, Rattus norvegicus, Testis (tubules\, without capsule)

description: Library name: itox000256

source_name: Testis (tubules\, without capsule)

value: Testis (tubules\, without capsule)


title: 1283, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001283


title: 209, Rattus norvegicus, Stomach (glandular)

description: Library name: itox000209

source_name: Stomach (glandular)

value: Stomach (glandular)


title: 1483, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001483


title: 257, Rattus norvegicus, Brain - Cerebellum

description: Library name: itox000257

source_name: Brain - Cerebellum

value: Brain - Cerebellum


title: mia.paca_2_g12ci_2

description: Library name: Sample-29


title: mia.paca_2_g12ci_1

description: Library name: Sample-28


title: 1284, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001284


title: 1484, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001484


title: mia.paca_2_vehicle_3

description: Library name: Sample-27

value: No


title: 258, Rattus norvegicus, Epididymus (head)

description: Library name: itox000258

source_name: Epididymus (head)

value: Epididymus (head)


title: 1485, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001485

value: Adrenal Gland,Adrenal Gland


title: 1486, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001486


title: 260, Rattus norvegicus, Epididymus (tail)

description: Library name: itox000260

source_name: Epididymus (tail)

value: Epididymus (tail)


title: 1487, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001487


title: 1287, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001287


title: 1285, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001285


title: 259, Rattus norvegicus, Seminal Vesicles

description: Library name: itox000259

source_name: Seminal Vesicles

value: Seminal Vesicles


title: mia.paca_2_vehicle_2

description: Library name: Sample-26


title: mia.paca_2_vehicle_1

description: Library name: Sample-25


title: HPAC_MRTX11_3

description: Library name: Sample-24

source_name: HPAC

value: HPAC

value: HPAC (KRASG12D)


title: HPAC_MRTX11_2

description: Library name: Sample-23


title: 1489, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001489


title: 984, Macaca fascicularis, MammaryGland,MammaryGland

description: Library name: itox000984

value: MammaryGland,MammaryGland


title: 262, Rattus norvegicus, Brain - Cortex

description: Library name: itox000262

source_name: Brain - Cortex

value: Brain - Cortex


title: 1288, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001288

value: Trachea,Trachea


title: 1559, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001559


title: HPAC_Cont_3

description: Library name: Sample-21

value: Pancreatic cancer


title: 1286, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001286


title: 1344, Macaca fascicularis, WholeBlood,WholeBlood

description: Library name: itox001344

source_name: WholeBlood,WholeBlood

value: WholeBlood,WholeBlood


title: 264, Rattus norvegicus, Muscle - Skeletal (gastrocnemius)

description: Library name: itox000264

source_name: Muscle - Skeletal (gastrocnemius)

value: Muscle - Skeletal (gastrocnemius)


title: 1343, Macaca fascicularis, WholeBlood,WholeBlood

description: Library name: itox001343


title: HPAC_Cont_1

description: Library name: Sample-19


title: HPAC_MRTX11_1

description: Library name: Sample-22

value: YES


title: 261, Rattus norvegicus, Prostate

description: Library name: itox000261

source_name: Prostate

value: Prostate


title: 263, Rattus norvegicus, Eyes-cornea

description: Library name: itox000263

source_name: Eyes-cornea

value: Eyes-cornea


title: 1560, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001560


title: 1289, Macaca fascicularis, Trachea,Trachea

description: Library name: itox001289


title: 1558, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001558


title: HPAC_Cont_2

description: Library name: Sample-20


title: 266, Rattus norvegicus, Peripheral Nerve (tibial)

description: Library name: itox000266

source_name: Peripheral Nerve (tibial)

value: Peripheral Nerve (tibial)


title: 990, Macaca fascicularis, MesentericLymphNode,MesentericLymphNode

description: Library name: itox000990

source_name: MesentericLymphNode,MesentericLymphNode

value: MesentericLymphNode,MesentericLymphNode


title: Pa014c_MRTX11_3

description: Library name: Sample-18

value: Pa14C (KRASG12D)


title: 265, Rattus norvegicus, Peripheral Nerve (sciatic)

description: Library name: itox000265

source_name: Peripheral Nerve (sciatic)

value: Peripheral Nerve (sciatic)


title: 1561, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001561


title: 1488, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001488

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 267, Rattus norvegicus, Heart - Atrium

description: Library name: itox000267

source_name: Heart - Atrium

value: Heart - Atrium


title: 954, Macaca fascicularis, Liver,Liver

description: Library name: itox000954

source_name: Liver,Liver

value: Liver,Liver


title: 268, Rattus norvegicus, Lung (left lobe)

description: Library name: itox000268

source_name: Lung (left lobe)

value: Lung (left lobe)


title: 1563, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001563


title: Pa014c_MRTX11_1

description: Library name: Sample-16


title: 1001, Macaca fascicularis, MotorCortex,MotorCortex

description: Library name: itox001001

source_name: MotorCortex,MotorCortex

value: MotorCortex,MotorCortex


title: Pa014c_Cont_3

description: Library name: Sample-15

value: No


title: Pa014c_MRTX11_2

description: Library name: Sample-17


title: 991, Macaca fascicularis, MesentericLymphNode,MesentericLymphNode

description: Library name: itox000991


title: 1566, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001566


title: 272, Rattus norvegicus, Trachea

description: Library name: itox000272

source_name: Trachea

value: Trachea


title: gene_expression_3

first: Simon

last: Davis

address: MRC Weatherall Institute of Molecular Medicine

department: Radcliffe Department of Medicine

description: Library name: Sample 4

library_source: transcriptomic single cell

data_processing:
Fastq files were aligned and quantified using Cell Ranger v8.0.1.
Assembly: mm10-1.2.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Immune cells

extract_protocol:
The following BioLegend hashtag antibodies were used: TotalSeq-C0301 (ACCCACCAGTAAGAC), TotalSeq-C0302 (GGTCGAGAGCATTCA), TotalSeq-C0303 (CTTGCCGCATGTCAT), TotalSeq-C0304 (AAAGCATTCTTCACG), TotalSeq-C0305 (CTTTGTCTTTGTGAG), TotalSeq-C0306 (TATGCTGCCACGGTA), TotalSeq-C0307 (GAGTCTGCCAGTATC), TotalSeq-C0308 (TATAGAACGCCAGGC), TotalSeq-C0309 (TGCCTATGAAACAAG).
Library was performed according to the manufacturer's instructions (Single Cell 5' PE HT).

value: Immune cells


title: 1562, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001562


title: gene_expression_2

description: Library name: Sample 3


title: 270, Rattus norvegicus, Thymus

description: Library name: itox000270

source_name: Thymus

value: Thymus


title: 273, Rattus norvegicus, Salivary Gland (mandibular)

description: Library name: itox000273

source_name: Salivary Gland (mandibular)

value: Salivary Gland (mandibular)


title: 1565, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001565


title: 1564, Mus musculus, Skeletal Muscle (gastrocnemius),Skeletal Muscle (gastrocnemius)

description: Library name: itox001564


title: 274, Rattus norvegicus, Artery - Aorta (thoracic)

description: Library name: itox000274

source_name: Artery - Aorta (thoracic)

value: Artery - Aorta (thoracic)


title: 269, Rattus norvegicus, Brain - Hypothalamus

description: Library name: itox000269

source_name: Brain - Hypothalamus

value: Brain - Hypothalamus


title: Pa03c_MRTX11_1

description: Library name: Sample-10

value: Pancreatic cancer

value: Pa03C (KRASG12D)

value: YES


title: 994, Macaca fascicularis, MesentericLymphNode,MesentericLymphNode

description: Library name: itox000994

value: MesentericLymphNode,MesentericLymphNode


title: gene_expression_4

description: Library name: Sample 5


title: Pa014c_Cont_2

description: Library name: Sample-14

value: Pa14C (KRASG12D)


title: Pa03c_MRTX11_2

description: Library name: Sample-11


title: 1571, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001571

source_name: Brain - Cerebellum,Brain - Cerebellum

value: Brain - Cerebellum,Brain - Cerebellum


title: gene_expression_1

description: Library name: Sample 2


title: 1567, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001567


title: Immune cells (CD45+) from digested lung tumors pool4; ADT

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
Library name: mm_lung_CD45pos_pool4_ADT
CD11C_GTTATGGACGCTTGC; CD19_CTGGGCAATTACTCG; CD326_ACCCGCGTTAGTATG; IGG2B_ATATGTATCACGCGA; MERTK_AGTAGAGCAACTCGT; XCR1_TCCATTACCCACGTT
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds

library_source: other

data_processing:
Demultiplexing, preprocessing, gene counting and aggregation were done using CellRanger v6.1.2.
Assembly: mm10
Supplementary files format and content: h5; feature barcode count matrix
Library strategy: CITE-seq

molecule: protein

source_name: lung

extract_protocol:
Single-cell suspensions from lung tissues were obtained, as described above. Samples were broad- ly enriched for CD45POS cells by fluorescence-activated cell sorting, and these cells were suspended in PBS supplemented with 0.5% BSA.
Samples were loaded onto the 10x Genomics Next GEM 3’ V3 assay, as per the manufacturer’s instructions, for a target cell recovery of 10,000 cells per lane. Libraries were constructed, according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer and KAPA library quantification kit (Roche, Cat. #0797014001).

value: lung

value: immune (CD45+)

value: WT

value: mixed samples (chemo; chemo + RT)


title: Pa03c_MRTX11_3

description: Library name: Sample-12


title: 1573, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001573


title: 1570, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001570


title: Pa03c_Cont_2

description: Library name: Sample-8

value: No


title: Immune cells (CD45+) from digested lung tumors pool4; HTO

description:
Library name: mm_lung_CD45pos_pool4_HTO
mm_lung_CD45pos_chemo_rep1 (CMO301_ATGAGGAATTCCTGC); mm_lung_CD45pos_chemo_rep2 (CMO302_CATGCCAATAGAGCG); mm_lung_CD45pos_chemo_rep3 (CMO303_CCGTCGTCCAAGCAT); mm_lung_CD45pos_chemo_RT_rep1 (CMO304_AACGTTAATCACTCA); mm_lung_CD45pos_chemo_RT_rep2 (CMO305_CGCGATATGGTCGGA); mm_lung_CD45pos_chemo_RT_rep3 (CMO306_AAGATGAGGTCTGTG) mm_lung_CD45pos_chemo_RT_rep4 (CMO307_AAGCTCGTTGGAAGA); mm_lung_CD45pos_chemo_RT_rep5 (CMO308_CGGATTCCACATCAT)
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: pa01c_g12di_3

description: Library name: Sample-6


title: 271, Rattus norvegicus, Thyroid/parathyroid

description: Library name: itox000271

source_name: Thyroid/parathyroid

value: Thyroid/parathyroid


title: 1569, Mus musculus, Muscle - Skeletal (gastrocnemius),Muscle - Skeletal (gastrocnemius)

description: Library name: itox001569


title: 73, Rattus norvegicus, Peripheral Nerve (tibial)

description: Library name: itox000073

source_name: Peripheral Nerve (tibial)

value: Peripheral Nerve (tibial)


title: 275, Rattus norvegicus, Artery- Aorta (abdominal descending)

description: Library name: itox000275

source_name: Artery- Aorta (abdominal descending)

value: Artery- Aorta (abdominal descending)


title: Immune cells (CD45+) from digested lung tumors pool3; ADT

description:
Library name: mm_lung_CD45pos_pool3_ADT
CD11C_GTTATGGACGCTTGC; CD19_CTGGGCAATTACTCG; CD326_ACCCGCGTTAGTATG; IGG2B_ATATGTATCACGCGA; MERTK_AGTAGAGCAACTCGT; XCR1_TCCATTACCCACGTT
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: 74, Rattus norvegicus, Esophagus (mid)

description: Library name: itox000074

source_name: Esophagus (mid)

value: Esophagus (mid)


title: hashtag

description: Library name: Sample 1

value: Immune cells


title: Pa03c_Cont_3

description: Library name: Sample-9


title: 1575, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001575


title: pa01c_g12di_2

description: Library name: Sample-5

value: Pa01C (KRASG12D)


title: Pa014c_Cont_1

description: Library name: Sample-13

value: Pancreatic cancer


title: 1572, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001572


title: Immune cells (CD45+) from digested lung tumors pool4; GEX

description:
Library name: mm_lung_CD45pos_pool4_GEX
GEX
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: 61, Rattus norvegicus, Liver (left lateral lobe)

description: Library name: itox000061

source_name: Liver (left lateral lobe)

value: Liver (left lateral lobe)


title: Pa03c_Cont_1

description: Library name: Sample-7

value: Pa03C (KRASG12D)


title: 60, Rattus norvegicus, Colon (mid)

description: Library name: itox000060

source_name: Colon (mid)

value: Colon (mid)


title: 1574, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001574


title: 75, Rattus norvegicus, Heart - Atrium

description: Library name: itox000075

source_name: Heart - Atrium

value: Heart - Atrium


title: pa01c_g12di_1

description: Library name: Sample-4

value: YES


title: Immune cells (CD45+) from digested lung tumors pool3; GEX

description:
Library name: mm_lung_CD45pos_pool3_GEX
GEX
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds

value: lung


title: 76, Rattus norvegicus, Heart - Ventricle (left)

description: Library name: itox000076

source_name: Heart - Ventricle (left)

value: Heart - Ventricle (left)


title: pa01c_vehicle_3

description: Library name: Sample-3


title: 1578, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001578

value: Brain - Cerebellum,Brain - Cerebellum


title: 77, Rattus norvegicus, Lung (left lobe)

description: Library name: itox000077

source_name: Lung (left lobe)

value: Lung (left lobe)


title: 78, Rattus norvegicus, Brain - Hypothalamus

description: Library name: itox000078

value: Brain - Hypothalamus


title: 1645, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001645


title: pa01c_vehicle_1

description: Library name: Sample-1

value: No


title: 1644, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001644


title: pa01c_vehicle_2

description: Library name: Sample-2


title: Immune cells (CD45+) from digested lung tumors pool3; HTO

description:
Library name: mm_lung_CD45pos_pool3_HTO
mm_lung_CD45pos_chemo_rep1 (CMO301_ATGAGGAATTCCTGC); mm_lung_CD45pos_chemo_rep2 (CMO302_CATGCCAATAGAGCG); mm_lung_CD45pos_chemo_rep3 (CMO303_CCGTCGTCCAAGCAT); mm_lung_CD45pos_chemo_RT_rep1 (CMO304_AACGTTAATCACTCA); mm_lung_CD45pos_chemo_RT_rep2 (CMO305_CGCGATATGGTCGGA); mm_lung_CD45pos_chemo_RT_rep3 (CMO306_AAGATGAGGTCTGTG) mm_lung_CD45pos_chemo_RT_rep4 (CMO307_AAGCTCGTTGGAAGA); mm_lung_CD45pos_chemo_RT_rep5 (CMO308_CGGATTCCACATCAT)
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds

value: immune (CD45+)

value: WT

value: mixed samples (chemo; chemo + RT)


title: Immune cells (CD45+) from digested lung tumors pool2; HTO

description:
Library name: mm_lung_CD45pos_pool2_HTO
mm_lung_CD45pos_chemo_rep1 (CMO301_ATGAGGAATTCCTGC); mm_lung_CD45pos_chemo_rep2 (CMO302_CATGCCAATAGAGCG); mm_lung_CD45pos_chemo_rep3 (CMO303_CCGTCGTCCAAGCAT); mm_lung_CD45pos_chemo_RT_rep1 (CMO304_AACGTTAATCACTCA); mm_lung_CD45pos_chemo_RT_rep2 (CMO305_CGCGATATGGTCGGA); mm_lung_CD45pos_chemo_RT_rep3 (CMO306_AAGATGAGGTCTGTG) mm_lung_CD45pos_chemo_RT_rep4 (CMO307_AAGCTCGTTGGAAGA); mm_lung_CD45pos_chemo_RT_rep5 (CMO308_CGGATTCCACATCAT)
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: 1646, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001646


title: 79, Rattus norvegicus, Thymus

description: Library name: itox000079

value: Thymus


title: 1577, Mus musculus, Brain - Cerebellum,Brain - Cerebellum

description: Library name: itox001577


title: Pa14c-B

description: Library name: Sample 8

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Count,CPM,RPKM

value: Pa14C (KRASG12D)

value: Yes


title: Immune cells (CD45+) from digested lung tumors pool1; GEX

description:
Library name: mm_lung_CD45pos_pool1_GEX
GEX
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: Pa14c-A

description: Library name: Sample 7

value: Pancreatic cancer


title: Immune cells (CD45+) from digested lung tumors pool1; ADT

description:
Library name: mm_lung_CD45pos_pool1_ADT
CD11C_GTTATGGACGCTTGC; CD19_CTGGGCAATTACTCG; CD326_ACCCGCGTTAGTATG; IGG2B_ATATGTATCACGCGA; MERTK_AGTAGAGCAACTCGT; XCR1_TCCATTACCCACGTT
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: 1647, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001647


title: 81, Rattus norvegicus, Tongue

description: Library name: itox000081

source_name: Tongue

value: Tongue


title: Pa03c-B

description: Library name: Sample 6

value: Pa03C (KRASG12D)


title: Immune cells (CD45+) from digested lung tumors pool2; GEX

description:
Library name: mm_lung_CD45pos_pool2_GEX
GEX
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: Immune cells (CD45+) from digested lung tumors pool1; HTO

description:
Library name: mm_lung_CD45pos_pool1_HTO
mm_lung_CD45pos_chemo_rep1 (CMO301_ATGAGGAATTCCTGC); mm_lung_CD45pos_chemo_rep2 (CMO302_CATGCCAATAGAGCG); mm_lung_CD45pos_chemo_rep3 (CMO303_CCGTCGTCCAAGCAT); mm_lung_CD45pos_chemo_RT_rep1 (CMO304_AACGTTAATCACTCA); mm_lung_CD45pos_chemo_RT_rep2 (CMO305_CGCGATATGGTCGGA); mm_lung_CD45pos_chemo_RT_rep3 (CMO306_AAGATGAGGTCTGTG) mm_lung_CD45pos_chemo_RT_rep4 (CMO307_AAGCTCGTTGGAAGA); mm_lung_CD45pos_chemo_RT_rep5 (CMO308_CGGATTCCACATCAT)
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: Immune cells (CD45+) from digested lung tumors pool2; ADT

description:
Library name: mm_lung_CD45pos_pool2_ADT
CD11C_GTTATGGACGCTTGC; CD19_CTGGGCAATTACTCG; CD326_ACCCGCGTTAGTATG; IGG2B_ATATGTATCACGCGA; MERTK_AGTAGAGCAACTCGT; XCR1_TCCATTACCCACGTT
mm_lung_CD45pos_chemo_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep1_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep2_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep3_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep4_feature_bc_matrix.rds
mm_lung_CD45pos_chemo_RT_rep5_feature_bc_matrix.rds


title: 1648, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001648


title: 82, Rattus norvegicus, Artery - Aorta (thoracic)

description: Library name: itox000082

value: Artery - Aorta (thoracic)


title: 80, Rattus norvegicus, Thyroid/parathyroid

description: Library name: itox000080

value: Thyroid/parathyroid


title: 70, Rattus norvegicus, Eyes-cornea

description: Library name: itox000070

source_name: Eyes-cornea

value: Eyes-cornea


title: Pa02c-B

description: Library name: Sample 4

value: Pa02C (KRASG12D)


title: 1650, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001650


title: eq_TGFbeta1

city: Neustadt am Rübenberge

first: Claudia

last: Klein

state: Lower Saxony

address: Höltystraße 10

department: Biotechnology

country: Germany

institute: Friedrich-Loeffler-Institut

description:
Library name: L127048
10X Genomics

data_processing:
Cell Ranger count tool (v.7.1.0) was used for alignment to the reference genome
Using Souporcell, pooled data sets for each treatment group were separated into the four individual animals.
Cells with at least 20,000 unique molecular identifiers (UMIs), at least 3,500 genes, and containing less than 4% mitochondrial genes were kept for further analyses.
Data sets were then merged into a single Seurat object and normalized using Seurat.
Following the integration of data (Seurat v.5), visualization was performed through the generation of uniform manifold approximation and projection (UMAP, resolution of 0.5) and multi-dimensional scaling (MDS) plots. Differential gene expression analysis was conducted in edgeR 4.2.2.
Assembly: Equus_caballus.EquCab3.0.109
Supplementary files format and content: count matrix for each treatment (control, MFGE8, TGFB); mtx.gz

organism: Equus caballus

source_name: Endometrium

growth_protocol: Cells were incubated for 24 hours in a humidified atmosphere at 38 °C and 5% CO₂ using our DMEM/F-12 medium supplemented with 10% FBS. After 24 hours, the serum concentration was reduced to 4% FBS.

extract_protocol:
Cells were harvested using trypsin and processed for single cell sequencing using Chromium Next GEM Single Cell 3’Reagent Kits v3.1, Dual Index (10x Genomics, CA, USA).
Chromium Next GEM Single Cell 3’Reagent Kits v3.1, Dual Index. Resulting libraries were subjected to paired-end (100 bp) sequencing as multiplexed pools on a NovaSeq 6000 using an S4 Reagent Kit v1.5 4XP (290 pM, 200 cycles; Illumina, CA, USA).

treatment_protocol: From 48 hours to 72 hours , cells were incubated using cell culture medium containing 0.1% BSA instead of FBS and received either (1) no further supplementation (control), (2) were supplemented with 10 ng/ml human recombinant TGF-β1, or (3) were supplemented with 10 ng/ml mouse recombinant MFGE8.

value: Endometrium

tag: Sex

value: female

value: Fibroblast

value: 10 ng/ml human recombinant TGF-β1


title: eq_MFGE8

description:
Library name: L127049
10X Genomics

value: 10 ng/ml mouse recombinant MFGE8


title: Pa02c-A

description: Library name: Sample 3

value: No


title: 1651, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001651


title: 83, Rattus norvegicus, Artery- Aorta (abdominal descending)

description: Library name: itox000083

value: Artery- Aorta (abdominal descending)


title: eq_control

description:
Library name: L127047
10X Genomics

value: none; control


title: 1652, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001652


title: Pa03c-A

description: Library name: Sample 5


title: MRE-seq Vehicle replicate 3

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

description: MRE-seq

library_source: genomic

data_processing:
MRE reads were normalized to account for differences in enzyme efficiency and scoring consisted of tabulating reads with CpGs at each fragment end.
Genome_build: mm9

molecule: genomic DNA

source_name: femoral head

growth_protocol: Following digestion, chondrocytes were harvested and cultured in complete high-glucose Dulbecco’s modified Eagle’s medium (DMEM; Gibco; #31053028) supplemented with 10% fetal bovine serum (FBS; Gibco; #10437), 2 mM L-Glutamine (Gibco; #A2916801), and 1% penicillin/streptomycin.

extract_protocol:
Genomic DNA from caltured cells was extracted using the DNeasy Tissue kit (Qiagen, Valencia, CA).
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, as described in previous study (Maunakea et al. 2010).

treatment_protocol: Primary chondrocytes were seeded at a density of 50 x 104 cells/well in 12-well plates and treated with vehicle, 5 ng/ml TGFβ1 (R&D Systems; #240-B-010) and 100ng/ml BMP2 (R&D Systems; #355-BM-010) for 24 hours.

value: articular chondrocytes

tag: disease condition

value: Vehicle


title: 85, Rattus norvegicus, Mammary Gland/Tissue (female only)

description: Library name: itox000085

source_name: Mammary Gland/Tissue (female only)

value: Mammary Gland/Tissue (female only)


title: MRE-seq Vehicle replicate 2

description: MRE-seq


title: 1653, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001653


title: 84, Rattus norvegicus, Brown Fat (intrascapular)

description: Library name: itox000084

source_name: Brown Fat (intrascapular)

value: Brown Fat (intrascapular)


title: 1654, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001654


title: MRE-seq Vehicle replicate 1

description: MRE-seq


title: 1655, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001655


title: 1649, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001649


title: Pa01c-A

description: Library name: Sample 1

value: Pancreatic cancer

value: Pa01C (KRASG12D)


title: MRE-seq TGFb replicate 3

description: MRE-seq

value: TGFb


title: Salinity 383, 18 hours, Replicate 3

city: Berkeley

first: Lisa

last: Alvarez-Cohen

state: CA

address: Davis Hall

department: Department of Civil and Environmental Engineering

institute: University of California, Berkeley

description: Library name: s383_18h_Rep3

data_processing:
The sequence reads were first preprocessed by "scythe" for adapter trimming and "sickle" for quality trimming.
The trimmed sequence reads were then aligned to the genome of Dhc195, using the aligner "STAR".
The count data from reads alignment was then collated into raw count files that include the counts of every gene in each sample, followed by statistical analysis using R.
Assembly: Dehalococcoides mccartyi strain 195 (Assembly ASM1190v1)
Supplementary files format and content: Tab-delimited text file containing raw read counts for each gene across all samples.

organism: Dehalococcoides mccartyi

source_name: Salinity 383 perturbation at 18 hours

extract_protocol:
RNA was extracted from cells collected from ~100 mL of culture filtered onto MDI Nylon-66 Disc membranes (47 mm, 0.2 mm, Fisher Scientific). RNA extraction and purification was done using Qiagen RNase kit.
Library construction and RNA-Seq were performed at QB3 Functional Genomics Laboratory at UC Berkeley (http://qb3.berkeley.edu/qb3/fgl/) following their protocol.

value: Bacterial

value: WT

value: Salinity 383

tag: timepoint

value: 18 hours


title: Pa01c-B

description: Library name: Sample 2

value: Yes


title: 87, Rattus norvegicus, Skin (inguinal)

description: Library name: itox000087

source_name: Skin (inguinal)

value: Skin (inguinal)


title: 86, Rattus norvegicus, Brain - Spinal cord (cervical)

description: Library name: itox000086

source_name: Brain - Spinal cord (cervical)

value: Brain - Spinal cord (cervical)


title: Salinity 383, 18 hours, Replicate 1

description: Library name: s383_18h_Rep1


title: 1656, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001656


title: 89, Rattus norvegicus, Adrenal Gland

description: Library name: itox000089

source_name: Adrenal Gland

value: Adrenal Gland


title: MRE-seq TGFb replicate 2

description: MRE-seq


title: 1657, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001657


title: MRE-seq TGFb replicate 1

description: MRE-seq


title: Salinity 383, 18 hours, Replicate 2

description: Library name: s383_18h_Rep2


title: 90, Rattus norvegicus, DRG-L4

description: Library name: itox000090


title: Salinity 383, 12 hours, Replicate 3

description: Library name: s383_12h_Rep3

source_name: Salinity 383 perturbation at 12 hours

value: 12 hours


title: Salinity 383, 12 hours, Replicate 2

description: Library name: s383_12h_Rep2


title: 1658, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001658


title: Salinity 383, 12 hours, Replicate 1

description: Library name: s383_12h_Rep1


title: MRE-seq BMP2 replicate 3

description: MRE-seq


title: 91, Rattus norvegicus, Brain-Striatum

description: Library name: itox000091

source_name: Brain-Striatum

value: Brain-Striatum


title: 1659, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001659


title: 88, Rattus norvegicus, Urinary Bladder

description: Library name: itox000088

source_name: Urinary Bladder

value: Urinary Bladder


title: 93, Rattus norvegicus, Spleen

description: Library name: itox000093

source_name: Spleen

value: Spleen


title: 92, Rattus norvegicus, Pituitary

description: Library name: itox000092

source_name: Pituitary

value: Pituitary


title: 1661, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001661


title: Salinity 293, 18 hours, Replicate 3

description: Library name: s293_18h_Rep3

source_name: Salinity 293 perturbation at 18 hours

value: Salinity 293


title: MRE-seq BMP2 replicate 1

description: MRE-seq

value: articular chondrocytes


title: Salinity 293, 18 hours, Replicate 2

description: Library name: s293_18h_Rep2


title: RNA-seq Vehicle replicate 2

description: Bulk RNA-seq

data_processing:
RNA-Seq reads were trimmed by cutadapt first, then trimmed read were aligned against mouse genome (mm10) using STAR v2.4.2a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread: featureCount (5) with mouse GENCODE gene annotation (M15).
All gene-level transcript counts were then imported into DESeq2, and normalization method was used to adjust for differences in library size

extract_protocol:
Total RNA was extracted using E.Z.N.A. Total RNA kit (Omega Bio-Tek, R6834) with DNase 1 following the manufacturer’s instructions.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq4000 at the Genome Technology Access Center of Washington University in St. Louis.

value: Vehicle


title: Salinity 293, 18 hours, Replicate 1

description: Library name: s293_18h_Rep1


title: 94, Rattus norvegicus, Stomach (glandular)

description: Library name: itox000094

source_name: Stomach (glandular)

value: Stomach (glandular)


title: MRE-seq BMP2 replicate 2

description: MRE-seq


title: RNA-seq Vehicle replicate 1

description: Bulk RNA-seq


title: 1662, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001662


title: 1660, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001660


title: 1663, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001663


title: 95, Rattus norvegicus, Cecum

description: Library name: itox000095

source_name: Cecum

value: Cecum


title: 96, Rattus norvegicus, Colon (mid)

description: Library name: itox000096

source_name: Colon (mid)

value: Colon (mid)


title: RNA-seq TGFb replicate 3

description: Bulk RNA-seq

value: TGFb


title: Salinity 293, 12 hours, Replicate 3

description: Library name: s293_12h_Rep3

source_name: Salinity 293 perturbation at 12 hours

value: Bacterial

value: WT


title: RNA-seq TGFb replicate 1

description: Bulk RNA-seq

source_name: femoral head


title: Salinity 293, 12 hours, Replicate 1

description: Library name: s293_12h_Rep1


title: 1361, Mus musculus, Artery- Aorta (abdominal descending),Artery- Aorta (abdominal descending)

description: Library name: itox001361


title: RNA-seq BMP2 replicate 3

description: Bulk RNA-seq


title: Salinity 293, 12 hours, Replicate 2

description: Library name: s293_12h_Rep2


title: Control, 18 hours, Replicate 3

description: Library name: Control_18h_Rep3

source_name: Control condition at 18 hours

value: Control

value: 18 hours


title: 1362, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001362


title: 99, Rattus norvegicus, Vagina

description: Library name: itox000099

source_name: Vagina

value: Vagina


title: 97, Rattus norvegicus, Liver (left lateral lobe)

description: Library name: itox000097

source_name: Liver (left lateral lobe)

value: Liver (left lateral lobe)


title: RNA-seq BMP2 replicate 1

description: Bulk RNA-seq


title: 1363, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001363


title: 1664, Mus musculus, Brain - Hypothalamus,Brain - Hypothalamus

description: Library name: itox001664


title: 100, Rattus norvegicus, Ovary (left)

description: Library name: itox000100

source_name: Ovary (left)

value: Ovary (left)


title: Control, 18 hours, Replicate 2

description: Library name: Control_18h_Rep2


title: 1364, Mus musculus, Artery- Aorta (abdominal descending),Artery- Aorta (abdominal descending)

description: Library name: itox001364


title: 101, Rattus norvegicus, Oviduct (Fallopian tube)

description: Library name: itox000101

source_name: Oviduct (Fallopian tube)

value: Oviduct (Fallopian tube)


title: 1366, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001366


title: Control, 12 hours, Replicate 3

description: Library name: Control_12h_Rep3

source_name: Control condition at 12 hours

value: 12 hours


title: M520 Rep2

city: Milwaukee

first: Anooj

last: Arkatkar

state: WI

address: 8701 W Watertown Plank Rd.

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

description:
Library name: M520 2
10X Genomics

data_processing:
Demultiplexing, barcode processing, and counting was done using CellRanger v.9.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: mRatBN7.2
Supplementary files format and content: h5 archive file of CellRanger feature barcode matrices

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Hearts were digested through Langendorf perfusion of Collagenase II and ventricular tissue was transferred to lysis buffer (320 mM sucrose, 10mM Tris-HCl pH 8, 5 mM CaCl2, 5 mM Magnesium Acetate, 2 mM EDTA, 0.5 mM EGTA, 1 mM DTT, 1x Halt Protease Inhibitor, 0.2 U/μL RNAse inhibitor, 0.1% Triton X-100). Tissue was homogenized by dounce (20x A pestle, 20x B pestle) and Tissue-Tearor (BioSpec), and strained through successive 70, 40, and 20 μm filters. Nuclei were resuspended in FACS buffer (1x PBS, 1% BSA, 0.2 U/μL RNAse inhibitor), labeled with DAPI, and isolated using a FACSMelody (BD Biosciences).
Library construction was performed according to manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1). Briefly, nuclei were added to master mix and loaded onto a Chromium Next GEM Chip G targeting along with partitioning oil and barcoded gel beads to generate Gel Beads-in-emulsion (GEMs). Partitioned nuclei were lysed and GEM incubation produced full-length cDNA from polyadenylated mRNA containing an Illumina R1 primer sequence, unique molecular identifier (UMI), and a 10X barcode. The pooled barcoded cDNA was purified by Silane magnetic beads and amplified by PCR. Final libraries were generated by enzymatic fragmentation, size selection, and addition of P5, P7, i7, and i5 sample indices and an Illumina R2 primer sequence.

value: Heart

value: Female

tag: strain


title: RNA-seq BMP2 replicate 2

description: Bulk RNA-seq

value: articular chondrocytes


title: M520 Rep1

description:
Library name: M520 1
10X Genomics


title: Control, 18 hours, Replicate 1

description: Library name: Control_18h_Rep1


title: 98, Rattus norvegicus, Brain - Cerebellum

description: Library name: itox000098

source_name: Brain - Cerebellum

value: Brain - Cerebellum


title: 146, Rattus norvegicus, Eyes-cornea

description: Library name: itox000146

source_name: Eyes-cornea

value: Eyes-cornea


title: 147, Rattus norvegicus, Muscle - Skeletal (gastrocnemius)

description: Library name: itox000147

source_name: Muscle - Skeletal (gastrocnemius)

value: Muscle - Skeletal (gastrocnemius)


title: Control, 12 hours, Replicate 2

description: Library name: Control_12h_Rep2


title: 1367, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001367


title: F344 Rep2

description:
Library name: F344 2
10X Genomics


title: 148, Rattus norvegicus, Peripheral Nerve (sciatic)

description: Library name: itox000148

source_name: Peripheral Nerve (sciatic)

value: Peripheral Nerve (sciatic)


title: F344 Rep1

description:
Library name: F344 1
10X Genomics


title: 1368, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001368


title: 1365, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001365


title: BN-Lx Rep2

description:
Library name: BN 2
10X Genomics

value: BN-Lx


title: 1369, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001369


title: 149, Rattus norvegicus, Peripheral Nerve (tibial)

description: Library name: itox000149

source_name: Peripheral Nerve (tibial)

value: Peripheral Nerve (tibial)


title: BN-Lx Rep1

description:
Library name: BN 1
10X Genomics

value: WT


title: Mouse cortex snRNA-seq, pregnant female (E13.5), replicate 1

city: Ecublens

first: Luca

last: Fusar Bassini

state: Vaud

address: EPFL - SV Building

department: BMI

country: Switzerland

institute: EPFL

description:
Library name: LBA_Pregnant_Female_1
Element Biosciences AVITI24 sequencer; 10x Chromium Next GEM Single Cell 3' v4 (GEMX); condition: pregnant E13.5; sex: female; age: ~12 weeks; strain: C57BL/6JRj; tissue: cortex; nuclei recovered: 6680; mean reads per cell: 50555; median genes per cell: 4088; sequencing saturation: 28.3%

data_processing:
Cell Ranger 10.0.0 (10x Genomics) with intronic reads included for nuclear RNA quantification
Reference genome: GRCm39-2024-A (mouse genome GRCm39 with Ensembl gene annotations, filtered by 10x Genomics)
Assembly: GRCm39
Supplementary files format and content: Tab-delimited MEX format (10x Genomics Cell Ranger filtered_feature_bc_matrix): barcodes.tsv.gz contains cell barcodes, features.tsv.gz contains gene identifiers (Ensembl ID and gene symbol), matrix.mtx.gz contains the filtered UMI count matrix in Matrix Market format

source_name: cortex

extract_protocol:
Nuclei were isolated from microdissected cortex tissue using ice-cold materials and buffers. Tissue pieces were resuspended in 2 mL of nuclear isolation medium (NIM: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl pH 7.5, 5 ng/mL actinomycin D, 1 mM DTT, 100 U/mL murine RNase inhibitor, supplemented with 0.1% v/v NP-40). Tissue was homogenized on a MACS OctoDissociator (Miltenyi) using the 4C_nuclei_1 programme, then passed through a 100 um strainer and centrifuged at 1000g for 8 min. The pellet was resuspended in 500 uL NIM, mixed with 600 uL of 50% iodixanol to a final concentration of 30%, and centrifuged at 10,000g for 20 min to pellet nuclei. Nuclei were resuspended in storage buffer (0.5% w/v BSA, 2 mM MgCl2, 1 mM DTT, 200 U/mL murine RNase inhibitor, 5 ng/mL actinomycin D) to ~1200 nuclei/uL and filtered through a 40 um Flowmi strainer (Bel-Art).
Single-nucleus encapsulation and library preparation were performed by the Gene Expression Core Facility (GECF) at EPFL. Nuclei were loaded into a Chromium X controller (10x Genomics) targeting ~8,000 nuclei per sample. Libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v4 (GEMX) following manufacturer protocol (CG000731 Rev B). cDNA amplification: 11 PCR cycles. Library quality was assessed by Qubit and Fragment Analyzer. Final indexing PCR: 12-13 cycles with 10x Genomics Dual Index Kit TT Set A. Libraries were pooled and sequenced on an Element Biosciences AVITI24 system (Cloudbreak Freestyle chemistry) with read configuration 28, 10i, 10i, 90 bp. Total yield: ~1,388 million read pairs (Q30: 96.9%).

treatment_protocol: Non-pregnant control and pregnant (embryonic day E13.5) female C57BL/6JRj mice (~12 weeks old) were used. For pregnant mice, timed matings were set up and pregnancy was confirmed. Mice were sacrificed at E13.5.

value: cortex

value: wildtype

value: pregnant E13.5


title: 150, Rattus norvegicus, Bone marrow - femoral scoop

description: Library name: itox000150

source_name: Bone marrow - femoral scoop

value: Bone marrow - femoral scoop


title: Mouse cortex snRNA-seq, pregnant female (E13.5), replicate 2

description:
Library name: LBA_Pregnant_Female_2
Element Biosciences AVITI24 sequencer; 10x Chromium Next GEM Single Cell 3' v4 (GEMX); condition: pregnant E13.5; sex: female; age: ~12 weeks; strain: C57BL/6JRj; tissue: cortex; nuclei recovered: 6847; mean reads per cell: 49375; median genes per cell: 4102; sequencing saturation: 30%


title: 1370, Mus musculus, Artery - Aorta (thoracic),Artery - Aorta (thoracic)

description: Library name: itox001370


title: 151, Rattus norvegicus, Esophagus (mid)

description: Library name: itox000151

source_name: Esophagus (mid)

value: Esophagus (mid)


title: Control, 12 hours, Replicate 1

description: Library name: Control_12h_Rep1

value: Bacterial

value: Control


title: WY_input,input

city: Nantong

first: Xingmin

last: Wang

state: Jiangsu

address: 399 Century Ave.

department: Institute of Genetics and Reproductive Medicine

institute: Nantong Maternity and Child Healthcare Hospital

data_processing:
ChIP-Seq reads were trimmed using Trimmomatic v0.33, discarding reads left with < 20bp
ChIP-Seq reads were aligned to the Rattus_norvegicus.Rnor_5.0.77 using Bowtie version 2.5.1
The aligned bam were converted to bigwig file using deeptools v3.5.1
Assembly: Rattus_norvegicus.Rnor_5.0.77
Supplementary files format and content: bigWig

source_name: Small intestine

extract_protocol:
Cells were harvested using PBS containing the Proteinase Inhibitor Cocktail (Cell Signaling Technology, Shanghai, China). Cells were then crosslinked using 1% formaldehyde at room temperature for 10 min. The reaction was terminated by adding 1.25 M glycine. Cells were then resuspended in lysis buffer and kept on ice for 10 min. Cell lysates were sonicated at 30% power in 3 second intervals for a total of 7 sessions using a VCX150 ultrasonic cell crusher (Sonics & Materials, Newton, CT, USA). Following centrifugation at 14,000 ×g and 4°C for 10 min, the supernatant was subjected to chromatin immunoprecipitation (ChIP) using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. Acetyl-Histone H3 (Lys27) (D5E4) XP rabbit monoclonal antibody (Abmart, Shanghai, China) was employed for the ChIP assay.
After determining the yield and the band type, purified and constructed the library

value: Small intestine

value: epithelial cells


title: 1371, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001371

source_name: Heart - Atrium,Heart - Atrium

value: Heart - Atrium,Heart - Atrium


title: WY_h3k27,ChIP


title: Shroom3 1073S rep1

description: Library name: S338

data_processing:
Raw sequencing data was processed using Nextflow v.25.10.2 with the nf-core/rnaseq pipeline version 3.22.2 for quality control (FastQC v0.12.1), read trimming (Trimgalore v0.6.10), alignment (STAR v2.7.10a), and quantification (salmon v.1.10.3).
Quantification files were loaded into DESeq2 (v1.44.0) using tximport (v1.32.0) for differential expression analysis.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file is the quantification file output from salmon. Columns correspond to transcript ID, transcript length (bp), estimated effective transcript length (bp), transcript abundance (transcripts per million or TPM), and transcript counts.

source_name: Neonatal rat ventricular cardiomyocyte

growth_protocol: Cardiomyocytes were isolated from the neonatal HXB23 rats (postnatal day 0) and maintained with DMEM supplemented with 15% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Cells were lysed in 1 mL TRIzol solution. The total RNA was isolated using TRIzol RNA isolation protocol (Invitrogen).
Libraries were prepared using the Takara SMART-Seq mRNA LP kit P/N 634769 according to the manufacturer’s directions.  Final libraries were QC’d using the Agilent Fragment Analyzer.

treatment_protocol: Cells were transduced with GFP, Shroom3 variant 1073G, and Shroom3 variant 1073S AAVs for 48 hours

value: Neonatal rat ventricular cardiomyocyte


title: un_input,input,input


title: 152, Rattus norvegicus, Heart - Atrium

description: Library name: itox000152

source_name: Heart - Atrium

value: Heart - Atrium


title: 1372, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001372

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human


title: 153, Rattus norvegicus, Heart - Ventricle (left)

description: Library name: itox000153

source_name: Heart - Ventricle (left)

value: Heart - Ventricle (left)


title: Mouse cortex snRNA-seq, non-pregnant female, replicate 1

description:
Library name: LBA_Female_1
Element Biosciences AVITI24 sequencer; 10x Chromium Next GEM Single Cell 3' v4 (GEMX); condition: non-pregnant control; sex: female; age: ~12 weeks; strain: C57BL/6JRj; tissue: cortex; nuclei recovered: 6932; mean reads per cell: 41064; median genes per cell: 3940; sequencing saturation: 26.1%

value: non-pregnant control


title: 1374, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001374


title: Shroom3 1073G rep3

description: Library name: S337


title: un_h3k27,ChIP


title: Shroom3 1073G rep2

description: Library name: S336


title: 155, Rattus norvegicus, Brain - Hypothalamus

description: Library name: itox000155

source_name: Brain - Hypothalamus

value: Brain - Hypothalamus


title: 1373, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001373


title: OG_input,input


title: 156, Rattus norvegicus, Thymus

description: Library name: itox000156

source_name: Thymus

value: Thymus


title: 154, Rattus norvegicus, Lung (left lobe)

description: Library name: itox000154

source_name: Lung (left lobe)

value: Lung (left lobe)


title: 1376, Mus musculus, Heart - Ventricle (left),Heart - Ventricle (left)

description: Library name: itox001376


title: 1375, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001375


title: Mouse cortex snRNA-seq, non-pregnant female, replicate 2

description:
Library name: LBA_Female_2
Element Biosciences AVITI24 sequencer; 10x Chromium Next GEM Single Cell 3' v4 (GEMX); condition: non-pregnant control; sex: female; age: ~12 weeks; strain: C57BL/6JRj; tissue: cortex; nuclei recovered: 6357; mean reads per cell: 57284; median genes per cell: 4527; sequencing saturation: 36%

value: cortex


title: OG_h3k27,ChIP


title: Shroom3 1073G rep1

description: Library name: S335


title: 1379, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001379


title: 1377, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001377


title: ctl_input,input


title: 158, Rattus norvegicus, Tongue

description: Library name: itox000158

source_name: Tongue

value: Tongue


title: GFP rep3

description: Library name: S334

value: Ad-GFP


title: ctl_h3k27,ChIP


title: Shroom3 1073S rep3

description: Library name: S340


title: 160, Rattus norvegicus, Artery - Aorta (thoracic)

description: Library name: itox000160

source_name: Artery - Aorta (thoracic)

value: Artery - Aorta (thoracic)


title: 1381, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001381


title: 12286, Sus scrofa, Temporal lobe,Temporal lobe

description: Library name: itox012286

organism: Sus scrofa

source_name: Temporal lobe,Temporal lobe

value: Temporal lobe,Temporal lobe


title: 1382, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001382


title: 162, Rattus norvegicus, Brown Fat (intrascapular)

description: Library name: itox000162

source_name: Brown Fat (intrascapular)

value: Brown Fat (intrascapular)


title: 12284, Sus scrofa, Vagina,Vagina

description: Library name: itox012284

source_name: Vagina,Vagina

value: Vagina,Vagina


title: 159, Rattus norvegicus, Trachea

description: Library name: itox000159

source_name: Trachea

value: Trachea


title: 157, Rattus norvegicus, Thyroid/parathyroid

description: Library name: itox000157

source_name: Thyroid/parathyroid

value: Thyroid/parathyroid


title: 12287, Sus scrofa, Blood,Blood

description: Library name: itox012287

source_name: Blood,Blood

value: Blood,Blood


title: 1380, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001380

value: Heart - Atrium,Heart - Atrium


title: 3p WT cell, ribosome profiling, biological replicate 1

city: West Haven

first: Wenxue

state: CT     Connecticut

address: 300 Heffernernan Dr Bldg A42,, Bldg 840, Room ABC 367

institute: Yale University

description:
Library name: Sample 13
Chr3_isogenic_Riboseq.xlsx

data_processing:
Total mRNA:RNA sequencing from chromosoe 3/chromosome 8 aneuploidy system data was processed using the nf-core/rnaseq pipeline (v3.14.0). The RNAseq were also aligned to the human genome GRCh38. Ribosome Profiling: The analysis of ribosome footprint data was performed using RiboDoc (v0.9.1.1) on Podman (v3.4.4). RPFs ranging from 25 to 45 nucleotides were aligned to the human genome (GRCh38) within the analysis pipeline. For identification and removal of human rRNA contaminants, the SILVA database was utilized.
Assembly: GRCh38
Supplementary files format and content: TPM values:Chr8_isogenic_system_mRNA.xlsx
Supplementary files format and content: TPM values:Chr3_isogenic_system_mRNA.xlsx
Supplementary files format and content: raw counts for each sample:Chr3_isogenic_Riboseq.xlsx
Library strategy: Ribo-Seq

source_name: lung epithelial cell

extract_protocol:
Total mRNA:Cells from the chromosome 3 isogenic aneuploidy system (3p loss/3q gain/WT) were washed three times with PBS, snap-frozen, and then lysed with the QIAShredder columns (#79654, QIAGEN) according to the manufacturer’s instructions. For each cell line, three biological replicates were processed. Total RNA was isolated with the Qiagen RNeasy Mini Kit (#74104, QIAGEN), including the DNA digestion step using the RNAase-Free DNAase set kit (#79254, QIAGEN). Ribosome Profiling:3p loss cells and 3p WT cells were subjected to ribosome profiling. For each cell line, three biological replicates were processed. Cells were cultured under standard conditions until they reached 80% confluency. They were then treated with 10 µg/µL cycloheximide for 5 minutes at 37°C. Following treatment, cells were harvested and lysed. Ribosome-protected fragments (RPFs) were generated and purified using RiboLace Pro (Immagina Biotech; catalog # RL00P-12). The RPFs underwent end repair using the Small RNA Library Prep Kit (NEB; catalog # E7300S) and size selection using the RNA Clean & Concentrator-5 Kit (Zymo; catalog # R1015) to enrich RNA fragments sized smaller than 200 nt.
Total mRNA:PolyA isolation and sequencing library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit (#E7760, NEB). Each set of samples were pooled and sequenced in one lane of HiSeq2500 RR, 100 basepair paired end. For the transcriptome analysis of chromosome 8 isogenic aneuploidy system (8p loss/8p WT), total mRNA samples were prepared as described above with three biological replicates, and the following library preparation was conducted in Yale Center for Genomic Analysis (YCGA). Sequencing was conducted on NovaSeq X Plus platform (Illumina). Ribosome Profiling:RPFs were reverse transcribed and tagged by Small RNA Library Prep Kit (NEB; catalog # E7300S) following the recommended conditions. RPF libraries were then amplified by Phusion High-Fidelity PCR Kit (NEB; E0553L). Further size selection and purification of RPF libraries was conducted using Mag-Bind TotalPure NGS beads (Omega Bio-tek; catalog # M1378-01) at a beads-to-product ratio of 1.3:1. The NGS libraries were quantified using the sparQ Universal Library Quant Kit (Quantabio; catalog # 95210-100) and analyzed using a TapeStation (Agilent) before being sequenced with NovaSeq X Plus (Illumina) in YCGA or NextSeq 1000 system in Quintara Biosciences. The target sequencing depth for the RPF libraries was 200 million reads per library.

value: lung epithelial cell

value: 3p WT


title: 3p loss cell, ribosome profiling, biological replicate 1

description:
Library name: Sample 10
Chr3_isogenic_Riboseq.xlsx

value: 3p loss


title: GFP rep1

description: Library name: S332

value: Neonatal rat ventricular cardiomyocyte


title: 161, Rattus norvegicus, Artery- Aorta (abdominal descending)

description: Library name: itox000161

source_name: Artery- Aorta (abdominal descending)

value: Artery- Aorta (abdominal descending)


title: Shroom3 1073S rep2

description: Library name: S339


title: GFP rep2

description: Library name: S333


title: 12288, Sus scrofa, Temporal Lobe,Temporal Lobe

description: Library name: itox012288

source_name: Temporal Lobe,Temporal Lobe

value: Temporal Lobe,Temporal Lobe


title: 12285, Sus scrofa, Thyroid Gland,Thyroid Gland

description: Library name: itox012285

source_name: Thyroid Gland,Thyroid Gland

value: Thyroid Gland,Thyroid Gland


title: 1378, Mus musculus, Heart - Atrium,Heart - Atrium

description: Library name: itox001378

source_name: Heart - Atrium,Heart - Atrium


title: 1491, Mus musculus, Adrenal Gland,Adrenal Gland

description: Library name: itox001491

source_name: Adrenal Gland,Adrenal Gland

value: Adrenal Gland,Adrenal Gland


title: 163, Rattus norvegicus, Mammary Gland/Tissue (female only)

description: Library name: itox000163

source_name: Mammary Gland/Tissue (female only)

value: Mammary Gland/Tissue (female only)


title: VICs, CALD1 siRNA, Osteogenesis medium-3

city: Toon

first: Tomohisa

last: Sakaue

address: Shitsukawa

department: Cardiovascular and Thoracic Surgery

country: Japan

institute: Ehime University

description: Library name: Sample 9

data_processing:
Raw reads were quality-checked using FastQC, trimmed using Trimmomatic, and aligned to the human genome (GRCh38) using CLC Genomics Workbench (QIAGEN). The sequencing data were processed to calculate the number of fragments per kilobase of exon per million fragments mapped or transcripts per million for relative expression analysis.
Assembly: human genome (GRCh38)
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: Valve interstitial cells

growth_protocol: VICs at 80% confluency, at passage number two were stimulated with StemPro™ Osteogenesis Differentiation Medium　(Thermo Fisher Scientific., Catalog No. A10007201) or MesenPRO RS™ Medium　(Thermo Fisher Scientific, Catalog No. 12746012) as a control for 4 w under normoxic condition.

extract_protocol:
Control VICs and CALD1-knockdown VICs cultured in Osteogenesis Differentiation Medium or MesenPRO RS™ Medium for 4 w were collected using 700 µL of QIAzol Lysis Reagent (QIAGEN). Total RNA was purified using the miRNeasy Micro Kit (QIAGEN) according to the manufacturer’s instructions.
for library preparation, the KAPA mRNA Capture Kit (KAPA, Catalog No. KK8440) and MGIEasy Fast RNA Library Prep Set (MGI, Catalog No. 940-000889-00) were used. The constructed RNA libraries were sequenced on a DNBSEQ-T7RS using the DNBSEQ-T7RS High-throughput Sequencing Set.

treatment_protocol: Transfection of 25 nM small interfering RNA (siRNA) for Control (Sigma-Aldrich, MISSION® siRNA Universal Negative Control #1), 25 nM CALD1#1 siRNA (Sigma-Aldrich, SASI_Hs01_0010-3337/CALD1), or 25 nM CALD1#2 siRNA (Sigma-Aldrich, SASI_Hs01_0010-3339/CALD1) was performed using Lipofectamine RNAiMAX reagent (Thermo Fisher Scientific) according to the manufacturer’s protocol. siRNA transfection and medium change were performed every week.

value: Valve interstitial cells


title: 164, Rattus norvegicus, Brain - Spinal cord (cervical)

description: Library name: itox000164

source_name: Brain - Spinal cord (cervical)

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

value: Brain - Spinal cord (cervical)


title: 165, Rattus norvegicus, Skin (inguinal)

description: Library name: itox000165

source_name: Skin (inguinal)

value: Skin (inguinal)


title: 12290, Sus scrofa, Thymus Gland,Thymus Gland

description: Library name: itox012290

source_name: Thymus Gland,Thymus Gland

value: Thymus Gland,Thymus Gland


title: VICs, CALD1 siRNA, Osteogenesis medium-1

description: Library name: Sample 7


title: 1494, Mus musculus, Pituitary,Pituitary

description: Library name: itox001494

source_name: Pituitary,Pituitary

value: Pituitary,Pituitary


title: 1492, Mus musculus, Pituitary,Pituitary

description: Library name: itox001492


title: VICs, CALD1 siRNA, Osteogenesis medium-2

description: Library name: Sample 8


title: 1493, Mus musculus, Pituitary,Pituitary

description: Library name: itox001493


title: 12295, Sus scrofa, Uterus,Uterus

description: Library name: itox012295

source_name: Uterus,Uterus

value: Uterus,Uterus


title: VICs, Control siRNA, Osteogenesis medium-3

description: Library name: Sample 6


title: 167, Rattus norvegicus, Urinary Bladder

description: Library name: itox000167

source_name: Urinary Bladder

value: Urinary Bladder


title: 1495, Mus musculus, Pituitary,Pituitary

description: Library name: itox001495


title: VICs, Control siRNA, Osteogenesis medium-1

description: Library name: Sample 4


title: 12291, Sus scrofa, Tongue,Tongue

description: Library name: itox012291

source_name: Tongue,Tongue

value: Tongue,Tongue


title: 1496, Mus musculus, Pituitary,Pituitary

description: Library name: itox001496


title: 12293, Sus scrofa, Trachea,Trachea

description: Library name: itox012293

source_name: Trachea,Trachea

value: Trachea,Trachea


title: VICs, Control siRNA, Osteogenesis medium-2

description: Library name: Sample 5


title: 166, Rattus norvegicus, Ureter

description: Library name: itox000166

source_name: Ureter

value: Ureter


title: 12294, Sus scrofa, Bladder,Bladder

description: Library name: itox012294

source_name: Bladder,Bladder

value: Bladder,Bladder


title: 212, Rattus norvegicus, Lymph node (mesenteric)

description: Library name: itox000212

source_name: Lymph node (mesenteric)

value: Lymph node (mesenteric)


title: VICs, Control siRNA, basal medium-2

description: Library name: Sample 2


title: VICs, Control siRNA, basal medium-3

description: Library name: Sample 3


title: 211, Rattus norvegicus, Colon (mid)

description: Library name: itox000211

source_name: Colon (mid)

value: Colon (mid)


title: 12275, Sus scrofa, Temporal Lobe,Temporal Lobe

description: Library name: itox012275

source_name: Temporal Lobe,Temporal Lobe

value: Temporal Lobe,Temporal Lobe


title: 1498, Mus musculus, Pituitary,Pituitary

description: Library name: itox001498


title: 12296, Sus scrofa, Uterus,Uterus

description: Library name: itox012296


title: 213, Rattus norvegicus, Liver (left lateral lobe)

description: Library name: itox000213

source_name: Liver (left lateral lobe)

value: Liver (left lateral lobe)


title: 1499, Mus musculus, Pituitary,Pituitary

description: Library name: itox001499


title: 1497, Mus musculus, Pituitary,Pituitary

description: Library name: itox001497


title: 1500, Mus musculus, Pituitary,Pituitary

description: Library name: itox001500


title: 11765, Sus scrofa, Pancreas,Pancreas

description: Library name: itox011765

source_name: Pancreas,Pancreas

value: Pancreas,Pancreas


title: 12276, Sus scrofa, Thalamus,Thalamus

description: Library name: itox012276

source_name: Thalamus,Thalamus

value: Thalamus,Thalamus


title: TA muscle from control (Cre) male mouse 4

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

description:
Library name: R318_M_Cre_TA
Column name in gene_counts_matrix.txt: R318_M_Cre_TA

data_processing:
Paired-end sequencing (read length: 2x150 bp) was performed by NovoGene using an Illumina sequencer.
Raw RNA-seq reads were quality filtered and trimmed using Trimmomatic.
Trimmed reads were aligned to the mouse reference genome using STAR.
Gene-level count summaries were generated from STAR output and differential expression analysis was performed using DESeq2.
Submitted FASTQ files correspond to quality-filtered and trimmed reads used for alignment.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing gene-level raw counts for all samples (gene_counts_matrix.txt).
Supplementary files format and content: Tab-delimited text file containing sample-level correlation/QC summary values (sample_correlation_matrix.tsv).

source_name: tibialis anterior muscle

growth_protocol: Specific skeletal muscle TRF2 KO mice (HSA-Cre+/-; Terf2-/-) were generated as previously described (Robin et al., 2020). TRF2 floxed mice from the Jackson Laboratory (strain B6;129P2-Terf2tm1Tdl/J) were backcrossed with C57BL/6 for 6 generations and crossed with the HSA-Cre+/- strain expressing Cre recombinase under the control of the Human Skeletal Actin promoter, specifically expressed in striated muscle fibers. Animal procedures were approved by the appropriate ethics committees and regulatory authorities.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.
Libraries were prepared by NovoGene from total RNA for paired-end Illumina sequencing.

treatment_protocol: Mice were euthanized by isoflurane-induced loss of consciousness followed by cervical dislocation. Gastrocnemius-plantaris-soleus and tibialis anterior muscles were dissected, snap-frozen in liquid nitrogen, and stored at -80°C.

value: tibialis anterior muscle

value: HSA-Cre+/-

value: Male

tag: age

value: 8 months


title: 1501, Mus musculus, Pituitary,Pituitary

description: Library name: itox001501

value: Pituitary,Pituitary


title: 215, Rattus norvegicus, Adipose - Visceral (Omentum)

description: Library name: itox000215

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read counts mapped to human

source_name: Adipose - Visceral (Omentum)

value: Adipose - Visceral (Omentum)


title: 214, Rattus norvegicus, Ileum

description: Library name: itox000214

source_name: Ileum

value: Ileum


title: 11766, Sus scrofa, Cerebral Cortex,Cerebral Cortex

description: Library name: itox011766

source_name: Cerebral Cortex,Cerebral Cortex

value: Cerebral Cortex,Cerebral Cortex


title: TA muscle from control (Cre) male mouse 5

description:
Library name: R319_M_Cre_TA
Column name in gene_counts_matrix.txt: R319_M_Cre_TA


title: 11767, Sus scrofa, Skin,Skin

description: Library name: itox011767

source_name: Skin,Skin

value: Skin,Skin


title: 216, Rattus norvegicus, Testis (tubules\, without capsule)

description: Library name: itox000216

source_name: Testis (tubules\, without capsule)

value: Testis (tubules\, without capsule)


title: 11768, Sus scrofa, Duodenum,Duodenum

description: Library name: itox011768

source_name: Duodenum,Duodenum

value: Duodenum,Duodenum


title: 217, Rattus norvegicus, Epididymus (head)

description: Library name: itox000217

source_name: Epididymus (head)

value: Epididymus (head)


title: 1502, Mus musculus, Pituitary,Pituitary

description: Library name: itox001502

source_name: Pituitary,Pituitary


title: 218, Rattus norvegicus, Seminal Vesicles

description: Library name: itox000218

source_name: Seminal Vesicles

value: Seminal Vesicles


title: VICs, Control siRNA, basal medium-1

description: Library name: Sample 1

source_name: Valve interstitial cells

value: Valve interstitial cells


title: 1503, Mus musculus, Pituitary,Pituitary

description: Library name: itox001503


title: 11885, Sus scrofa, Heart,Heart

description: Library name: itox011885

source_name: Heart,Heart

value: Heart,Heart


title: 1504, Mus musculus, Pituitary,Pituitary

description: Library name: itox001504


title: 11751, Sus scrofa, Hippocampus,Hippocampus

description: Library name: itox011751

source_name: Hippocampus,Hippocampus

value: Hippocampus,Hippocampus


title: TA muscle from control (Cre) male mouse 2

description:
Library name: R245_M_Cre_TA
Column name in gene_counts_matrix.txt: R245_M_Cre_TA


title: 1505, Mus musculus, Pituitary,Pituitary

description: Library name: itox001505


title: TA muscle from control (Cre) male mouse 1

description:
Library name: R321_M_Cre_TA
Column name in gene_counts_matrix.txt: R321_M_Cre_TA


title: TA muscle from control (Cre) female mouse 5

description:
Library name: R320_F_Cre_TA
Column name in gene_counts_matrix.txt: R320_F_Cre_TA

value: Female


title: 219, Rattus norvegicus, Epididymus (tail)

description: Library name: itox000219

source_name: Epididymus (tail)

value: Epididymus (tail)


title: 11769, Sus scrofa, Adipose,Adipose

description: Library name: itox011769

source_name: Adipose,Adipose

value: Adipose,Adipose


title: TA muscle from control (Cre) female mouse 4

description:
Library name: R249_F_Cre_TA
Column name in gene_counts_matrix.txt: R249_F_Cre_TA

value: tibialis anterior muscle

value: HSA-Cre+/-


title: 221, Rattus norvegicus, Eyes-cornea

description: Library name: itox000221

source_name: Eyes-cornea

value: Eyes-cornea


title: 11770, Sus scrofa, Adipose,Adipose

description: Library name: itox011770


title: TA muscle from control (Cre) female mouse 3

description:
Library name: R248_F_Cre_TA
Column name in gene_counts_matrix.txt: R248_F_Cre_TA

value: 8 months


title: 220, Rattus norvegicus, Prostate

description: Library name: itox000220

source_name: Prostate

value: Prostate


title: 11869, Sus scrofa, Brainstem,Brainstem

description: Library name: itox011869

source_name: Brainstem,Brainstem

value: Brainstem,Brainstem


title: 1509, Mus musculus, Thyroid/parathyroid,Thyroid/parathyroid

description: Library name: itox001509

source_name: Thyroid/parathyroid,Thyroid/parathyroid

value: Thyroid/parathyroid,Thyroid/parathyroid


title: TA muscle from control (Cre) male mouse 3

description:
Library name: R317_M_Cre_TA
Column name in gene_counts_matrix.txt: R317_M_Cre_TA

source_name: tibialis anterior muscle

value: Male


title: 1506, Mus musculus, Pituitary,Pituitary

description: Library name: itox001506

value: Pituitary,Pituitary


title: 223, Rattus norvegicus, Peripheral Nerve (sciatic)

description: Library name: itox000223

source_name: Peripheral Nerve (sciatic)

value: Peripheral Nerve (sciatic)


title: 1507, Mus musculus, Pituitary,Pituitary

description: Library name: itox001507


title: 11753, Sus scrofa, Kidney,Kidney

description: Library name: itox011753

source_name: Kidney,Kidney

value: Kidney,Kidney


title: 224, Rattus norvegicus, Peripheral Nerve (tibial)

description: Library name: itox000224

source_name: Peripheral Nerve (tibial)

value: Peripheral Nerve (tibial)