title: 488-14_36562_MesLN_HTO


title: KO1-LSC Ribo-seq

status: Public on Sep 24 2024

type: SRA

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

country: China

institute: Wuhan university

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole transcriptome using hisat v2.1.0 with default parameters
FeatureCounts were used to summary raw counts from bam files
differential genes' expression  were performed by  DESeq2 and Riborex
Supplementary files format and content: Translation efficience calculated by Riborex
Library strategy: Ribo-seq

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
3 millions cells were lysed with 300μl lysis buffer (CaCl2 4 mM, MgCl 10 mM, K-HEPES pH 7.2 25 mM, KOAc 200 mM and NP-40 1%) for 5 min on ice and then centrifuged at 9000rpm for 5 min. Collect supernatant and 100 μl of lysate was mixed with TRIzol and saved as input. Adjust KOAc concentration of the lysate to 100 mM by 1:1 dilution with water and then incubated with 10μg/ml micrococcal nuclease for 30 min at 37°C. RNA was extracted with TRIzol. Followed by PNK treatment, ribosome-protected fragments (RPFs), 25 to 40 nucleotides long, was purified with 15% TBE-Urea Gel. Libraries were then prepared using the VAHTSTM Small RNA Library Prep Kit for Illumina® following manufacturer’s instructions.
Libraries were prepared using the VAHTSTM Small RNA Library Prep Kit for Illumina® following manufacturer’s instructions.

tag: tissue

value: bone marrow

tag: cell line

tag: disease state

value: leukemia

tag: genotype


title: 488-14_36562_MesLN_GEX

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

country: USA

library_source: transcriptomic single cell

data_processing:
CellRanger/Seurat
Assembly: Mmul_10
Supplementary files format and content: Count Matrix / Seurat Object

molecule: polyA RNA

organism: Macaca mulatta

source_name: MesLN

extract_protocol:
N/A
10x Genomics 5' Chemistry

tag: cdna library_id

tag: subjectid

value: MesLN

tag: cell type

value: Primary cells

tag: plateid

tag: hto


title: WT2-LSC Ribo-seq

value: WT


title: WT1-LSC Ribo-seq


title: KO2-LSC Ribo-seq


title: Larvae, 60 hours post fertilization

status: Public on Sep 23 2024

city: DURHAM

first: Alejandro

last: Berrio

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

description: 10X Genomics

data_processing:
Raw sequencing data was processed using the Cellranger 3.1.0  pipeline (10X Genomics) to generate FASTQ files.
FASTQ files were aligned to the reference genome (H. erythrogramma 1.0 Genome) and gene expression matrices were generated using Cell Ranger.
Quality control, normalization, and clustering were performed using Seurat (v4.0).
Differential expression analysis was conducted using the FindMarkers function in Seurat.
Assembly: GCA_025617745.1 (Davidson et al., 2022)
Supplementary files format and content: Processed data files are provided in TSV and MTX format, containing gene expression matrices. TSV files include  files with cell metadata and gene annotations.

organism: Heliocidaris erythrogramma

source_name: Larvae

extract_protocol:
Single-cell suspensions were prepared, to do this,  larvae were washed twice in calcium-free artificial seawater (CFASW) then resuspended in dissociation buffer [1.0 M glycine and 0.25 mM EDTA (pH 8.0)] at 4°C. The embryos were then dissociated by gentle trituration. Following dissociation, cells were resuspended in CFASW, and fixed at a final concentration of 80% methanol in CFASW for 1 h, at 4°C. Following fixation, cells were stored at −20°C and all cell libraries were processed within 1 month of dissociation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kits v3.1 (10X Genomics) according to the manufacturer's protocol. Briefly, single cells were encapsulated into Gel Bead-In-Emulsions (GEMs) using the Chromium Controller, followed by reverse transcription, cDNA amplification, and library construction.
Libraries were titered and pooled at Duke University’s Sequencing and Genomic Technologies Core Facility, then sequenced in one S1 flow cell on an Illumina NovaSeq 6000 with 28 x 8 x 91 bp.

value: Larvae

tag: age

value: 60 hours post fertilization


title: Larvae, 56 hours post fertilization

description: 10X Genomics

value: 56 hours post fertilization


title: Larvae, 42 hours post fertilization

description: 10X Genomics

value: 42 hours post fertilization


title: Larvae, 48 hours post fertilization

description: 10X Genomics

value: 48 hours post fertilization


title: Larvae, 36 hours post fertilization

description: 10X Genomics

value: 36 hours post fertilization


title: Testis, Input, sample TAC-1, rep1

city: Montpellier

first: Bernard

last: de Massy

address: 141, rue de la Cardonille

country: France

institute: Institute of Human Genetics - UMR9002 CNRS

library_source: genomic

data_processing:
The libraries were sequenced at Novogene Europe using the NovaSeq6000 PE150 whit S4 flow cells.
DMC1 ChIP-seq data was analysed through the hotSSDS v1.0 pipeline; v2.0 is available at https://github.com/jajclement/hotSSDS. H3K4me3 and H3K36me3 ChIP-seq data was analysed through the nf-core/chipseq v1.2.1 pipeline, accessible at https://github.com/nf-core/chipseq.
DMC1 ChIP-seq reads were mapped on the reference genome using a modified BWA algorithm (BWA Right Align), to align and recover ssDNA fragments (Khil et al., 2012; Brick et al., 2018). H3K4me3 and H3K36me3 ChIP-seq reads were aligned to the reference genome using BWA v0.7.17-r1188. Only non-duplicated and high-quality uniquely mapping reads were retained.
DMC1 peak calling was performed using MACS2 v2.2.7.1 under relaxed conditions (--pvalue=1e-2, --bw=1000, --nomodel, --slocal=5000, --extsize=800) for each replicate, with input provided. Peak calling was also performed on the pooled dataset, generated by subsampling half the reads. IDR analysis (threshold: 0.01) was applied to identify highly reproducible peaks, which were then recentered and normalized based on ssDNA fragment distribution. H3K4me3 and H3K36me3 peaks were called using MACS2 v2.2.7.1 (--pvalue=1e-5, --narrow_peak) on both replicates, with input control. Peaks within 1000 bp were merged using Bedtools (-d 1000 -c 5 -o mean). Reproducible peaks were identified using Bedtools intersect (-f 0.25 -r -u).
Assembly: USDA_OmykA_1.1 (NCBI RefSeq assembly: GCF_013265735.2)
Supplementary files format and content: bigWig (files generated by the pipelines used, not edited)
Supplementary files format and content: bed (4 columns files edited from the original files generated by the pipelines)

molecule: genomic DNA

organism: Oncorhynchus mykiss

source_name: Testis

extract_protocol:
Frozen tissue was fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and lysis, chromatin was sheared using a Bioruptor UCD-300 sonicator (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II kit (NEB, E7645S-E7103S) for H3K4me and H3K36me3 experiments, or using the Illumina TruSeq kit (Illumina, IP-202-9001DOC) for DMC1 experiments. 90 ng of DNA was used as starting material for DMC1 ip samples, while 180 ng was used for input. 100-200 ng of DNA was used as starting material for H3K4me3 and H3K36me3 ip samples and input. DMC1 libraries were amplified using 18 cycles on the thermocycler, while H3K4me3 and H3K36me3 libraries were amplified using 9-12 cycles. Post amplification libraries were size selected by excision from agarose gel within the range of 200 to 400 bp followed by DNA purification using MinElute columns from Qiagen.

value: Testis

tag: maturation stage

value: III

tag: strain

value: INRA-AUT

tag: chip antibody


title: Testis, H3K36me3, sample TAC-1, ChIP, rep1


title: Testis, H3K36me3, sample TAC-1, ChIP, rep2


title: Testis, H3K4me3, sample TAC-1, ChIP, rep1

value: H3K4me3 (Abcam, ab8580)


title: Testis, Input, sample TAC-3, rep2


title: Testis, H3K36me3, sample TAC-3, ChIP, rep2


title: Testis, H3K4me3, sample TAC-3, ChIP, rep2


title: Testis, H3K36me3, sample TAC-3, ChIP, rep1


title: Testis, DMC1, sample TAC-3, ChIP, rep2


title: Testis, H3K4me3, sample TAC-3, ChIP, rep1


title: Testis, H3K4me3, sample TAC-1, ChIP, rep2


title: Testis, DMC1, sample TAC-1, ChIP, rep1


title: Testis, DMC1, sample TAC-1, ChIP, rep2


title: Testis, DMC1, sample RT-52, ChIP, rep1

value: IV


title: Testis, Input, sample RT-52, rep1


title: Testis, DMC1, sample TAC-3, ChIP, rep1


title: Testis, DMC1, sample RT-52, ChIP, rep2


title: 488-14_36562_MesLN_ADT


title: MDA-MB-231 cells cultured in endosteal bone seeded with mesenchymal stem cells and endothelial cells sample 4

city: New York

first: Richard

middle: A

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

data_processing:
Bases2fastq version 1.7.0.1196148384 was used for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment to a kallisto index created from transcriptomes (Ensembl v111, Human:GRCh38.p14) was performed using kallisto (0.50.1).
Assembly: Human:GRCh38.p14
Supplementary files format and content: tab delimited text file includes raw counts for each file

organism: Homo sapiens

source_name: Breast; Mammary gland

growth_protocol: Decellularized 8 mm x 4 mm x 1 mm bovine bone scaffolds were seeded with 1'000'000 primary bone marrow-derived mesenchymal stem/stromal cells (BM-MSCs; ATCC) each, and cultured in MSC media consisting of 4.5 g/L DMEM (Gibco) with 1% P/S (Gibco), 10% FBS (Corning), and 1 ng/mL bFGF (Peprotech) during 1 wk of MSC expansion. Bone tissues were then matured over 3 wk in osteogenic media containing 1 g/L DMEM (Gibco), 1% P/S (Gibco), 10% FBS (Corning), 10 mM β-glycerophosphate disodium salt hydrate (Sigma), 100 nM dexamethasone (Sigma), and 50 ug/mL L-ascorbic acid (Sigma).

extract_protocol:
At day 10, adherent fractions were digested with 10 mg/mL collagenase II (Worthington) and 10 mg/mL Nattokinase (Japan BioSciences) for 1 h on a rocker at 37°C. Tissues were further digested a second iteration if not completely detached. Isolated cells were washed and resuspended in FACS buffer 2X and filtered with 40 μm Flowmi® Cell Strainers (Sigma).
Cells were then sorted for tdTomato signal using a Sony MA900 cell sorter, collected in RNA lysis buffer, and processed using RNeasy Micro Kit (Qiagen), according to the manufacturer's instructions. RNA was analyzed for quality and quantity using an Agilent Qubit 2.0 bioanalyzer at the Herbert Irving Comprehensive Cancer Center Molecular Pathology Shared Resource at Columbia University (all RIN > 9.5). Samples were sequenced by the Columbia Genome Center.

treatment_protocol: 150'000 BM-MSCs, 150'000 human umbilical vein endothelial cells (HUVECs; Lonza), and 30’000 CB-HSPCs, with 5'000 MDA-MB-231 cancer cells (with tdTomato reporter) per tissue were seeded with 11 mg/mL fibrinogen (F3879, Sigma) on ultra-low attachment plates (Corning). All cells were expanded (i.e., not used directly from thaw) prior to seeding onto tissues. After seeding cell-fibrinogen suspensions, 33 U/mL of thrombin (T6884, Sigma) were added to the tissues, which were then left to polymerize for 25-30 minutes at 37°C. After this, tissues were re-hydrated with SFEM II media supplemented with 5% heat- inactivated FBS (Corning), 1% P/S (Gibco), selected EGM-2 bullet kit (Lonza) components (at 50% manufacturer’s concentration: FGF-2, Heparin, VEGF, R3-IGF-1, hEGF, ascorbic acid), and 50 ng/mL each of SCF, TPO, and FLT-3L (PeproTech). Until day 5, media was supplemented with 33 μg/mL of cell culture graded aprotinin (A3428, Sigma). eBM tissues were kept on a rocker at 37°C with 5% CO2 for the duration of the experiment.

value: Breast; Mammary gland

value: epithelial

value: ER-/PR-/HER-

tag: treatment


title: MDA-MB-231 cells cultured in endosteal bone containing only osteoblasts (OB) sample 4


title: MDA-MB-231 cells cultured in endosteal bone containing only osteoblasts (OB) sample 3


title: MDA-MB-231 cells cultured in endosteal bone seeded with mesenchymal stem cells and endothelial cells sample 1


title: MDA-MB-231 cells cultured in endosteal bone seeded with mesenchymal stem cells and endothelial cells sample 3


title: MDA-MB-231 cells cultured in endosteal bone seeded with mesenchymal stem cells and endothelial cells sample 2


title: MDA-MB-231 cells cultured in endosteal bone containing only osteoblasts (OB) sample 2


title: MDA-MB-231 cells cultured in endosteal bone containing only osteoblasts (OB) sample 1


title: Testis, Input, sample TAC-3, rep1


title: Substantia Nigra_P4_77

city: Los Angeles

first: Ting

state: CA

address: 2506 Gonda Bldg, 695 Charles E.Young Dr. South

department: Pathology and laboratory medicine

institute: University of California, Los Angeles

description:
Retry #3|029|Full ROI
processed_data2.txt

data_processing:
Following sequencing, the processing and normalization of data involves matching the raw probe counts to sequencing results to filter out unused probes and remove outliers, then subjected to third quartile Q3 normalization to the negative probes. The negative probes include probes for whole transcriptomic atlas and SARS-CoV2 (Neg-WTA and SARS-CoV2-Neg).
Processed data: Q3 normalized counts
Library strategy: Spatial Transcriptomics

source_name: PATIENT

extract_protocol:
5-6 µm were mounted on glass slides and subjected to an overnight baking at 37°C, followed by a 3-hour baking at 65°C. The slides underwent antigen retrieval for 20 minutes at 100°C and 0.25 µg/mL proteinase K treatment for 20 minutes.
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail. Immunofluorescent cell type/morphology markers, anti-NeuN antibody (Millipore) for neurons, anti-GFAP antibody (Invitrogen) for astrocyte, anti-IBA1 antibody (Millipore) for microglia, and Syto83 (Invitrogen) for nuclei were then applied to the slides.
The GeoMx Deep Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by senior neuropathologists. Probe barcodes were UV cleaved, collected, and sequenced on the Illumina NovaSeq 6000 platform with paired end reads.

value: postmortem brain

tag: tissue type

value: FFPE

tag: area

value: Substantia Nigra

tag: region

value: Midbrain

tag: grey/whitematter

value: Grey

tag: lotid

value: Retry #3

tag: roi

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

value: Yes

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq

tag: pkc file


title: Periaqueduct GrayMatter_P4_76

description:
Retry #3|028|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

value: Periaqueduct GrayMatter

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration


title: Red Nucleus_P4_75

description:
Retry #3|027|Full ROI
processed_data2.txt

value: Red Nucleus

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Periaqueduct GrayMatter_P4_79

description:
Retry #3|031|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: scanoffsetx

tag: scanoffsety

tag: loq

tag: pkc file


title: Red Nucleus_P4_73

description:
Retry #3|025|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: HCT116, Valine deprivation, MAB-seq

city: Shanghai

first: Yu

last: Yuanyuan

address: No. 1239, Siping Road, Shanghai

institute: Tongji University

data_processing:
*library strategy: methylase-assisted bisulfite sequencing (MAB-seq)
MAB-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
MAB-seq reads were aligned to hg38 using Bismark (v0.22.1) in paired-end mode. Duplicates were removed using deduplicate_bismark.
5fC in the CpG contexts were extracted by MethPipe software package (v3.4.3)
Cytosines sites with at least 5 reads coverage and a 5fC level > 20% were retained.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
500 ng of DNA extracted from HCT116 cells with or without the treatment of valine deprivation was first spiked-in with unmethylated lambda DNA (1:500), and break the DNA to 600-700 bp. The broken DNA was treated by M.SssI (New England Biolabs, M0226M) in a 50 μL reaction. In the treatment, DNA was first incubated with 1.0 unit/μl M.SssI methylase (New England Biolabs, M0226M) for 4 h in 50 μL reaction (1 μL of 4 U/μL M.SssI, 5 μL of 1.6 mM SAM, 5 μL of 10×Methyltransferase Reaction Buffer, add ddH2O up to 50 μL). DNA was purified by using DNA Clean & Concentrator kit (Zymo，D4013). M.SssI-treated DNA was then subjected to bisulfite conversion using EZ DNA Methylation-Direct kit (Zymo，D5021).
Bisulfite-treated DNA were purified and subjected to library construction with EpiArt DNA Methylation Library Kit (Vazyme, NE103) and VAHTS Multiplex Oligos Set 4 (Vazyme, N321) according to the instruction manual (Illumina). Briefly, the single-stranded heat-denatured DNA fragments were ligated to the 3' adapter ligation and 5' adapter ligation. Next, the ligated DNA was extended to the second strand synthesis and the methylated adapters were ligated. The DNA was ampliﬁed for 10 cycles using Illumina 8-bp dual index primers. Finally, the MAB-seq libraries were analyzed by Agilent 2100 Bioanalyzer and sequenced on an Illumina NovaSeq 6000 platform by 150 bp paired-end sequencing.

tag: cell line

tag: treatment

value: valine deprivation


title: Periaqueduct GrayMatter_P4_78

description:
Retry #3|030|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: HCT116, MAB-seq


title: HCT116, H3K4me1-ChIP

data_processing:
ChIP-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
ChIP-seq reads were aligned to hg38 using Bowtie2 (v2.3.5.1) with parameters: --no-unal --no-mixed --no-discordant, and were further filtered with mapping quality of at least 20
PCR duplicates were removed using Sambamba (v0.7.0)
Peaks were called using  MACS2 (v2.1.2) to call peaks with parameter --broad -q0.01 --cut-off 0.01
bigWig files were generated by bamCoverage in deepTools (v3.3.0) with 25 bp bin size and normalized as FPKM
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
HCT116 cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were precleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-H3K4me1 antibodies. After reverse crosslinking, ChIPed and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adapter ligation with the NEBNext Ultra Ligation Module (E7445, NEB).
Sequencing libraries were generated by Genefund Biotech (Shanghai, China). The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with 150 bp paired-end protocol.


title: Substantia Nigra_P4_72

description:
Retry #3|024|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Red Nucleus_P4_74

description:
Retry #3|026|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Substantia Nigra_P4_71

description:
Retry #3|023|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Substantia Nigra_P4_70

description:
Retry #3|022|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Cerebral Peduncle_C4_69

description:
Retry #3|021|Full ROI
processed_data2.txt

source_name: CONTROL

value: Cerebral Peduncle

value: White

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

value: No

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Cerebral Peduncle_C4_68

description:
Retry #3|020|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Cerebral Peduncle_C4_67

description:
Retry #3|019|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Red Nucleus_C4_64

description:
Retry #3|016|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Red Nucleus_C4_65

description:
Retry #3|017|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Substantia Nigra_C4_63

description:
Retry #3|015|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Substantia Nigra_C4_62

description:
Retry #3|014|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Periaqueduct GrayMatter_P3_57

description:
Retry #3|009|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Substantia Nigra_C4_61

description:
Retry #3|013|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Periaqueduct GrayMatter_P3_58

description:
Retry #3|010|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Periaqueduct GrayMatter_P3_56

description:
Retry #3|008|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Red Nucleus_P3_55

description:
Retry #3|007|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Cerebral Peduncle_P3_60

description:
Retry #3|012|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Red Nucleus_P3_54

description:
Retry #3|006|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Red Nucleus_P3_53

description:
Retry #3|005|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Substantia Nigra_P3_52

description:
Retry #3|004|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Substantia Nigra_C3_45

description:
Retry #1|021|Full ROI
processed_data2.txt

value: Retry #1

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Substantia Nigra_P3_49

description:
Retry #3|001|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Substantia Nigra_P3_50

description:
Retry #3|002|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Substantia Nigra_C3_43

description:
Retry #1|019|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Red Nucleus_C3_48

description:
Retry #1|024|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Red Nucleus_C3_46

description:
Retry #1|022|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Substantia Nigra_P3_51

description:
Retry #3|003|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Red Nucleus_C4_66

description:
Retry #3|018|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Periaqueduct GrayMatter_P2_41

description:
Retry #1|017|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

value: Female

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Periaqueduct GrayMatter_P2_42

description:
Retry #1|018|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Periaqueduct GrayMatter_P2_39

description:
Retry #1|015|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: Red Nucleus_P2_38

description:
Retry #1|014|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Cerebral Peduncle_P3_59

description:
Retry #3|011|Full ROI
processed_data2.txt

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety


title: Periaqueduct GrayMatter_P2_40

description:
Retry #1|016|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: deduplicatedreads

tag: trimmedreads

tag: loq

tag: pkc file


title: SPN_D39_Dccn_1_BHI_Zn

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: rRNA depleted

data_processing:
Adapters and low quality bases were trimmed using Cutadapt
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2
Read counting was performed with HTSeq
Differential Gene expression analysis performed with DESeq2
Assembly: Streptococcus pneumoniae D39  (Genbank CP000410.1) genome and Streptococcus pneumoniae TIGR4 (Genbank AE005672.3) genome
Supplementary files format and content: WT_vs_ccn_DESeq2.xlsx: differentially expressed genes

organism: Streptococcus pneumoniae D39

source_name: bacterial cell

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth alone or supplmented with 0.2 mM zinc sulfate at 37oC in atmosphere of 5% CO2 to an OD620 of 0.2

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
Library was generated  with NEBNext Ultra II RNA Library Prep Kit for library preparation after removing DNA by DNase treatment and depleting rRNA with FastSelect Bacteria kit for rRNA depletion.

treatment_protocol: BHI Broth with 0.2 mM zinc sulfate at 37 degrees celsius under atmosphere of 5% carbon dioxide

tag: cell type

value: bacterial cell

tag: genotype

value: rpsL1 DccnABCDE

tag: treatment


title: SPN_D39_Dccn_2_BHI_Zn

description: rRNA depleted


title: Red Nucleus_P2_37

description:
Retry #1|013|Full ROI
processed_data2.txt

value: postmortem brain

value: FFPE

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: SPN_D39_2_BHI_Zn

description: rRNA depleted

tag: cell type

tag: genotype


title: Red Nucleus_P2_36

description:
Retry #1|012|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

value: Midbrain

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: deduplicatedreads

tag: trimmedreads

tag: scanoffsety

tag: loq

tag: pkc file


title: Substantia Nigra_P2_35

description:
Retry #1|011|Full ROI
processed_data2.txt

value: Substantia Nigra

value: Grey

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Substantia Nigra_C3_44

description:
Retry #1|020|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

value: Male

tag: deduplicatedreads

tag: trimmedreads

tag: scanoffsety


title: Red Nucleus_C3_47

description:
Retry #1|023|Full ROI
processed_data2.txt

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

value: Yes

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: stitchedreads

tag: loq

tag: pkc file


title: SPN_D39_1_BHI_Zn

description: rRNA depleted

treatment_protocol: BHI Broth at 37 degrees celsius under atmosphere of 5% carbon dioxide

tag: cell type

tag: genotype

tag: treatment


title: SPN_D39_Dccn_3_BHI

description: rRNA depleted

value: BHI


title: SPN_D39_Dccn_3_BHI_Zn

description: rRNA depleted


title: Cerebral Peduncle_C2_33

description:
Retry #1|009|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: SPN_D39_Dccn_2_BHI

description: rRNA depleted

tag: cell type

tag: genotype


title: SPN_D39_Dccn_1_BHI

description: rRNA depleted

tag: treatment


title: Cerebral Peduncle_C2_34

description:
Retry #1|010|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: stitchedreads

tag: scanoffsety

tag: loq

tag: pkc file


title: Cerebral Peduncle_C2_32

description:
Retry #1|008|Full ROI
processed_data2.txt

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: deduplicatedreads

tag: trimmedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Red Nucleus_C2_31

description:
Retry #1|007|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

value: Red Nucleus

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: stitchedreads


title: Red Nucleus_C2_29

description:
Retry #1|005|Full ROI
processed_data2.txt

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: deduplicatedreads

tag: trimmedreads

tag: scanoffsety

tag: loq

tag: pkc file


title: Substantia Nigra_C2_28

description:
Retry #1|004|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: SPN_D39_1_BHI

description: rRNA depleted

tag: cell type

tag: genotype

tag: treatment


title: SPN_D39_2_BHI

description: rRNA depleted


title: SPN_D39_3_BHI_Zn

description: rRNA depleted


title: Substantia Nigra_C2_25

description:
Retry #1|001|Full ROI
processed_data2.txt

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanoffsety

tag: loq


title: Substantia Nigra_C2_26

description:
Retry #1|002|Full ROI
processed_data2.txt

tag: tissue

tag: tissue type

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: pkc file


title: Red Nucleus_C2_30

description:
Retry #1|006|Full ROI
processed_data2.txt

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: HT29 cells, siALDOA, biol rep 3

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

data_processing:
All libraries were sequenced on the Illumina NovaSeq X Plus instrument, and 150 bp paired-end reads were generated.
Sequencing reads were aligned back to the human genome (version: hg38) by TopHat 2 software.
Read count extraction was performed using GFOLD software.
The expression matrix of all samples was subjected to the Bayesian workflow for differential gene modeling based on the “edgeR” and “limma” R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads count for each Sample

extract_protocol:
Total RNA was isolated from the colorectal cancer cells using Trizol reagent (Invitrogen; ThermoFisher) according to the manufacturer’s instructions.
RNA-Seq libraries (with each treatment in triplicate) were constructed according to standard Illumina protocols.

treatment_protocol: HT29 cells were treated with a siRNA targeting ALDOA, and a scrambled siRNA was used as a control. 48 h later, RNA was isolated.

tag: cell line

tag: cell type

value: a human colorectal adenocarcinoma cell line with epithelial morphology.

tag: genotype

value: ALDOA KD

tag: treatment

value: siALDOA


title: HT29 cells, siALDOA, biol rep 2


title: HT29 cells, siControl, biol rep 3

value: WT

value: CTRL


title: HT29 cells, siControl, biol rep 2


title: Red Nucleus_P1_24

description:
9_MidBrain_Pons-COVID|024|Full ROI
processed_data1.txt

tag: tissue

tag: tissue type

tag: gender

tag: immunocompromised status

value: No

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq

tag: pkc file


title: SPN_D39_3_BHI

description: rRNA depleted

tag: cell type

value: bacterial cell

tag: genotype

tag: treatment


title: HT29 cells, siControl, biol rep 1

tag: cell line


title: Red Nucleus_P1_23

description:
9_MidBrain_Pons-COVID|023|Full ROI
processed_data1.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: Substantia Nigra_C2_27

description:
Retry #1|003|Full ROI
processed_data2.txt

value: Retry #1

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq

tag: pkc file


title: HT29 cells, siALDOA, biol rep 1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Red Nucleus_P1_22

description:
9_MidBrain_Pons-COVID|022|Full ROI
processed_data1.txt

tag: tissue

value: postmortem brain

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: Periaqueduct GrayMatter_P1_21

description:
9_MidBrain_Pons-COVID|021|Full ROI
processed_data1.txt

value: FFPE

value: Periaqueduct GrayMatter

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq

tag: pkc file


title: 46D,B

city: Urbana

first: Tina

last: Barbasch

address: 505 S Goodwin Ave

department: Evolution, Ecology, and Behavior

institute: University of Illinois Urbana Champaign

data_processing:
Reads were aligned using STAR to the G. aculeatus reference genome (Ensembl release 95). Gene transcript counts were generated using HTSeq.
Assembly: Ensembl release 95
Supplementary files format and content: .txt files of counts generated from HTSeq

organism: Gasterosteus aculeatus

source_name: Diencephalon

extract_protocol:
One hour after the trial, males were sacrificed (n = 8 after a courtship opportunity, n = 8 after predation risk, n = 8 after a tradeoff, n = 7 after a control) and their telencephalon and diencephalon were rapidly dissected and deep frozen at -80°C until extraction. RNA was extracted using Invitrogen PureLink RNA extraction kits (Invitrogen Corporation, Carlsbad, CA) and quality was checked using Agilent Bioanalyzer chips.
Library prep and sequencing was performed by the Functional Genomics Unit of the W.M. Keck Center (University of Illinois Urbana Champaign). Libraries were prepared using the ‘Kapa Hyper Stranded mRNA library kit’ (Roche) and pooled, quantitated by qPCR and sequenced on one S4 lane on a NovaSeq6000 to a depth of >30M reads.

treatment_protocol: Behavioral trials were conducted between July 12 – July 29, 2022. Males were placed in experimental tanks (53L x 33W x 24H cm) with sand and algae provided for nesting material. Once males built their nests, they were assigned one of four treatments: courtship opportunity alone (F), predation risk alone (P), a tradeoff consisting of a courtship opportunity and predation risk together (B), and a control (C). The courtship opportunity consisted of a live gravid female stickleback in a cage, the predation risk consisted of a model trout plus odor cues in a cage, the tradeoff consisted of both a live gravid female and a model trout, and the control consisted of empty cages.

tag: tissue

value: Diencephalon

tag: treatment

value: B


title: 44T,P

source_name: Telencephalon

value: Telencephalon

value: P


title: Periaqueduct GrayMatter_P1_20

description:
9_MidBrain_Pons-COVID|020|Full ROI
processed_data1.txt

tag: tissue type

tag: area

tag: region

value: Midbrain

tag: grey/whitematter

value: Grey

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

value: Yes

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: Periaqueduct GrayMatter_P1_19

description:
9_MidBrain_Pons-COVID|019|Full ROI
processed_data1.txt

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 44D,P

tag: tissue

tag: treatment


title: 42T,P


title: 42D,P


title: Substantia Nigra_P1_17

description:
9_MidBrain_Pons-COVID|017|Full ROI
processed_data1.txt

tag: tissue type

tag: area

value: Substantia Nigra

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: roicoordinatey

tag: rawreads

tag: pkc file


title: Substantia Nigra_P1_16

description:
9_MidBrain_Pons-COVID|016|Full ROI
processed_data1.txt

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: 41T,F

tag: tissue

tag: treatment

value: F


title: Cerebral Peduncle_P1_15

description:
9_MidBrain_Pons-COVID|015|Full ROI
processed_data1.txt

tag: tissue type

tag: area

value: Cerebral Peduncle

tag: region

tag: grey/whitematter

value: White

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: roicoordinatey

tag: rawreads

tag: loq


title: 41D,F


title: 40T,C

value: C


title: Cerebral Peduncle_P1_14

description:
9_MidBrain_Pons-COVID|014|Full ROI
processed_data1.txt

value: No

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: pkc file


title: Cerebral Peduncle_P1_13

description:
9_MidBrain_Pons-COVID|013|Full ROI
processed_data1.txt

tag: tissue

value: postmortem brain

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: scanoffsety


title: Red Nucleus_C1_12

description:
8_MidBrain-Control|012|Full ROI
processed_data1.txt

value: FFPE

value: Red Nucleus

value: Female

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: loq


title: 40D,C

tag: tissue

value: Diencephalon

tag: treatment


title: 46T,B

value: Telencephalon

value: B


title: 39T,B


title: Red Nucleus_C1_11

description:
8_MidBrain-Control|011|Full ROI
processed_data1.txt

tag: tissue type

tag: area

tag: region

value: Midbrain

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: pkc file


title: Periaqueduct GrayMatter_C1_9

description:
8_MidBrain-Control|009|Full ROI
processed_data1.txt

value: Periaqueduct GrayMatter

value: Grey

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanoffsety


title: 39D,B

tag: tissue

tag: treatment


title: Periaqueduct GrayMatter_C1_7

description:
8_MidBrain-Control|007|Full ROI
processed_data1.txt

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

value: Yes

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: loq


title: 38D,F


title: 38T,F


title: 35T,F


title: 37T,P

value: P


title: 37D,P


title: Substantia Nigra_P1_18

description:
9_MidBrain_Pons-COVID|018|Full ROI
processed_data1.txt

value: Substantia Nigra

value: Male

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: pkc file


title: Substantia Nigra_C1_5

description:
8_MidBrain-Control|005|Full ROI
processed_data1.txt

tag: tissue

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: scanwidth

tag: scanoffsety


title: Substantia Nigra_C1_6

description:
8_MidBrain-Control|006|Full ROI
processed_data1.txt

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: loq


title: 34T,P

tag: tissue

tag: treatment


title: 35D,F

value: F


title: 34D,P


title: 33T,P


title: Cerebral Peduncle_C1_2

description:
8_MidBrain-Control|002|Full ROI
processed_data1.txt

tag: tissue type

tag: area

value: Cerebral Peduncle

tag: region

tag: grey/whitematter

value: White

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: pkc file


title: Periaqueduct GrayMatter_C1_8

description:
8_MidBrain-Control|008|Full ROI
processed_data1.txt

value: postmortem brain

tag: immunocompromised status

tag: duration

tag: ventilation

value: No

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Cerebral Peduncle_C1_1

description:
8_MidBrain-Control|001|Full ROI
processed_data1.txt

tag: tissue

tag: tissue type

value: FFPE

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: trimmedreads

tag: loq


title: 32T,F

tag: treatment


title: Cerebral Peduncle_C1_3

description:
8_MidBrain-Control|003|Full ROI
processed_data1.txt

value: Female

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: pkc file


title: Tegmentum_P3_3

description: 9_MidBrain_Pons-COVID|12|Full ROI

data_processing:
Following sequencing, the processing and normalization of data involves matching the raw probe counts to sequencing results to filter out unused probes and remove outliers, then subjected to third quartile Q3 normalization to the negative probes. The negative probes include probes for whole transcriptomic atlas and SARS-CoV2 (Neg-WTA and SARS-CoV2-Neg).
Processed data includes Q3 normalized counts
Library strategy: Spatial Transcriptomics

extract_protocol:
5-6 µm were mounted on glass slides and subjected to an overnight baking at 37°C, followed by a 3-hour baking at 65°C. The slides underwent processing on the Leica automation platform, including antigen retrieval for 20 minutes at 100°C and proteinase K treatment.
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail, targeting 18,702 genes including 3 SARS-CoV2 targets. Immunofluorescent cell type/morphology markers, anti-NeuN antibody (Millipore) for neurons, anti-GFAP antibody (Invitrogen) for astrocyte, anti-IBA1 antibody (Millipore) for microglia, and Syto83 (Invitrogen) for nuclei were then applied to the slides.
The GeoMx Deep Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by senior neuropathologists. Probe barcodes were UV cleaved, collected, and sequenced on the Illumina NovaSeq 6000 platform with paired end reads.

tag: tissue

tag: tissue type

tag: area

value: Tegmentum

tag: region

value: Pons

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: 30D,C

value: Diencephalon

tag: treatment

value: C


title: 33D,P

tag: tissue


title: Red Nucleus_C1_10

description:
8_MidBrain-Control|010|Full ROI
processed_data1.txt

tag: tissue type

value: Red Nucleus

value: Midbrain

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq

tag: pkc file


title: Tegmentum_P3_2

description: 9_MidBrain_Pons-COVID|11|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

value: Yes

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Tegmentum_P3_1

description: 9_MidBrain_Pons-COVID|9|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq


title: 29D,F

tag: tissue

tag: treatment


title: 28T,B

value: Telencephalon

value: B


title: Tegmentum_P5_1

description: Pons|27|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Tegmentum_P2_2

description: 7_Pons|23|Full ROI

tag: tissue type

value: Male

tag: immunocompromised status

tag: duration

tag: ventilation

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq


title: 30T,C

tag: tissue

tag: treatment


title: 32D,F

value: F


title: 26T,C


title: Tegmentum_P2_1

description: 7_Pons|22|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Tegmentum_P4_1

description: Pons|15|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq


title: 26D,C

tag: tissue

tag: treatment


title: 29T,F


title: 25T,B


title: Tegmentum_P2_3

description: 7_Pons|24|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Substantia Nigra_C1_4

description:
8_MidBrain-Control|004|Full ROI
processed_data1.txt

tag: tissue type

value: Substantia Nigra

value: Grey

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq

tag: pkc file


title: Tegmentum_C3_3

description: 7_Pons-Control|12|Full ROI

tag: tissue

value: postmortem brain

tag: area

tag: region

tag: grey/whitematter

value: White

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: 24T,P

tag: treatment

value: P


title: Tegmentum_P1_2

description: 5_Pons|11|Full ROI

tag: tissue type

value: FFPE

tag: immunocompromised status

value: No

tag: duration

tag: ventilation

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq


title: 28D,B

tag: tissue


title: 25D,B


title: Tegmentum_C3_1

description: 7_Pons-Control|10|Full ROI

tag: area

value: Tegmentum

tag: region

value: Pons

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

value: Female

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Tegmentum_C2_3

description: 6_Pons|24|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: 24D,P

tag: tissue

value: Diencephalon

tag: treatment


title: 21T,F


title: Tegmentum_C3_2

description: 7_Pons-Control|11|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight

tag: scanoffsetx

tag: loq


title: 23D,P


title: Tegmentum_C2_1

description: 6_Pons|22|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanoffsety


title: Tegmentum_C2_2

description: 6_Pons|23|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanheight


title: Tegmentum_P1_1

description: 5_Pons|10|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: loq


title: Tegmentum_P1_3

description: 5_Pons|12|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: sequencingsaturation

tag: scanwidth

tag: scanoffsety


title: 23T,P

tag: treatment


title: Tegmentum_C1_2

description: 5_Pons|23|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanheight


title: 21D,F

tag: tissue


title: Pontine nuclei_P6_5

description: Pons|28|Full ROI

tag: area

value: Pontine nuclei

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: sequencingsaturation

tag: scanwidth

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 20T,C

tag: treatment

value: C


title: Tegmentum_C1_3

description: 5_Pons|24|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

value: Yes

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanheight


title: 18T,F

tag: tissue

value: Telencephalon


title: Tegmentum_C1_1

description: 5_Pons|22|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

value: Male

tag: lung disease

tag: sequencingsaturation

tag: scanwidth

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 18D,F

tag: treatment

value: F


title: 20D,C


title: Pontine nuclei_P6_3

description: Pons|19|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanheight


title: 17D,P

tag: tissue


title: Pontine nuclei_P6_2

description: Pons|18|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: sequencingsaturation

tag: scanwidth

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 15T,C

tag: treatment


title: Pontine nuclei_P6_1

description: Pons|17|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanheight


title: 15D,C

tag: tissue


title: Pontine nuclei_P5_4

description: Pons|16|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: sequencingsaturation

tag: scanwidth

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontine nuclei_P5_3

description: Pons|9|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Pontine nuclei_P5_2

description: Pons|8|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: 13T,B

tag: treatment

value: B


title: 13D,B


title: Pontine nuclei_P6_4

description: Pons|20|Full ROI

tag: tissue type

value: Grey

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 12T,C

tag: tissue


title: 12D,C


title: Pontine nuclei_P5_1

description: Pons|6|Full ROI

value: postmortem brain

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontine nuclei_P4_1

description: 9_MidBrain_Pons-COVID|3|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanoffsetx

tag: scanoffsety


title: Pontine nuclei_P4_3

description: 9_MidBrain_Pons-COVID|10|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: loq


title: 11T,B

tag: treatment


title: 17T,P


title: Pontine nuclei_P4_2

description: 9_MidBrain_Pons-COVID|5|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: 07D,F

tag: tissue


title: 07T,F


title: 06T,B


title: Pontine nuclei_P3_4

description: 7_Pons|10|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontine nuclei_P3_5

description: 7_Pons|11|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth


title: Pontine nuclei_P3_3

description: 7_Pons|9|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: scanheight


title: 11D,B

tag: treatment


title: Pontine nuclei_P3_2

description: 7_Pons|8|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontine nuclei_P3_1

description: 7_Pons|7|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: 04D,C

tag: treatment


title: Pontine nuclei_P2_4

description: 6_Pons|12|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: 04T,C

tag: tissue


title: Pontine nuclei_P2_3

description: 6_Pons|11|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq


title: 01D,B

tag: treatment


title: Pontine nuclei_P2_2

description: 6_Pons|10|Full ROI

tag: tissue type

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: 22Rv1-C1111S-SF3B1, WX43, ATAC-Seq, rep2

city: La Jolla

first: Yuxiang

address: 10550 N. Torrey Pines Rd.

department: Chemistry

institute: The Scripps Research Institute

data_processing:
Reads were were aligned to the human genome build hg19 with Bowtie2. Blacklist regions were excluded using data file wgEncodeDacMapabilityConsensusExcludable.bed.gz. Unmapped/low quality and duplicated reads were filtered with sambamba.
Peaks were called by MACS2 with pareameters: -q 0.01 --nomodel --shift -100 --extsize 150.
Assembly: hg19
Supplementary files format and content: narrowPeak

source_name: Prostate

growth_protocol: All 22Rv1 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 2 mM L-alanyl-L-glutamine (GlutaMAX), penicillin (100 U/ml), and streptomycin (100 μg/ml) and maintained at 37 °C with 5% CO2.

extract_protocol:
ATAC-seq fragmentes were extracted with ATAC-Seq Kit (Active Motif, Cat#: 53150) following manufacturer's instruction.
ATAC-seq libraries were prepared with ATAC-Seq Kit (Active Motif, Cat#: 53150) following manufacturer's instruction.

treatment_protocol: Cells were treated with DMSO (0.1%), stereoprobes (WX-02-23, WX-02-43, 20 uM), PladB (10 nM and 100 nM for parental 22Rv1, 10 nM for 22Rv1_SF3B1-C1111S, 100 nM for engineered 22Rv1) for 3 h.

tag: tissue

value: Prostate

tag: cell line

tag: genotype

value: Gene-edited to express C1111S-SF3B1


title: Pontine nuclei_P3_6

description: 7_Pons|12|Full ROI

tag: tissue type

value: FFPE

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq


title: 22Rv1-C1111S-SF3B1, WX43, ATAC-Seq, rep1

tag: tissue

tag: cell line

tag: treatment


title: Pontine nuclei_P1_3

description: 5_Pons|9|Full ROI

tag: tissue type

tag: area

tag: immunocompromised status

value: No

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: 06D,B

tag: tissue


title: 22Rv1-C1111S-SF3B1, WX23, ATAC-Seq, rep2

tag: cell line

tag: genotype

tag: treatment


title: Pontine nuclei_P1_1

description: 5_Pons|7|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: lung disease

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: loq


title: Pontine nuclei_C4_2

description: 7_Pons-Control|8|Full ROI

tag: tissue

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Pontine nuclei_C4_3

description: 7_Pons-Control|9|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: lung disease

tag: trimmedreads

tag: stitchedreads


title: 22Rv1-C1111S-SF3B1, WX23, ATAC-Seq, rep1

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: 22Rv1-C1111S-SF3B1, DMSO, ATAC-Seq, rep3

value: DMSO


title: Pontine nuclei_C4_1

description: 7_Pons-Control|7|Full ROI

tag: tissue type

value: Pons

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 01T,B

tag: tissue

tag: treatment


title: 22Rv1-C1111S-SF3B1, DMSO, ATAC-Seq, rep1

tag: cell line

tag: genotype


title: 22Rv1-C1111S-SF3B1, PladB, rep3

data_processing:
Raw sequencing data in FASTQ format was processed using the SLAMdunk pipeline for alignment to the human genome (hg19), counting nucleotide conversions, and generating mutation profiles specific to SLAM-seq.
Assembly: hg19
Supplementary files format and content: TSV files containing columns for gene identifiers, counts of nucleotide conversions, expression levels (CPM)

extract_protocol:
The SLAMseq Kinetics Kit-Anabolic Kinetics module (Lexogen) was used to process samples according to manufacturer’s guidelines. Briefly, RNA isolation was performed in dark with RNeasy Kit (Qiagen) with 0.1 mM DTT in all buffers. 4 mg of purified RNA was alkylated with 2.5 mM iodoacetamide and after ethanol precipitation, samples were processed for the sequencing library preparation using QuantSeq 3’ mRNA-seq V2 Library Prep Kit (Lexogen). Samples were multiplex sequenced on the Illumina NextSeq 2000.
QuantSeq 3’ mRNA-seq V2 Library Prep Kit (Lexogen) accoding to manufacturer's guidelines.
QuantSeq 3’ mRNA-seq V2 Library Prep Kit (Lexogen)

treatment_protocol: Cells were treated with DMSO (0.1% v/v), stereoprobes (WX-02-23, WX-02-43, 20 uM, 3h), PladB (10 nM, 3h) followed by 100 uM 4-thiouridine (S4U, 1h)

value: PladB, 10 nM


title: 22Rv1-C1111S-SF3B1, DMSO, ATAC-Seq, rep2


title: Pontine nuclei_C3_2

description: 7_Pons|20|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

value: Female

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads


title: Pontine nuclei_C2_3

description: 6_Pons|21|Full ROI

tag: tissue

value: Pontine nuclei

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 22Rv1-C1111S-SF3B1, PladB, rep2

tag: cell line

tag: genotype

tag: treatment


title: Pontine nuclei_C3_3

description: 7_Pons|21|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads


title: 22Rv1-C1111S-SF3B1, PladB, rep1

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: Pontine nuclei_C3_1

description: 7_Pons|19|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontine nuclei_P2_1

description: 6_Pons|9|Full ROI

tag: tissue

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads


title: Pontine nuclei_C2_2

description: 6_Pons|20|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: 22Rv1-C1111S-SF3B1, WX43, ATAC-Seq, rep3

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: 22Rv1-C1111S-SF3B1, WX43, rep2


title: Pontine nuclei_C2_1

description: 6_Pons|19|Full ROI

tag: tissue type

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontine nuclei_P1_2

description: 5_Pons|8|Full ROI

tag: tissue

tag: area

tag: region

tag: grey/whitematter

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: 22Rv1-C1111S-SF3B1, WX23, ATAC-Seq, rep3

tag: cell line

tag: genotype

tag: treatment


title: 22Rv1-C1111S-SF3B1, WX43, rep1


title: Pontine nuclei_C1_3

description: 5_Pons|21|Full ROI

tag: tissue type

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 22Rv1-C1111S-SF3B1, WX23, rep3

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: 22Rv1-C1111S-SF3B1, WX23, rep2


title: Pontocerebellar Tract_P6_2

description: Pons|25|Full ROI

tag: tissue type

tag: area

value: Pontocerebellar Tract

tag: region

tag: grey/whitematter

value: White

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontocerebellar Tract_P6_1

description: Pons|24|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

value: Yes

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 22Rv1-C1111S-SF3B1, WX43, rep3

tag: cell line

tag: genotype

tag: treatment


title: Pontocerebellar Tract_P5_3

description: Pons|13|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontocerebellar Tract_P5_2

description: Pons|12|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 22Rv1-C1111S-SF3B1, DMSO, rep1

tag: cell line

tag: genotype

tag: treatment


title: Pontocerebellar Tract_P6_3

description: Pons|26|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontine nuclei_C1_1

description: 5_Pons|19|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: 22Rv1-C1111S-SF3B1, DMSO, rep2

tag: cell line

tag: genotype

tag: treatment


title: 22Rv1-C1111S-SF3B1, WX23, rep1


title: 22Rv1-C1111S-SF3B1, DMSO, rep3


title: Pontocerebellar Tract_P5_1

description: Pons|11|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontocerebellar Tract_P4_3

description: 9_MidBrain_Pons-COVID|6|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontocerebellar Tract_P4_2

description: 9_MidBrain_Pons-COVID|2|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Pontocerebellar Tract_P3_3

description: 7_Pons|6|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontocerebellar Tract_P4_1

description: 9_MidBrain_Pons-COVID|1|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontocerebellar Tract_P3_2

description: 7_Pons|5|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Pontine nuclei_C1_2

description: 5_Pons|20|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontocerebellar Tract_P2_4

description: 6_Pons|8|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontocerebellar Tract_P2_2

description: 6_Pons|6|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Pontocerebellar Tract_P2_3

description: 6_Pons|7|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Pontocerebellar Tract_P2_1

description: 6_Pons|5|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontocerebellar Tract_P1_3

description: 5_Pons|6|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos1/2DKO mice, biological rep 2

type: RNA

city: Salamanca

first: Fernando

middle: C

last: Baltanas

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigacion del Cancer

hyb_protocol: Protocol was developed following GeneChip® WT PLUS Reagent Kit userguide.

scan_protocol: Affymetrix GeneChip Command Console 3.2

data_processing: R version 3.6.3 was used for statistical analyses along with Python version 3.9 for text file processing. Signal intensity values were obtained from expression microarray CEL files after robust multichip average (RMA)

label: Biotin

source_name: Mouse primary fibroblasts

label_protocol: Fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA is required for fragmentation and labeling

growth_protocol: Sos1WT, Sos1KO, Sos2KO and Sos1/2DKO primary MEFs were isolated from E13.5 embryos of the corresponding genotypes and used as primary (low passage) cultured cells and they were grown in DMEM with 10% FBS, glutamine and antibiotics

extract_protocol: RNA was isolated from subconfluent MEFs with Nyzol and QIAGEN RNeasy Mini kit (74104, QIAGEN) following the manufacturer’s indications

treatment_protocol: Mouse Embryonic Fibroblasts were treated with 4-hydroxytamoxifen for 12 days

tag: strain


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos2KO mice, biological rep 1


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos1KO mice, biological rep 3


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos1KO mice, biological rep 2


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos2KO mice, biological rep 3


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos2KO mice, biological rep 2


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos1/2DKO mice, biological rep 3


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos1/2DKO mice, biological rep 1


title: Pontocerebellar Tract_P1_2

description: 5_Pons|5|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Pontocerebellar Tract_P3_1

description: 7_Pons|4|Full ROI

tag: tissue

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: scanoffsety

tag: loq


title: dyW1 muscle fibers E17.5

city: Lisboa

first: Ana Rita

last: Carlos

address: FCUL, Campo Grande

country: Portugal

institute: Faculty of Sciences, University of Lisbon

data_processing:
Galaxy Europe platform
Quality of fastq.gz reads was analyzed fastq.gzC
Reads was trimmed and filtered using Cutadapt
Reads were aligned against the mouse reference genome using RNA STAR
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include normalized counts for each sample
Supplementary files format and content: tab-delimited text files include DeSeq2 analysis of wildtype versus dyW/dyW samples

source_name: skeletal muscle

extract_protocol:
Muscle fibers were directly incubated with RTL lysis buffer
Nextera library preparation protocol (Nextera XT DNA Library Preparation kit, Illumina) was used for library preparation, including cDNA ‘tagmentation’, PCR-mediated dT adaptor addition, and library amplification
The libraries were sequenced using the NextSeq 2000 P2 Reagents (100 cycles) (Illumina)

value: skeletal muscle

tag: developmental stage

tag: cell type

value: muscle fibers

tag: genotype

value: dyW/dyW


title: Pontocerebellar Tract_P1_1

description: 5_Pons|4|Full ROI

tag: tissue

value: postmortem brain

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: wt1 muscle fibers E17.5

tag: developmental stage

tag: cell type

tag: genotype

value: wt


title: 12 days 4OHT-treated mouse primary fibroblasts from Sos1KO mice, biological rep 1

tag: strain


title: 12 days 4OHT-treated mouse primary fibroblasts from Wild-Type mice, biological rep 3


title: 12 days 4OHT-treated mouse primary fibroblasts from Wild-Type mice, biological rep 1


title: wt3 muscle fibers E17.5

tag: tissue


title: wt2 muscle fibers E17.5


title: wt4 muscle fibers E17.5


title: Pontocerebellar Tract_C4_2

description: 7_Pons-Control|5|Full ROI

tag: tissue type

tag: area

tag: region

tag: grey/whitematter

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: scanoffsety

tag: loq


title: Pontocerebellar Tract_C3_3

description: 7_Pons|18|Full ROI

tag: tissue

tag: tissue type

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx


title: Pontocerebellar Tract_C4_1

description: 7_Pons-Control|4|Full ROI

tag: area

tag: region

tag: grey/whitematter

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Slc16a11fl/fl x CD4Cre Texh #3

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5115 Centre Ave.

institute: University of Pittsburgh

description:
KO_3_Texh
MCT11 cKO CD8+ Tex from B16 tumor

data_processing:
Partek-Flow
Adapter Trimming with Cutadapt.
Alignment to mm38 with STAR 2.7.
Differential expression analysis with DESeq2.
Assembly: mm38
Supplementary files format and content: Tab-separated text file includes an RPKM gene count matrix.
Supplementary files format and content: Microsoft Excel spreadsheet (xls) containing fold change and differential expression analysis.

source_name: B16 melanoma tumor

extract_protocol:
mRNA extraction and cDNA synthesis were performed using Takara SMARTer ultra-low input RNA isolation kit for Illumina Sequencing.
Libraries were generated using the Illumina Nextera XT kit as per manufacturer's instructions.

tag: genotype

value: MCT11 cKO

tag: tissue

value: B16 melanoma tumor

tag: cell type

value: Sorted tumor-infiltrating lymphocytes (CD8+ exhausted T cells)


title: 12 days 4OHT-treated mouse primary fibroblasts from Wild-Type mice, biological rep 2

tag: strain


title: Pontocerebellar Tract_C3_2

description: 7_Pons|17|Full ROI

tag: tissue type

value: FFPE

tag: area

tag: lotid

tag: roi

tag: age

value: No

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pontocerebellar Tract_C4_3

description: 7_Pons-Control|6|Full ROI

tag: tissue

tag: region

value: Pons

tag: grey/whitematter

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Slc16a11fl/fl x CD4Cre Texh #2

description:
KO_2_Texh
MCT11 cKO CD8+ Tex from B16 tumor

tag: genotype

tag: cell type


title: Pontocerebellar Tract_C3_1

description: 7_Pons|16|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: age

value: Female

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Pontocerebellar Tract_C2_2

description: 6_Pons|17|Full ROI

tag: tissue

tag: region

tag: grey/whitematter

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: loq


title: Slc16a11fl/fl x CD4Cre Texh #1

description:
KO_1_Texh
MCT11 cKO CD8+ Tex from B16 tumor

tag: genotype

tag: cell type


title: Pontocerebellar Tract_C2_3

description: 6_Pons|18|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: Pontocerebellar Tract_C2_1

description: 6_Pons|16|Full ROI

tag: tissue

tag: region

tag: grey/whitematter

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: loq


title: Pontocerebellar Tract_C1_3

description: 5_Pons|18|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: HCC_TMA_20210804_09_20703_ROI029_Tumor

city: Boston

first: Joseph

last: Franses

state: Massachusetts

department: Cancer Center

institute: Massachusetts General Hospital

description: (v1.0) Cancer Transcriptome Atlas

data_processing:
Raw sequencing data were processed using the GeoMx NGS Pipeline to generate fastq files followed by dcc files
Sequences were aligned to the Cancer Transcriptome Atlas probe set using default settings
Assembly: hg38
Supplementary files format and content: rawCounts.tsv: gene count matrix file in tsv format
Supplementary files format and content: qnormCounts.tsv: Q3 normalized gene count matrix file in tsv format
Library strategy: GeoMx Spatial Transcriptomics

source_name: Liver cancer resection

extract_protocol:
We followed published experimental methods (NanoString) with modifications as noted below. Briefly, slides were baked at 60 °C for one hour, deparaffinized with CitriSolv (DECON), rehydrated, antigen-retrieved in 1x Tris-EDTA/pH 9 in a steamer for 15 min at 100 °C, proteinase K (Thermo Fisher Scientific, AM2548) digested at 0.1 ng/ml for 15 min at 37 °C, and postfixed in neutral-buffered formalin for 10 min, hybridized to UV-photocleavable barcode-conjugated RNA in situ hybridization probe set (CTA with 1,779 gene targets and 32 reference genes) overnight at 37 °C, washed to remove off-target probes and then counterstained with morphology markers for 2 h at room temperature. The morphology markers consisted of: 1:50 CD31 (Abcam, ab47063) and 1:50 Arginase-1 (Cell Signaling Technology, 93668S) in blocking buffer W (NanoString). The anti-CD31 antibody was conjugated using the Alexa Fluor 555 Lightning-Link kit (Abcam, ab269820) and the anti-Arginase-1 antibody with the Alexa Fluor 647 Lightning-Link kit (Abcam, ab269823). These two morphology markers allowed distinction between vessel areas of interest (AOIs) and tumor regions of interest (AOIs) within a microscopic region of interest (ROI). 22 Immunofluorescence images, ROI selection, segmentation into marker-specific AOIs and 23 spatially indexed barcode cleavage and collection were performed on a GeoMx DSP instrument 24 (NanoString). Typical exposure times were 400 ms for CD31 and 300 ms for Arg 1. Approximately 25 4 AOIs on average were collected per specimen (details in Table 1)
Library preparation was performed according to the manufacturer’s instructions and involved PCR amplification to add Illumina adapter sequences and unique dual sample indices. A minimum sequencing depth of 2 150–200 reads per square micron of illumination area was achieved by sequencing all CTA AOIs on a NovaSeq S2 (100 cycles, read 1: 27 nt, read 2: 27 nt, index 1: 8 nt, index 2: 8 nt).

tag: tissue

value: Liver cancer resection

tag: slide name

value: HCC TMA 04

tag: pool

tag: aoi type

value: Tumor


title: HCC_TMA_20210804_09_20703_ROI030_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_09_25860_ROI028_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Vessel


title: HCC_TMA_20210804_09_20703_ROI030_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_09_20703_ROI029_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_P6_3

description: Pons|23|Full ROI

tag: tissue type

value: Corticospinal Tract

tag: region

tag: grey/whitematter

value: White

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

value: Yes

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Corticospinal Tract_P6_2

description: Pons|22|Full ROI

tag: tissue

tag: area

tag: lotid

tag: roi

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: HCC_TMA_20210804_09_25860_ROI028_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210804_09_25860_ROI027_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Pontocerebellar Tract_C1_1

description: 5_Pons|16|Full ROI

tag: tissue type

value: Pontocerebellar Tract

tag: region

tag: grey/whitematter

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_25860_ROI027_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Pontocerebellar Tract_C1_2

description: 5_Pons|17|Full ROI

value: postmortem brain

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Corticospinal Tract_P6_1

description: Pons|21|Full ROI

tag: tissue

tag: area

tag: roi

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Corticospinal Tract_P5_2

description: Pons|10|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads


title: HCC_TMA_20210804_09_19181_ROI026_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_09_19181_ROI025_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_P4_3

description: 9_MidBrain_Pons-COVID|8|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_19181_ROI025_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Corticospinal Tract_P4_2

description: 9_MidBrain_Pons-COVID|7|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads


title: Corticospinal Tract_P3_3

description: 7_Pons|3|Full ROI

tag: tissue

tag: area

tag: roi

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_20703_ROI024_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210804_09_13084_ROI022_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_09_20703_ROI023_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_P3_2

description: 7_Pons|2|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads


title: Corticospinal Tract_P3_1

description: 7_Pons|1|Full ROI

tag: tissue

tag: area

tag: roi

tag: aoisurfacearea

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Corticospinal Tract_P5_3

description: Pons|14|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoinucleicount

tag: roicoordinatex


title: HCC_TMA_20210804_09_19181_ROI026_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area