title: B16F10 cells treated with BVT948, CD45+, Mer-Stat1 PLA+ area, replicate 2

description:
Library name: DSP-1001660020082-D-E01
Nanostring GeoMx DSP

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

tag: cell type

value: Melanoma murine cells

value: BVT948, 10 mg/kg, ip, qd

tag: primer used

value: GeoMx Seq Code D E01


title: C_HC_Sc0155

status: Public on Feb 07 2025

type: RNA

city: Brighton

first: Sarah

last: Unterberger

address: Biology Road

country: United Kingdom

institute: BSMS

hyb_protocol: For each sample, 25ng RNA was hybridised for 20 hours at 65°C with XT Hs HostResponse CSO code set containing 785 human genes including 12 internal reference genes using Nanostring’s nCounter XT Code-Set Gene Expression Assay protocol.

scan_protocol: Samples were loaded onto an nCounter cartridge and run on the Nanostring nCounter SPRINT™ Profiler. The digital analysis system is imaging the immobilised fluorescent reporters on the cartridge with a CCD camera through a microscope objective lens. Within each sample lane, multiple fields of view are imaged which are processed internally, fluorescent reporter tag counts are collected (Reporter Code Count; RCC).

data_processing: A quality check of raw data (RCC) was performed, followed by normalisation using the nSolver Analysis Software v4.0 (NanoString Technologies, Inc.). Only housekeeping genes with a raw probe count above 100 were included in the normalisation process. For normalisation, the background threshold was defined as mean+2SD of all negative controls for each sample separately and substracted from the counts. Samples were normalised by using the sample specific mRNA positive normalisation factor (PNF) and mRNA content normalisation factor (CNF) according to this formula: normalized count = count x PNF x CNF.

label: Reporter and capture probesets

molecule: total RNA

organism: Homo sapiens

source_name: Primary human peripheral blood monocytes

label_protocol: not applicable

extract_protocol: Whole venous blood was collected into sodium heparinised vacutainers (Becton Dickinson, Oxford, UK) and peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque gradients (Cedarlane, Burlington, Canada). Monocytes were then isolated using CD14+ selection beads (Miltenyi Biotec, Cologne, Germany) as per the manufacturer’s instructions. RNA was extracted using the RNeasy Mini Kit (QIAGEN, Stockach, Germany) according to manufacturer’s instructions.

tag: disease

value: Healthy Control

tag: Sex

value: female

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

value: not applicable

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: macrophage, wild type 5

type: SRA

city: Cambridge

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

description:
macrophage_WT_5
RNAseq_GPR35_macrophages.txt

library_source: transcriptomic

data_processing:
Sequencing of libraries was performed using an Illumina HiSeq 2500 platform generating 1x50bp reads.
Assembly: GRCm38 Mus musculus
Supplementary files format and content: tab-delimited txt files include RPKM for each sample

organism: Mus musculus

source_name: bone marrow-derived macrophage

extract_protocol:
RNA was extracted using the QIAGEN Rneasy kit (QIAGEN).
RNA libraries were prepared using TruSeq® Stranded mRNA Library Prepas per manufacturer's instructions

tag: tissue

value: bone marrow-derived macrophage

tag: genotype

value: Wild type

tag: treatment


title: SL470539

city: Ann Arbor

first: Elaine

last: Hebda-Bauer

state: Michigan

address: 205 Zina Pitcher Place

department: Michigan Neuroscience Institute

country: USA

institute: University of Michigan

data_processing:
Alignment: STAR: 2.7.3a
Quantification of gene-level counts: Subread version 2.0.0
Quality control and filtering: Rstudio (v.1.4.1717, R v. 4.1.1)
Differential expression analysis: limma v.3.48.3
Assembly: Rnor6, annotation: Ensembl v.103
Supplementary files format and content: Filtered log(2) cpm per Ensembl-annotated gene for each F2 hippocampal sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: hippocampus

growth_protocol: Selectively breeding rats for a high or low propensity to explore a novel environment produced the bHR and bLR lines, respectively, at the University of Michigan (Stead et al., 2006). After 37 generations, an initial set (“F0”) of bHRs and bLRs were chosen from 24 distinct families (12 bHR, 12 bLR) to cross-breed for creating 12 intercross families. Their “F1” offspring were screened for novelty-induced locomotion, and individuals with similarly high or low LocoScores were bred with each other to produce a re-emergence of diverse behavioral phenotypes in the “F2” generation. These 48 F2 litters generated 540 rats, 323 of which were phenotyped as young adults (2-4 months old). Our current study used a subset of these animals (F0: n=24, n=6/phenotype per sex; F2: n=250, n=125/sex) that overlapped with those in previous genetic studies (Chitre et al., 2022; Z. Zhou et al., 2019a) but was distinct from those included in our previous male-only RNA-Seq meta-analysis (Birt et al., 2021).  All procedures were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Animals and approved by the Institutional Animal Care and Use Committee at the University of Michigan.

extract_protocol:
Adults (postnatal days 113-132) were decapitated without anesthesia and brains extracted within two minutes. For the F0s, whole HPC was immediately dissected and flash frozen. For the F2s, whole brains were flash frozen, and then later hole punches from the dorsal and ventral HPC were pooled from four hemisected coronal slabs (-2.12 to -6.04 mm Bregma; (Paxinos & Watson, 2013)) for each animal. RNA was extracted using the Qiagen RNeasy Plus Mini Kit.
A Ribogreen Assay was performed using 2 ml of a 7X dilution to measure RNA concentration and total RNA amount. To measure RNA quality, 2 ml of various dilutions were loaded onto a HS RNA Fragment Analyzer chip. The samples were then normalized to 500ng input into 50ml volume for use in Poly A RNA-seq library reactions that were completed through Second Strand Synthesis and Purification. Diluted samples were used for a PicoGreen assay and loaded onto a HS Caliper chip for quality analysis of the cDNA libraries. Following Kapa qPCR, samples were sequenced on a NovaSeq S4 101PE flowcell targeting an average of 25 million reads.

treatment_protocol: Behavioral data analysis: All F0 and F2 rats were tested for locomotor activity in a novel environment (“LocoScore,” protocol: (Stead et al., 2006)). Exploratory and anxiety-related behaviors were measured on an Elevated Plus Maze (protocol: (Chitre et al., 2022)), including distance traveled (cm), time immobile (sec), and percent time in the open arms. A subset of F2s (n=209) was subsequently tested for Sign Tracking vs. Goal Tracking behavior during the last two days of a week-long Pavlovian Conditioned Approach task (protocol: (Meyer et al., 2012)) using a combined score (“PavCA Index”) summarizing behaviors indicating preference for the conditioned stimuli (lever) vs. unconditioned stimuli (food magazine).

value: hippocampus

tag: hippocampal siide used

value: left

value: Male

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: One

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: C_HC_Sc0151

tag: disease

tag: Sex

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: SL470526

tag: tissue

tag: hippocampal siide used

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial


title: C_HC_RIO007

tag: disease

tag: Sex

value: male

tag: age (years)

value: unknown

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: macrophage, GPR35 knockout 2

description:
macrophage_KO_2
RNAseq_GPR35_macrophages.txt

tag: tissue

tag: genotype

value: GPR35 knockout

tag: treatment


title: SL470531

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: DNA from TeSR condition cultured H1 cells repeat 2

type: genomic

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

country: China

institute: Zhejiang University School of Medicine

hyb_protocol: Hybridize the resuspended DNA sample with the prepared chip and place it in the hybridization oven to react overnight. During the hybridization process, the fragmented DNA is denatured and anneals with the site-specific bases, with the specific bases binding to the beads on the chip.

scan_protocol: Place the processed chip into the scanner, where laser excitation is used to excite the fluorescent tags on the single-base extension products on the chip. The scanner captures the fluorescence emitted by the fluorescent tags and generates high-resolution images

data_processing: An Infinium MethylationEPIC BeadChip (Illumina) was used to interrogate the genome-wide methylation profile following the Infinium HD methylation assay protocol.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: embryonic stem cell

label_protocol: Zymo EZ DNA Methylation kit (Zymo Research, CA, USA) following the manufacturer's recommendations for bisulfide conversion

growth_protocol: Primed Cells were grown in TeSR, Naïve cells were grown in 4iL and FINE conditions

extract_protocol: Genomic DNA was isolated by a DNeasy Blood & Tissue Kit (Qiagen)

tag: tissue

value: embryonic stem cell

tag: cell line

tag: cell type


title: CRISPRcut_Day12_TR1_B3_R2

city: Seattle

first: Jay

last: Shendure

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
SCF pilot gRNA-barcode library
pilot_count_table.csv

library_source: genomic

data_processing:
ORF-barcode subassembly. In order to associate ORFs to DNA barcodes, sequencing libraries were prepared from barcoded COMET libraries (see Subassembly of ORF-barcode pairs). Reads from tagmented COMET libraries were aligned to ORF sequences using bowtie2 v2.2.5 to determine which ORF was tagged. A custom bowtie2 index of ORF sequences was generated and aligned against. A summary output format of the data was then generated that included the read name, the degenerate barcode sequence, the bowtie2-determined tagged ORF and the mapping quality of the read, which was then used as input for further QC to determine the list of BC-associated ORFs. The initial list of barcodes and ORFs were filtered to exclude reads with a mapping quality score less than 31, barcodes that include any ‘N’ bases, and barcodes associated with common sequencing error modes (e.g., GGGGGGGGGGGGGGGGGGGGGGGGG). We then eliminated barcodes with fewer than 10 reads of supporting evidence, which guards against seemingly unique barcodes that actually include rarely occurring sequencing errors. Ambiguous barcodes were eliminated which mapped to more than one ORF, however, these were included if there was one ORF with more than 90% of the read evidence supporting one barcode. The remaining barcode-ORF pairs were then used to identify the ORF on a plasmid relying on the sequencing of just the barcode (Table S1).
Processing barcode-gRNA sequencing data. Amplicon sequencing reads of gDNA extracted from cells sorted by GFP:mCherry ratio contain two important pieces of information: the sequenced gRNA along with a barcode that was previously associated with a specific ORF. As a first step we convert the raw read data into a summary output format that includes ORF (determined with the previously generated barcode-ORF lookup table), the target identity of the sequenced gRNA, along with the raw sequencing information of the barcode and guide. Summary output files from libraries generated from different conditions and sorted bins are then combined into one file that is then used for statistical analysis.
Supplementary files format and content: TableS1_BC_ORF_associations.csv contains associations between barcodes and ORFs. The file contains associations for both the pilot SCF and short half-life TF screens, and associations from either screen can be subset from the file using the 'experiment' column.
Supplementary files format and content: pilot_count_table.csv contains read count data for the pilot SCF experiment. Read counts are provided for each barcode-target pair in each transfection replicate. Within individual transfection replicates, reads counts in each FACS bin are provided.
Supplementary files format and content: short_HL_TF_count_table.csv contains read count data for the short half-life transcription factor experiment. Read counts are provided for each barcode-target pair in each transfection replicate. Within individual transfection replicates, reads counts in each FACS bin are provided.
Library strategy: amplicon sequencing

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL).

extract_protocol:
Genomic DNA was extracted using the Qiagen Dneasy Blood and Tissue kit from sorted K562-rtTA-Cas9 cells that had been partitioned by FACS based on GFP:mCherry ratio.
Subassembly of ORF-barcode pairs: Plasmid libraries with gRNAs, barcodes, and ORFs were tagmented with N5 loaded Tn5 transposase (Diagenode). DNA fragments containing ORF-barcode information were enriched from the tagmented plasmid by two-step PCR. The first round of PCR utilized a primer that hybridizes upstream of the barcode region as well as an N5 specific primer that hybridizes to the tagmentation event. First round products were cleaned using Ampure beads and eluted in Qiagen EB. The second round completed the amplicon by adding sample indexes and Illumina sequencing adapters. PCR products were run on a pre-cast 6% TBE polyacrylamide gel (Thermo), and DNA fragments ranging in size from 400-1000 base pairs were excised from the gel and purified. The resulting library was quantified and sequenced on an Illumina instrument. Generation of gRNA-barcode Illumina amplicons: Genomic DNA was extracted from pellets of frozen cells using a DNEasy Blood and Tissue kit (Qiagen, 69504). Illumina amplicons containing gRNA and barcode information were amplified using two-step PCR. In the first round of PCR, genomic DNA from each bin was divided between eight 50 uL PCR reactions and amplified with primers that hybridize to the COMET construct upstream of the gRNA and downstream of the barcode. The eight PCRs were pooled, cleaned with 1X Ampure beads, and eluted in Qiagen EB. The eluted first round product was amplified with primers that added sample indexes and Illumina sequencing adapters. Final amplicons were again Ampure cleaned, quantified, and sequenced on an Illumina instrument.

value: lymphoblast

tag: genotype

value: Cas9 and rtTA

tag: group

tag: perturbation

value: CRISPRcut

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: B16F10 cells treated with BVT948, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 2

city: Birmingham

first: Nestor

last: Prieto-Dominguez

state: AL

department: Microbiology

institute: The University of Alabama at Birmingham (UAB)

description:
Library name: DSP-1001660020082-D-D10
Nanostring GeoMx DSP

data_processing:
fastq files were processed with GeoMx NGS pipeline in order to convert them to dcc files.
dcc files were loaded into the Nanostring DSP instrument. Raw data were filtered and normalized using the Nanostring built-in software and the GeoMxTools R Package (version 3.10.0). Count data were obtained at the end of the normalization process.
Assembly: Mus musculus NGS WTA v1.0
Supplementary files format and content: GeoMx counts from GeoMx DST groups.xlsx: List of the gene counts for each GeoMx-picked area.
Supplementary files format and content: GeoMX experiment ROI information and primer data.xlsx: List of the seq Code primers used for each ROI segment.
Supplementary files format and content: dcc: Processed count files.
Supplementary files format and content: stats: Stats obtained from GeoMX NGS pipeline.

source_name: Melanoma primary tumor

growth_protocol: B16F10 cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin at 37 degrees. When confluent, 1*10^5 cells were implanted subcutaneously into the right flank of C57Bl/6J mice (8 weeks old, both sexes at roughly equal numbers). Treatment started when tumors were palpable (about 8 days after implantation).

extract_protocol:
Tumors were collected 6 days after the start of the treatment and fixed using 10% neutral buffered formalin for 1 month. Replicate tumors were embedded on the same paraffin block and sliced into 5 µm thick slides. Slides were then immunoprobed for gH2Ax, Pros1 or assayed for Mer-Stat1 binding using Sigma Millipore PLA probes to determine the regions of interest (ROI).
Slides were deparaffined, rehydrated and incubated with proteinase K to unmask the cellular RNA targets. Tumors were then treated overnight with RNA Murine Whole Transcriptome Atlas (WTA) probes from Nanostring Technologies to detect the exposed RNAs. Slides were then incubated with Alexa fluor 532 labeled PanCK and Alexa fluor 594 labeled CD45 antibodies.
Slides were loaded into the GeoMx DSP instrument following the manufacturer's instructions. 4 representative regions of interest (positive for gH2Ax staining, positive for Pros1 staining, positive for Mer-Stat1 binding or negative for the three previous probes) were selected in each tumor section, manually separating CD45+ and PanCK+ areas inside each picked region. Oligos were then cleaved and collected in a DSP collection plate supplied by Nanostring Technologies. Libraries were prepared using Nanostring Seq code plates C and D and pooled for sequencing using Illumina NovaSeq 600

treatment_protocol: Tumors were treated with cisplatin (5mg/kg, ip, days 1-3 of the experiment), BVT948 (10mg/kg, ip, qd), or their combination. Mice in the vehicle group were treated with PBS (ip, qd).

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

value: Melanoma murine cells

tag: treatment

value: BVT948, 10 mg/kg, ip, qd

tag: primer used

value: GeoMx Seq Code D D10


title: Ileum, wild type 3

description:
Ileum_WT_3
RNAseq_GPR35_ileum.txt

source_name: Ileum

value: Ileum

value: Wild type


title: C_HC_AIM23

tag: disease

value: Healthy Control

tag: Sex

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

value: not applicable

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: C_HC_Sc0153

value: female


title: B16F10 cells treated with BVT948, CD45+, Pros1+ area, replicate 2

description:
Library name: DSP-1001660020082-D-D09
Nanostring GeoMx DSP

tag: tissue

tag: cell line

tag: cell type

value: GeoMx Seq Code D D09


title: B16F10 cells treated with BVT948, PanCK+, Mer-Stat1 PLA+ area, replicate 2

description:
Library name: DSP-1001660020082-D-D12
Nanostring GeoMx DSP

value: GeoMx Seq Code D D12


title: SL470524

value: hippocampus

tag: hippocampal siide used

value: right

value: Male

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: DNA from TeSR condition cultured H1 cells repeat 1

tag: tissue

value: embryonic stem cell

tag: cell line

tag: cell type


title: B16F10 cells treated with BVT948, PanCK+, Pros1+ area, replicate 2

description:
Library name: DSP-1001660020082-D-D08
Nanostring GeoMx DSP

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

value: Melanoma murine cells

tag: treatment

value: BVT948, 10 mg/kg, ip, qd

tag: primer used

value: GeoMx Seq Code D D08


title: SL470523

tag: hippocampal siide used

value: left

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial


title: SL470522

tag: tissue

tag: hippocampal siide used

tag: Sex

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: DNA from FINE condition cultured H1 cells repeat 1

tag: tissue

tag: cell line

tag: cell type


title: B16F10 cells treated with BVT948, CD45+, gH2Ax+ area, replicate 2

description:
Library name: DSP-1001660020082-D-D07
Nanostring GeoMx DSP

tag: mouse strain

tag: treatment

tag: primer used

value: GeoMx Seq Code D D07


title: DNA from 4iL condition cultured H1 cells repeat 2


title: SL470521

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial


title: C20_0917_076

tag: disease

value: Severe COVID-19

tag: Sex

value: female

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: B16F10 cells treated with BVT948, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 2

description:
Library name: DSP-1001660020082-D-D11
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code D D11


title: C20_0916_075


title: C20_0825_058


title: SL470525

value: hippocampus

tag: hippocampal siide used

value: right

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: DNA from 4iL condition cultured H1 cells repeat 1

tag: tissue

tag: cell line

tag: cell type


title: SL470520

tag: hippocampal siide used

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial


title: C20_0824_053

tag: disease

tag: Sex

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: C_HC_AIM22

value: Healthy Control

value: not applicable


title: SL470519

tag: tissue

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: B16F10 cells treated with BVT948, PanCK+, Mer-Stat1 PLA+ area, replicate 1

description:
Library name: DSP-1001660020082-D-D04
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

tag: cell type

value: Melanoma murine cells

tag: treatment

value: BVT948, 10 mg/kg, ip, qd

tag: primer used

value: GeoMx Seq Code D D04


title: B16F10 cells treated with BVT948, CD45+, Mer-Stat1 PLA+ area, replicate 1

description:
Library name: DSP-1001660020082-D-D05
Nanostring GeoMx DSP

value: GeoMx Seq Code D D05


title: C20_0820_050

tag: disease

value: Severe COVID-19

tag: Sex

value: female

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: DNA from FINE condition cultured H1 cells repeat 2

value: embryonic stem cell


title: SL470518

value: hippocampus

tag: hippocampal siide used

value: left

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch


title: B16F10 cells treated with BVT948, CD45+, Pros1+ area, replicate 3

description:
Library name: DSP-1001660020082-D-E05
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code D E05


title: 4xLPS-2-LPS

city: Montreal

first: Przemyslaw

last: Sapieha

state: Quebec

address: 5345 Assumption Blvd

country: Canada

institute: Maisonneuve-Rosemont Research Center

description: Sample 17

data_processing:
Analysis was performed using the Torrent Suite software v4.4 (Thermo Fisher) and the whole Transcriptome Analysis Plugin v 4.2-r7 (Thermo Fisher)
The whole Transcriptome Analysis Plugin aligns reads on mouse reference genome (mm10) using Tophat2 then unmapped reads are aligned using Bowtie2 and merged together.
FPKM are calculated using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

source_name: BMDM

growth_protocol: F12 DMEM growth medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from BMDMs using the RNeasy Mini Kit (Qiagen). The mRNA was then purified from 500 ng of total RNA using the Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific). Whole-transcriptome libraries were prepared using the Ion Total RNA-seq Kit v2. The yield and size distribution of the amplified libraries were assessed with the Agilent 2100 Bioanalyzer using the DNA 1000 Kit. Sequencing was performed on an Ion Proton (Thermo Fisher Scientific).
Analysis was performed using the Torrent Suite software v5.12 (Thermo Fisher). The whole Transcriptome Analysis Plugin aligns reads on mouse reference genome (mm10) using Tophat2 then unmapped reads are aligned using Bowtie2 and merged together. FPKM are calculate using Cufflinks.

tag: strain

tag: genotype

value: Wildtype

value: Bone Marrow-Derived Macrophage

value: PBS in vivo + in vitro LPS stimulation


title: B16F10 cells treated with BVT948, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 1

description:
Library name: DSP-1001660020082-D-D02
Nanostring GeoMx DSP

value: GeoMx Seq Code D D02


title: B16F10 cells treated with BVT948, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 1

description:
Library name: DSP-1001660020082-D-D03
Nanostring GeoMx DSP

value: GeoMx Seq Code D D03


title: SL470517

tag: hippocampal siide used

tag: Sex

value: Male

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco rack

tag: loco box

tag: dob

tag: dod


title: C20_0728_035

tag: disease

tag: Sex

value: male

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: 4xLPS-1-LPS

description: Sample 16

tag: strain

tag: genotype

tag: cell type

tag: treatment


title: B16F10 cells treated with BVT948, PanCK+, gH2Ax+ area, replicate 2

description:
Library name: DSP-1001660020082-D-D06
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

value: Melanoma murine cells

value: BVT948, 10 mg/kg, ip, qd

tag: primer used

value: GeoMx Seq Code D D06


title: 1xLPS-3-LPS

description: Sample 15

value: 1xLPS in vivo + in vitro LPS stimulation


title: B16F10 cells treated with BVT948, CD45+, Pros1+ area, replicate 1

description:
Library name: DSP-1001660020082-D-D01
Nanostring GeoMx DSP

value: GeoMx Seq Code D D01


title: B16F10 cells treated with BVT948, PanCK+, Pros1+ area, replicate 1

description:
Library name: DSP-1001660020082-D-C12
Nanostring GeoMx DSP

value: GeoMx Seq Code D C12


title: SL470515

value: hippocampus

tag: hippocampal siide used

value: right

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box


title: C20_0630_014

tag: disease

value: Severe COVID-19

tag: Sex

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: C20_0908_067

value: Mild COVID-19

value: female


title: C20_0908_069


title: 1xLPS-1-LPS

description: Sample 13

tag: strain

tag: genotype

value: Wildtype

tag: cell type

value: Bone Marrow-Derived Macrophage

tag: treatment


title: SL470514

tag: tissue

tag: hippocampal siide used

value: Male

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: dob

tag: dod


title: 4xLPS-3-LPS

description: Sample 18

tag: strain

tag: genotype

tag: cell type

tag: treatment

value: PBS in vivo + in vitro LPS stimulation


title: B16F10 cells treated with BVT948, PanCK+, gH2Ax+ area, replicate 1

description:
Library name: DSP-1001660020082-D-C10
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

value: Melanoma murine cells

value: BVT948, 10 mg/kg, ip, qd

tag: primer used

value: GeoMx Seq Code D C10


title: C20_0730_039

tag: disease

tag: Sex

value: male

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: SL470513

value: hippocampus

tag: hippocampal siide used

value: left

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box


title: C20_0827_062

tag: disease

value: Mild COVID-19

tag: Sex

value: female

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: B16F10 cells treated with BVT948, CD45+, gH2Ax+ area, replicate 1

description:
Library name: DSP-1001660020082-D-C11
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code D C11


title: SL470512

tag: hippocampal siide used

value: right

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: dob

tag: dod


title: B16F10 cells treated with PBS, CD45+, Mer-Stat4 PLA+ area, replicate 4

description:
Library name: DSP-1001660020082-D-C09
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D C09


title: B16F10 cells treated with PBS, PanCK+, Mer-Stat4 PLA+ area, replicate 4

description:
Library name: DSP-1001660020082-D-C08
Nanostring GeoMx DSP

value: GeoMx Seq Code D C08


title: PBS-3-LPS

description: Sample 12

tag: strain

tag: genotype

value: Wildtype

value: Bone Marrow-Derived Macrophage

value: 4xLPS in vivo + in vitro LPS stimulation


title: SL470511

tag: hippocampal siide used

tag: Sex

value: Female

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box


title: PBS-1-LPS

description: Sample 10

tag: strain

tag: genotype

tag: cell type

tag: treatment


title: B16F10 cells treated with PBS, CD45+, gH2Ax-/Pros1-/Mer-Stat4 PLA- area, replicate 4

description:
Library name: DSP-1001660020082-D-C07
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

value: Melanoma murine cells

tag: primer used

value: GeoMx Seq Code D C07


title: SL470510

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: dob

tag: dod


title: 4xLPS-3-NO

description: Sample 9

tag: strain

tag: genotype

tag: cell type

tag: treatment

value: PBS in vivo and no in vitro stimulation


title: SL470516

tag: tissue

tag: hippocampal siide used

value: right

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: GT

tag: pca index_days6and_7

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box


title: 1xLPS-2-LPS

description: Sample 14

tag: strain

tag: genotype

value: Wildtype

tag: cell type

value: Bone Marrow-Derived Macrophage

tag: treatment

value: 1xLPS in vivo + in vitro LPS stimulation


title: C20_0730_038

tag: disease

value: Mild COVID-19

tag: Sex

value: female

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: 4xLPS-2-NO

description: Sample 8


title: SL470508

tag: tissue

tag: hippocampal siide used

value: Female

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: One

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: dob

tag: dod


title: C20_0827_061

tag: disease

tag: Sex

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: B16F10 cells treated with PBS, PanCK+, Pros1+ area, replicate 4

description:
Library name: DSP-1001660020082-D-C04
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

tag: cell type

value: Melanoma murine cells

tag: treatment

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D C04


title: PBS-2-LPS

description: Sample 11

tag: strain

tag: genotype

value: 4xLPS in vivo + in vitro LPS stimulation


title: 1xLPS-2-NO

description: Sample 5

value: 1xLPS in vivo and no in vitro stimulation


title: C20_0629_013

value: male


title: B16F10 cells treated with PBS, CD45+, Pros1+ area, replicate 4

description:
Library name: DSP-1001660020082-D-C05
Nanostring GeoMx DSP

value: GeoMx Seq Code D C05


title: Sample 14 E-Cig

city: Winnipeg

first: Christopher

last: Pascoe

state: MB

address: 602-715 McDermot Avenue, Children's Hospital Research Institute of Manitoba

department: Physiology & Pathophysiology

institute: University of Manitoba

data_processing:
Raw reads were quality and adapter trimmed using cutadapt and then aligned to the Hg38 reference genome using STAR
Gene count matrix generated using FeatureCounts
Assembly: Hg38
Supplementary files format and content: csv file with raw counts for each sample

source_name: Lung

extract_protocol:
RNA extracted from lung tissue stored in RNAlater using Ambion PureLink RNA Mini Kit
Illumina's TruSeq mRNA Stranded kit

value: Lung

value: E-cig


title: SL470061

value: hippocampus

tag: hippocampal siide used

value: left

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box


title: 1xLPS-3-NO

description: Sample 6

tag: strain

tag: genotype

value: Wildtype

tag: cell type

value: Bone Marrow-Derived Macrophage

tag: treatment


title: SL470059

tag: tissue

tag: hippocampal siide used

tag: Sex

value: Female

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: dob

tag: dod


title: treated HCT116 input

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 predicted method with default parameters(Model-based analysis of ChIP-Seq (MACS), Genome Biol). MACS scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size.
Strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics. It is based on the fact that a high quality IP-seq experiment produces significant clustering of enriched DNA sequence tags at locations bound by the protein of interest, and that the sequence tag density accumulates on   forward and reverse strands centered around the binding site. get.binding.characteristics function of SPP R package was used to calculate the correlation between forward and reverse strands, which can reflect whether the chromatin immunoprecipitation effect is optimal.
After mapping reads to the reference genome, we used the MACS2 version 2.1.0 (model-based analysis of ChIP-seq) (Zhang et al., 2008) peak finding algorithm to indentify regions of IP enrichment over background. A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all   displayed.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: bigwig files

source_name: Human colon cancer cell

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA with stabilized G-Quadruplex were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: Cells were treated with 5-aza for 24 hours.

tag: cell line

tag: chip antibody

value: Not applied

tag: treatment

value: treated with 5-aza for 24h


title: Sample 12 E-Cig

tag: tissue


title: B16F10 cells treated with PBS, CD45+, gH2Ax+ area, replicate 4

description:
Library name: DSP-1001660020082-D-C03
Nanostring GeoMx DSP

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell type

value: Melanoma murine cells

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D C03


title: B16F10 cells treated with PBS, PanCK+, gH2Ax-/Pros1-/Mer-Stat4 PLA- area, replicate 4

description:
Library name: DSP-1001660020082-D-C06
Nanostring GeoMx DSP

value: GeoMx Seq Code D C06


title: SL470060

value: hippocampus

tag: hippocampal siide used

value: right

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: loco box


title: untreated HCT116 input

tag: cell line

tag: chip antibody

tag: treatment

value: untreated


title: treated HCT116 ChIP-seq rep3

value: Anti-Quadruplex DNA (5E11, Absolute Antibody Ltd.)


title: B16F10 cells treated with PBS, PanCK+, gH2Ax+ area, replicate 4

description:
Library name: DSP-1001660020082-D-C02
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell type

tag: primer used

value: GeoMx Seq Code D C02


title: 1xLPS-1-NO

description: Sample 4

tag: strain

tag: genotype

value: Wildtype

value: Bone Marrow-Derived Macrophage

value: 1xLPS in vivo and no in vitro stimulation


title: PBS-2-NO

description: Sample 2

value: 4xLPS in vivo and no in vitro stimulation


title: C20_0713_025

tag: disease

value: Mild COVID-19

tag: Sex

value: male

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: B16F10 cells treated with PBS, PanCK+, Mer-Stat1 PLA+ area, replicate 3

description:
Library name: DSP-1001660020082-D-B12
Nanostring GeoMx DSP

value: Melanoma primary tumor

value: GeoMx Seq Code D B12


title: SL470057

tag: hippocampal siide used

value: Male

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL470056

tag: tissue

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: loco box


title: SL470058

tag: tissue

tag: hippocampal siide used

value: right

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: C20_0727_030

tag: disease

tag: Sex

tag: age (years)

tag: igg against s1 spike protein (microg/ml)

tag: igm against s1 spike protein (microg/ml)

tag: days since positive pcr test


title: SL470509

tag: tissue

tag: hippocampal siide used

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: One

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: epm rawdatafile

tag: loco box


title: SL470055

tag: tissue

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: treated HCT116 ChIP-seq rep1

tag: cell line

tag: chip antibody

value: Anti-Quadruplex DNA (5E11, Absolute Antibody Ltd.)

tag: treatment

value: treated with 5-aza for 24h


title: 4xLPS-1-NO

description: Sample 7

tag: strain

tag: genotype

value: Wildtype

tag: cell type

value: Bone Marrow-Derived Macrophage

value: PBS in vivo and no in vitro stimulation


title: PBS-3-NO

description: Sample 3

value: 4xLPS in vivo and no in vitro stimulation


title: treated HCT116 ChIP-seq rep2


title: B16F10 cells treated with PBS, CD45+, Pros1+ area, replicate 3

description:
Library name: DSP-1001660020082-D-B09
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

value: Melanoma murine cells

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D B09


title: B16F10 cells treated with PBS, CD45+, Mer-Stat1 PLA+ area, replicate 3

description:
Library name: DSP-1001660020082-D-C01
Nanostring GeoMx DSP

value: GeoMx Seq Code D C01


title: SL470054

value: hippocampus

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: loco box


title: SL470053

tag: tissue

tag: hippocampal siide used

value: right

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: One

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: B16F10 cells treated with PBS, CD45+, gH2Ax+ area, replicate 3

description:
Library name: DSP-1001660020082-D-B07
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code D B07


title: B16F10 cells treated with PBS, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 3

description:
Library name: DSP-1001660020082-D-B11
Nanostring GeoMx DSP

value: GeoMx Seq Code D B11


title: HET-1A cells, Pepsin+APR, biol rep 2

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

description:
Library name: H_3B
Column name in HET1A_GeneCount.txt: H_Pepsin+APR_rep2_count

data_processing:
The MAPRSeq3 RNA-seq pipeline is used for counting.
EdgeR is used for differential gene expression analysis with FDR ≤ 0.05 and |log2 fold change| ≥ 0.375.
Ingenuity Pathway Analysis (IPA) was performed to identify the top significantly biological pathways.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: Het-1A and BAR-T cells were maintained in BEGM and KGM, respectively. BEGM was supplemented with 1x Antibiotic-Antimycotic. KGM was supplemented with hydrocortisone, insulin, and transferrin as provided, along with 180 μM adenine, 10 ng/ml cholera toxin, 70 μg/ml bovine pituitary extract, 5% fetal bovine serum, and 1x Antibiotic-Antimycotic. BAR-T cells were cultured on collagen-I coated plasticware, while Het-1A cells were cultured on uncoated plasticware. The cultures were incubated at 37°C in a 5% CO₂ atmosphere.

extract_protocol:
RNeasy
Illumina stranded total RNA, 500ng starting input

treatment_protocol: Unless noted, cultures were treated in triplicate with HBSS at pH 7, with or without 0.1 mg/mL porcine pepsin and/or 10 μM amprenavir (in DMSO) or equivalent volume of DMSO (solvent control) at 37°C and 5% CO2 for 1 hour. Following treatment, the cells were washed twice with HBSS and incubated in normal growth media at 37°C and 5% CO2 for an additional hour before harvest to extract the total RNA.

value: esophageal epithelium

value: pH 7.0 HBSS + pepsin + amprenavir


title: HET-1A cells, Pepsin+APR, biol rep 3

description:
Library name: H_3C
Column name in HET1A_GeneCount.txt: H_Pepsin+APR_rep3_count


title: untreated HCT116 ChIP-seq rep3

tag: chip antibody

value: Anti-Quadruplex DNA (5E11, Absolute Antibody Ltd.)

value: untreated


title: B16F10 cells treated with PBS, PanCK+, Pros1+ area, replicate 3

description:
Library name: DSP-1001660020082-D-B08
Nanostring GeoMx DSP

value: Melanoma primary tumor

value: C57bl/6J, 8-week old, both sexes.

value: Melanoma murine cells

value: GeoMx Seq Code D B08


title: untreated HCT116 ChIP-seq rep2


title: HET-1A cells, Pepsin+APR, biol rep 1

description:
Library name: H_3A
Column name in HET1A_GeneCount.txt: H_Pepsin+APR_rep1_count


title: Alveolar macrophage, Sdha-KO, rep3

city: Seoul

first: Seung Geun

last: Song

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University

description:
Library name: Alveolar macrophage, Sdha-KO3
Sdha-KO3

data_processing:
High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, Inc., USA). Raw sequencing data underwent quality trimming using BBDuk to retain high-quality reads with an average Phred quality score > Q20. Processed reads were mapped to the mouse reference genome (mm10) using Bowtie2. The resulting raw counts for each gene were obtained using Bedtools and exported for further analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from FACS-sorted mature AMs of Sdha-mKO and wildtype mice using TRIzol reagent (TR 188, MRC Inc, Cincinnati, USA). RNA quality was assessed by Agilent 2100 Bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Fisher Scientific Inc., DE, USA).
RNA sequencing libraries were constructed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen GmbH, Wien, Austria) according to the manufacturer’s protocol. In brief, each 500 ng total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components.

value: Lung

value: Alveolar macrophages

tag: genotype

value: Sdha-knockout

tag: batch


title: untreated HCT116 ChIP-seq rep1


title: HET-1A cells, Pepsin, biol rep 3

description:
Library name: H_2C
Column name in HET1A_GeneCount.txt: H_Pepsin_rep3_count

value: pH 7.0 HBSS + pepsin


title: PBS-1-NO

description: Sample 1

tag: strain

value: Wildtype

value: Bone Marrow-Derived Macrophage

value: 4xLPS in vivo and no in vitro stimulation


title: B16F10 cells treated with PBS, CD45+, Mer-Stat1 PLA+ area, replicate 2

description:
Library name: DSP-1001660020082-D-B05
Nanostring GeoMx DSP

value: PBS, ip, qd

value: GeoMx Seq Code D B05


title: SL470052

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

value: Female

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: One

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SL470050

tag: tissue

tag: hippocampal siide used

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: Alveolar macrophage, Sdha-KO, rep1

description:
Library name: Alveolar macrophage, Sdha-KO1
Sdha-KO1

tag: tissue

value: Lung

tag: cell type

tag: genotype

tag: batch


title: B16F10 cells treated with PBS, PanCK+, gH2Ax+ area, replicate 3

description:
Library name: DSP-1001660020082-D-B06
Nanostring GeoMx DSP

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

value: Melanoma murine cells

tag: treatment

tag: primer used

value: GeoMx Seq Code D B06


title: Alveolar macrophage, Sdha-KO, rep2

description:
Library name: Alveolar macrophage, Sdha-KO2
Sdha-KO2

value: Alveolar macrophages

value: Sdha-knockout


title: HET-1A cells, Control, biol rep 3

description:
Library name: H_1C
Column name in HET1A_GeneCount.txt: H_Control_rep3_count

value: esophageal epithelium

value: pH 7.0 HBSS


title: SL470048

value: hippocampus

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SL470051

tag: tissue

tag: hippocampal siide used

value: right

tag: Sex

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: Alveolar macrophage, wildtype, rep2

description:
Library name: Alveolar macrophage, Wildtype2
WT2

tag: tissue

tag: cell type

tag: genotype

value: Wildtype

tag: batch


title: SL470049

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: One

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: learningclassification

value: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: B16F10 cells treated with PBS, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 3

description:
Library name: DSP-1001660020082-D-B10
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: cell line

tag: cell type

tag: treatment

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D B10


title: HET-1A cells, Control, biol rep 2

description:
Library name: H_1B
Column name in HET1A_GeneCount.txt: H_Control_rep2_count


title: SL470046

tag: hippocampal siide used

value: left

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL470047

tag: tissue

value: hippocampus

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: B16F10 cells treated with PBS, CD45+, Pros1+ area, replicate 2

description:
Library name: DSP-1001660020082-D-B01
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

value: Melanoma murine cells

tag: treatment

tag: primer used

value: GeoMx Seq Code D B01


title: HET-1A cells, Pepsin, biol rep 1

description:
Library name: H_2A
Column name in HET1A_GeneCount.txt: H_Pepsin_rep1_count

value: esophageal epithelium

value: pH 7.0 HBSS + pepsin


title: HET-1A cells, Pepsin, biol rep 2

description:
Library name: H_2B
Column name in HET1A_GeneCount.txt: H_Pepsin_rep2_count


title: B16F10 cells treated with PBS, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 2

description:
Library name: DSP-1001660020082-D-B03
Nanostring GeoMx DSP

value: GeoMx Seq Code D B03


title: BAR-T cells, Pepsin+APR, biol rep 3

description:
Library name: B_3C
Column name in BART_GeneCount.txt: B_Pepsin+APR_rep3_count

source_name: BAR-T

value: BAR-T

value: pH 7.0 HBSS + pepsin + amprenavir


title: Alveolar macrophage, wildtype, rep1

description:
Library name: Alveolar macrophage, Wildtype1
WT1

value: Lung

value: Alveolar macrophages

tag: genotype

value: Wildtype

tag: batch


title: B16F10 cells treated with PBS, PanCK+, Mer-Stat1 PLA+ area, replicate 2

description:
Library name: DSP-1001660020082-D-B04
Nanostring GeoMx DSP

value: Melanoma primary tumor

value: C57bl/6J, 8-week old, both sexes.

value: GeoMx Seq Code D B04


title: Alveolar macrophage, wildtype, rep3

description:
Library name: Alveolar macrophage, Wildtype3
WT3


title: B16F10 cells treated with PBS, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 2

description:
Library name: DSP-1001660020082-D-B02
Nanostring GeoMx DSP

value: PBS, ip, qd

value: GeoMx Seq Code D B02


title: HET-1A cells, Control, biol rep 1

description:
Library name: H_1A
Column name in HET1A_GeneCount.txt: H_Control_rep1_count

value: pH 7.0 HBSS


title: wildtype GV oocyte RNA-seq biol rep3

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description: Library name: Ctr_GV_3_RME627

data_processing:
RNA-seq analysis was performed on the Galaxy platform. Sequence reads were mapped to the mouse genome build GRCm38.p6 (mm10) using STAR (Galaxy Version 2.7.11a), and gene-level transcript abundances were quantified by featureCounts (Galaxy Version 2.0.3) against the built-in gene annotation file (NCBI RefSeq)
Assembly: mm10/GRCm38
Supplementary files format and content: raw counts (generated by feature counts)
Supplementary files format and content: bigwig (signal tracks)

source_name: oocyte

extract_protocol:
For RNA-seq of MatKO and control oocytes RNA from ~10 pooled mouse oocytes per replicate was extracted with the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific).
cDNA libraries were generated from total RNA using the SMARTer Ultra Low Input RNA Kit for sequencing (Clontech), followed by sequencing library preparation with the NexteraXT DNA Sample Preparation Kit (Illumina) according to manufacturer’s instructions. Final libraries were amplified and pooled for single-end Illumina sequencing.

value: GV oocyte

value: wildtype


title: BAR-T cells, Pepsin+APR, biol rep 2

description:
Library name: B_3B
Column name in BART_GeneCount.txt: B_Pepsin+APR_rep2_count


title: B16F10 cells treated with PBS, CD45+, gH2Ax+ area, replicate 2

description:
Library name: DSP-1001660020082-D-A11
Nanostring GeoMx DSP

value: Melanoma murine cells

value: GeoMx Seq Code D A11


title: SL470044

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

value: Female

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: BAR-T cells, Pepsin+APR, biol rep 1

description:
Library name: B_3A
Column name in BART_GeneCount.txt: B_Pepsin+APR_rep1_count

tag: cell line

value: BAR-T

tag: cell type

value: esophageal epithelium

tag: treatment

value: pH 7.0 HBSS + pepsin + amprenavir


title: wildtype GV oocyte RNA-seq biol rep1

description: Library name: Ctr_GV_1_RME625

tag: genotype


title: B16F10 cells treated with PBS, PanCK+, Pros1+ area, replicate 2

description:
Library name: DSP-1001660020082-D-A12
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: primer used

value: GeoMx Seq Code D A12


title: B16F10 cells treated with PBS, PanCK+, gH2Ax+ area, replicate 2

description:
Library name: DSP-1001660020082-D-A10
Nanostring GeoMx DSP

value: PBS, ip, qd

value: GeoMx Seq Code D A10


title: BAR-T cells, Pepsin, biol rep 3

description:
Library name: B_2C
Column name in BART_GeneCount.txt: B_Pepsin_rep3_count

value: pH 7.0 HBSS + pepsin


title: SL470043

tag: hippocampal siide used

value: right

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SL470045

tag: tissue

value: hippocampus

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm time_immobile

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: B16F10 cells treated with PBS, CD45+, Mer-Stat1 PLA+ area, replicate 1

description:
Library name: DSP-1001660020082-D-A09
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

value: Melanoma murine cells

tag: treatment

tag: primer used

value: GeoMx Seq Code D A09


title: wildtype GV oocyte RNA-seq biol rep2

description: Library name: Ctr_GV_2_RME626

value: GV oocyte

tag: genotype

value: wildtype


title: B16F10 cells treated with PBS, PanCK+, Mer-Stat1 PLA+ area, replicate 1

description:
Library name: DSP-1001660020082-D-A08
Nanostring GeoMx DSP

value: GeoMx Seq Code D A08


title: Maternal Prdm10 knockout GV oocyte RNA-seq biol rep3

description: Library name: MatKO_GV_3_RME624

value: knock out


title: BAR-T cells, Pepsin, biol rep 2

description:
Library name: B_2B
Column name in BART_GeneCount.txt: B_Pepsin_rep2_count

value: BAR-T

value: esophageal epithelium


title: Maternal Prdm10 knockout GV oocyte RNA-seq biol rep2

description: Library name: MatKO_GV_2_RME623


title: B16F10 cells treated with PBS, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 1

description:
Library name: DSP-1001660020082-D-A07
Nanostring GeoMx DSP

value: Melanoma primary tumor

value: C57bl/6J, 8-week old, both sexes.

value: GeoMx Seq Code D A07


title: SL470040

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: B16F10 cells treated with PBS, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 1

description:
Library name: DSP-1001660020082-D-A06
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D A06


title: BAR-T cells, Control, biol rep 3

description:
Library name: B_1C
Column name in BART_GeneCount.txt: B_Control_rep3_count

value: pH 7.0 HBSS


title: BAR-T cells, Pepsin, biol rep 1

description:
Library name: B_2A
Column name in BART_GeneCount.txt: B_Pepsin_rep1_count

value: pH 7.0 HBSS + pepsin


title: SL470041

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL470038

tag: tissue

tag: hippocampal siide used

value: right

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

value: ST

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SL470039

tag: tissue

tag: hippocampal siide used

tag: Sex

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: BAR-T cells, Control, biol rep 2

description:
Library name: B_1B
Column name in BART_GeneCount.txt: B_Control_rep2_count

tag: cell line

value: BAR-T

tag: cell type

value: esophageal epithelium

tag: treatment


title: B16F10 cells treated with PBS, CD45+, Pros1+ area, replicate 1

description:
Library name: DSP-1001660020082-D-A05
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

value: Melanoma murine cells

tag: primer used

value: GeoMx Seq Code D A05


title: SL470042

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

value: F2 cross of bred Low Responders and bred High Responders

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SL470037

tag: tissue

value: hippocampus

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: response bias_day7

tag: prob diff_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: B16F10 cells treated with PBS, PanCK+, Pros1+ area, replicate 1

description:
Library name: DSP-1001660020082-D-A04
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D A04


title: HP, APP/Tau, 9months, Trained, sample4

city: Bellaterra, Barcelona

first: Arnaldo

last: Parra-Damas

address: Campus UAB, Edifici M, M2-003

department: Biochemistry and molecular biology

country: Spain

institute: Universitat Autònoma de Barcelona

data_processing:
Adapter removal and trimming were performed using Trimmomatic tool (v0.39) with default parameters. Alignment to the mouse reference genome (mm39) was performed using Rhisat2 with the QuasR package in Bioconductor (v3.16) (Kim et al., 2015; Gaidatzis et al., 2015) with default parameters. Counts per gene were obtained using the qCount function in QuasR and the annotation package TxDb.Mmusculus.UCSC.mm39.refGene in Bioconductor (v3.16) with default parameters.
Assembly: mm39
Supplementary files format and content: csv text file containing raw counts for each sample

source_name: Hippocampus

growth_protocol: APP/Tau Tg mice were obtained by crossing heterozygous APPSw,Ind (J9 line; genetic background C57BL/6; Hsia et al., 1999; Mucke et al., 2000) and Tau P301S mice (PS19 line, JAX #008169; background C57BL/6). We further generated APP/Tau; CaMKIIαCre mice by crossing APP/Tau and CaMKIIαCre Tg mice generated previously in Dr. E. Kandel lab, in which Cre-recombinase is expressed in glutamatergic (CaMKIIα) neurons of the postnatal forebrain (Yu et al., 2001). Heterozygous APP/Tau;CaMKIIαCre mice were bred with the RiboTag mouse line to generate WT; and APP/Tau; CaMKIIαCre; RiboTag mice, which express HA-tagged ribosome-bound mRNAs specifically in Cre-recombinase-expressing glutamatergic neurons (Sanz et al., 2009; Sanz et al., 2019). In this study, only input fractions were analyzed (Bulk RNA-seq).

extract_protocol:
Brains were mounted in a cutting chuck with Tissue-Tek® O.C.T. Compound before sectioning. Frozen coronal sections (300 μm) were obtained using a cryostat (Leica CM 3050s) and mounted on Superfrost Plus slides (J1800AMNT, Thermo Fisher Scientific). Next, hippocampi and BLA were obtained from eight and two consecutive slices (BLA: coronal plane from 1.3 to 1.9 mm behind Bregma), respectively. Both hippocampi were microdissected with a scalpel, and the BLA region was obtained using a 1 mm Ø diameter micropunch (BP-10F, Miltex kai Japan) (4 punches/mouse). Immediately after dissection, both hippocampi and amygdalae were placed individually in the ice-cold Dounce homogenizer (D8938-1SET, Sigma-Aldrich) vessel with a predetermined volume of pre-chilled homogenization buffer (50mM Tris pH 7.5, 100mM KCl, 12mM MgCl2, 1% Nonidet P-40, protease inhibitor, 1mM dl-Dithiothreitol (DTT), 1mg/ml heparin, 100ug/ml cycloheximide, 200U/ml RNAse Out in H2O RNAse free) to achieve a 2-10% w/v ratio; 750 μl of homogenization buffer were used for the hippocampus sample and 250 μl for the BLA sample. Both tissues were homogenized using 40 strokes with a large pestle (A) and 40 strokes more with a small pestle (B) to form the final homogenate. The lysate was centrifugated at 10,000 x g for 10 min at 4ºC to obtain a post-mitochondrial supernatant. A small aliquot of the cleared lysate (input) (100 μl from each tissue) was taken and stored at -80ºC for subsequent input analysis.
cDNA libraries were prepared using the NEBNext® Poly(A) mRNA magnetic isolation module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. In the case of hippocampus samples, cDNA libraries were prepared from 50 ng of RNA whereas, for BLA samples cDNA libraries were prepared from 10 ng of RNA. Libraries  were sequenced on an Illumina NextSeq 2000 instrument with 40 million reads per sample. Each fragment was sequenced paired-end 2 x 50 bp.

treatment_protocol: Naïve and fear-conditioned WT;CaMKIIαCre; RiboTag and APP/Tau;CaMKIIαCre; RiboTag mice were euthanized by cervical dislocation, and brains were immediately frozen in isopentane (-30ºC) and stored at −80 °C until sectioning. Trained mice were exposed to a cued fear conditioning consisted in a conditioned stimulus (CS, 2800 Hz, and 80 dB; 30 sec), which ended with an electric footshock (unconditioned stimulus, US: 0.8 mA, 2 sec). These mice were euthanized 1 hour after the US.

value: Hippocampus

value: Bulk

tag: genotype

value: Trained


title: HP, Control, 9months, Trained, sample6

value: Female


title: HP, APP/Tau, 9months, Trained, sample3


title: HP, APP/Tau, 9months, Naïve, sample4

value: Naïve


title: Hepatoblastoma sample 35

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

description:
Library name: H691
10X Genomics, Chromium Next GEM Single Cell Fixed RNA, Multiplex

library_source: transcriptomic single cell

data_processing:
NovaSeq 6000 binary base call (bcl) files were demultiplexed into individual library fastq files using the mkfastq program from the Cellranger v7.1.0  Suite (10X Genomics). Feature-barcode matrices and BAM files were obtained for each sample by aligning the raw fastq files to the GRCh38 reference genome using the cellranger multi pipeline (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files containing barcodes and features (genes) and matrix files containing count data.

extract_protocol:
Sample preparation for deparafinization and isolation of cells from FFPE tissue sections following 10x Genomics for Fixed RNA seq - protocol CGO000632 Rev B, using gentleMACS Octo dissociator with heaters (Miltenyi, Cat n. 140-004-386.06).
Protocol for probe hybridization, GEM generation and barcoding, amplification and library construction as per 10x Genomics Fixed RNA seq protocol CG000527 Rev E, for multiplexed library (16 rxns x 16 BC): 500,000 to 1 Mio nuclei per sample were taken for probe hybridization, followed by sample washing, pooling for pool preparation, and loading of 80,000 nuclei per library.


title: Hepatoblastoma sample 37

description:
Library name: H693
10X Genomics, Chromium Next GEM Single Cell Fixed RNA, Multiplex


title: HP, Control, 9months, Trained, sample5


title: SL470036

tag: hippocampal siide used

value: right

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: Hepatoblastoma sample 36

description:
Library name: H692
10X Genomics, Chromium Next GEM Single Cell Fixed RNA, Multiplex

tag: tissue


title: HP, APP/Tau, 9months, Naïve, sample5

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: B16F10 cells treated with PBS, CD45+, gH2Ax+ area, replicate 1

description:
Library name: DSP-1001660020082-D-A03
Nanostring GeoMx DSP

value: Melanoma primary tumor

tag: mouse strain

value: C57bl/6J, 8-week old, both sexes.

tag: primer used

value: GeoMx Seq Code D A03


title: No template control plate D

description:
Library name: DSP-1001660020082-D-A01
Nanostring GeoMx DSP

source_name: No template control

value: No template control

value: GeoMx Seq Code D A01