title: SL470580

tag: tissue

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

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 testorderbyday

tag: loco box

tag: dob

tag: dod


title: shortHL_CRISPRcut_Day12_TR2_B1_R1

status: Public on Feb 07 2025

type: SRA

city: Seattle

first: Jay

last: Shendure

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

description:
Short half-life TF gRNA-barcode library
short_HL_TF_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

molecule: genomic DNA

organism: Homo sapiens

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.

tag: cell line

tag: cell type

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: AdultSample15_Buccal

type: genomic

city: University Park

first: Idan

last: Shalev

state: PA

address: 219 Biobehavioral Health Building

institute: The Pennsylvania State University

description: Processed data file column header: 153

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the human Infinium MethylationEPICv2 BeadChip (Illumina) using standard Illumina protocols.

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

data_processing:
IDAT files were read into R statistical software using the read.metharray.exp function in the minfi package. Samples with probe detection p-values greater than 0.05 for more than 5% of probes or with bisulfite conversion rates of less than 80% were excluded from the current data (no IDAT files or processed data are included for these samples). CpG probes with a bead count of less than 3 in 5% or more samples or with an average detection p-value of > 0.05 across all samples were excluded. All samples were normalized using the beta-mixture quantile normalization (BMIQ) method. In order to remove duplicate probes in the EPIC v2 chip, we used the R package ENmix (using v1.36.08 or newer). This package has a function called rm.cgsuffix. This function both removes the suffix on EPIC v2 probe names (i.e., removes “_BC11” from “cg25324105_BC11”) and collapses duplicate probes by taking their averages.
Processed data files includes: Average Beta

label: Cy3 and Cy5

source_name: Cell-free DNA from Buccal tissue

label_protocol: Standard Illumina protocol.

extract_protocol: To minimize the impact of DNA extraction procedures, DNA was extracted from all tissue samples using the Gentra Puregene DNA Extraction Kit according to factory guidelines (Qiagen). Extracted DNA was stored at -80°C in Qiagen DNA Hydration Solution.

tag: tissue

value: Buccal

tag: Sex

value: Male

tag: age


title: AdultSample9_PBMC

description: Processed data file column header: 91

source_name: Cell-free DNA from PBMC tissue

value: PBMC

value: Female


title: AdultSample9_Buccal

description: Processed data file column header: 93


title: shortHL_CRISPRcut_Day12_TR1_B4_R4


title: SL470579

city: Ann Arbor

first: Elaine

last: Hebda-Bauer

state: Michigan

address: 205 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

library_source: transcriptomic

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

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: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: AdultSample9_DBS

description: Processed data file column header: 92

source_name: Cell-free DNA from DBS tissue

tag: tissue

value: DBS

tag: Sex

tag: age


title: AdultSample19_Buccal

description: Processed data file column header: 193


title: AdultSample8_Saliva

description: Processed data file column header: 84

source_name: Cell-free DNA from Saliva tissue

value: Saliva


title: SL470578

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: epm testorderbyday

tag: loco box

tag: dob

tag: dod


title: SL470577

tag: tissue

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

value: ST

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 testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: shortHL_CRISPRcut_Day12_TR1_B4_R3

tag: cell line

tag: cell type

value: lymphoblast

tag: genotype

value: Cas9 and rtTA

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: AdultSample8_Buccal

description: Processed data file column header: 83

tag: tissue

value: Buccal

tag: Sex

tag: age


title: AdultSample17_PBMC

description: Processed data file column header: 171


title: AdultSample8_DBS

description: Processed data file column header: 82


title: shortHL_CRISPRcut_Day12_TR1_B4_R2

value: CRISPRcut


title: SL470576

tag: hippocampal siide used

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

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

tag: dob

tag: dod


title: Gq3, LPS

city: Changsha

first: Dai

last: Ruping

state: Hunan

address: Ren-Min Central Road

department: Anesthesiology

country: China

institute: The Second Xiangya Hospital of Central South University

description:
Library name: Samples6
Gq3_tpm

data_processing:
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) following manufacturer’s recommendations.
Poly (A) RNA is purified from 1 μg total RNA using Dynabeads Oligo (dT) .Then the poly(A) RNA was fragmented and reverse-transcribed to create the cDNA.
Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA).
The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).
After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 4200 Bioanalyzer (Agilent, USA).
Assembly: Genome reference: Mus musculus (mm10) Annotation source: Gencode vMXX or Ensembl release XX
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: N/A (No in vitro cell culture; only lung tissue samples were used.)

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample.
The library was sequenced using the Illumina Xplus sequencing platform (Paired end150) to generate raw reads.

treatment_protocol: Mice were intranasally administered with LPS (20mg/kg) to induce acute lung injury

tag: tissue

value: Lung

tag: cell type

value: Neutrophils


title: Gq2, LPS

description:
Library name: Samples5
Gq2_tpm


title: AdultSample8_PBMC

description: Processed data file column header: 81

value: PBMC

tag: Sex

value: Female

tag: age


title: shortHL_CRISPRcut_Day12_TR1_B4_R1

tag: cell line

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: Gq1, LPS

description:
Library name: Samples4
Gq1_tpm


title: shortHL_CRISPRcut_Day12_TR1_B3_R4


title: mcherry2, LPS

description:
Library name: Samples2
mcherry2_tpm


title: SL470575

value: hippocampus

tag: hippocampal siide used

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

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 testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: SL470574

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

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: epm testorderbyday

tag: loco box

tag: dob

tag: dod


title: shortHL_CRISPRcut_Day12_TR1_B3_R2

tag: cell line

tag: cell type

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: shortHL_CRISPRcut_Day12_TR1_B3_R3


title: PFOA3

city: Beijing

first: Jianying

last: Hu

state: 北京

address: No. 5 Yiheyuan Road， Haidian District

institute: Peking University

description:
Library name: Sample6
PFOA3

data_processing:
Sequencing data were obtained from BGISEQ platform and ﬁltered using SOAPnuke (version 1.5.2; BGI-FlexLab).
Sequencing reads were mapped against GCF_000001635.27_GRCm39 reference genome using HISAT2 (version 2.0.4; Lady Hill Department of Bioinformatics) and Bowtie2 (version 2.2.5; Langmead lab at Johns Hopkins University).
The gene expression levels in each sample were calculated using RNA-Seq by Expectation-Maximization (version 1.2.8), and diﬀerentially expressed genes were identiﬁed using DEGseq2 (version 1.34.0; Mike Love).
Assembly: GRCm39 (GCF_000001635.27)
Supplementary files format and content: Tab-delimited text files containing FPKM values for each sample.

source_name: mouse expanded pluripotent stem cells

growth_protocol: Morula-like aggregate model derived from mouse expanded pluripotent stem cells was maintained in a N2B27LCDM medium followed by a induction medium under 5% CO2 and 20% O2 at 37°C

extract_protocol:
Total RNA was extracted using TRIzol Up ((ET111-01, Transgen)). 1.2 ug of total RNA was used for the construction of sequencing libraries.RNA quality was assessed by Agilent Bioanalyzer, with RIN values > 8.0.
RNA samples were enriched for poly A species, and the sequencing libraries were constructed and then sequenced on a BGISEQ-500 platform (Beijing Genomics Institute, BGI).

value: mouse expanded pluripotent stem cells


title: mcherry3, LPS

description:
Library name: Samples3
mcherry3_tpm

tag: tissue


title: SL470573

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

value: IN

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 testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: PFOA2

description:
Library name: Sample5
PFOA2

tag: cell type


title: mcherry1, LPS

description:
Library name: Samples1
mcherry1_tpm

tag: tissue


title: shortHL_CRISPRcut_Day12_TR1_B3_R1

tag: cell line

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: PFOA1

description:
Library name: Sample4
PFOA1


title: DMSO3

description:
Library name: Sample3
DMSO3


title: SL470571

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

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 testorderbyday

tag: loco box

tag: dob

tag: dod


title: shortHL_CRISPRcut_Day12_TR1_B2_R4

tag: cell line

tag: cell type

value: lymphoblast

tag: genotype

value: Cas9 and rtTA

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: DMSO2

description:
Library name: Sample2
DMSO2


title: DMSO1

description:
Library name: Sample1
DMSO1


title: shortHL_CRISPRcut_Day12_TR1_B2_R3

value: CRISPRcut


title: SL470570

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: 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: epm testdate

tag: epm testday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, gH2Ax+ area, replicate 4

city: Birmingham

first: Nestor

last: Prieto-Dominguez

state: AL

department: Microbiology

institute: The University of Alabama at Birmingham (UAB)

description:
Library name: DSP-1001660020083-C-F01
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).

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: Cisplaitn and BVT948. Similar regimes to the single-treated groups

tag: primer used

value: GeoMx Seq Code C F01


title: B16F10 cells treated with BVT948 and Cisplatin, CD45+, Pros1+ area, replicate 4

description:
Library name: DSP-1001660020083-C-E12
Nanostring GeoMx DSP

value: GeoMx Seq Code C E12


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, Pros1+ area, replicate 4

description:
Library name: DSP-1001660020083-C-E11
Nanostring GeoMx DSP

value: GeoMx Seq Code C E11


title: SL470569

value: hippocampus

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

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testorderbyday

tag: loco box

tag: dob

tag: dod


title: SL470568

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

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

value: IN

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: epm testdate

tag: epm testday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, Mer-Stat1 PLA+ area, replicate 4

description:
Library name: DSP-1001660020083-C-E09
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C E09


title: shortHL_CRISPRcut_Day12_TR1_B2_R1

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 and Cisplatin, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 4

description:
Library name: DSP-1001660020083-C-E08
Nanostring GeoMx DSP

value: Melanoma primary tumor

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

value: Melanoma murine cells

value: GeoMx Seq Code C E08


title: shortHL_CRISPRcut_Day12_TR1_B2_R2


title: shortHL_CRISPRcut_Day12_TR1_B1_R4


title: SL470567

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

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 box

tag: dob

tag: dod


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 4

description:
Library name: DSP-1001660020083-C-E07
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

value: Cisplaitn and BVT948. Similar regimes to the single-treated groups

tag: primer used

value: GeoMx Seq Code C E07


title: SL470572

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

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: loco testday

tag: loco batch

tag: loco rack


title: B16F10 cells treated with BVT948 and Cisplatin, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 3

description:
Library name: DSP-1001660020083-C-E06
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C E06


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 3

description:
Library name: DSP-1001660020083-C-E05
Nanostring GeoMx DSP

value: GeoMx Seq Code C E05


title: SL470566

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

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: IN

tag: pca index_days6and_7

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box

tag: dob

tag: dod


title: SL470565

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

value: ST

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: loco testday

tag: loco batch

tag: loco rack


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

description:
Library name: DSP-1001660020083-C-E04
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

tag: primer used

value: GeoMx Seq Code C E04


title: shortHL_CRISPRcut_Day12_TR1_B1_R3

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 and Cisplatin, CD45+, Mer-Stat1 PLA+ area, replicate 3

description:
Library name: DSP-1001660020083-C-E02
Nanostring GeoMx DSP

value: Melanoma murine cells

value: Cisplaitn and BVT948. Similar regimes to the single-treated groups

value: GeoMx Seq Code C E02


title: shortHL_CRISPRcut_Day12_TR1_B1_R2


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, Pros1+ area, replicate 3

description:
Library name: DSP-1001660020083-C-E03
Nanostring GeoMx DSP

value: GeoMx Seq Code C E03


title: SL470564

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

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 box

tag: dob

tag: dod


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, Mer-Stat1 PLA+ area, replicate 3

description:
Library name: DSP-1001660020083-C-E01
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C E01


title: shortHL_CRISPRcut_Day12_TR1_B1_R1

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: B16F10 cells treated with BVT948 and Cisplatin, CD45+, gH2Ax+ area, replicate 3

description:
Library name: DSP-1001660020083-C-D12
Nanostring GeoMx DSP

value: GeoMx Seq Code C D12


title: SL470563

tag: hippocampal siide used

value: left

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: 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

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


title: B16F10 cells treated with BVT948 and Cisplatin, PanCK+, gH2Ax+ area, replicate 3

description:
Library name: DSP-1001660020083-C-D11
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

tag: primer used

value: GeoMx Seq Code C D11


title: CRISPRcut_Day12_TR4_B4_R2

description:
SCF pilot gRNA-barcode library
pilot_count_table.csv

value: lymphoblast

tag: genotype

value: Cas9 and rtTA

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


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

description:
Library name: DSP-1001660020083-C-D10
Nanostring GeoMx DSP

value: Melanoma murine cells

value: GeoMx Seq Code C D10


title: SL470562

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: 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 box

tag: dob

tag: dod


title: B16F10 cells treated with BVT948 and Cisplatin, CD45+, Mer-Stat1 PLA+ area, replicate 4

description:
Library name: DSP-1001660020083-C-E10
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

value: Cisplaitn and BVT948. Similar regimes to the single-treated groups

tag: primer used

value: GeoMx Seq Code C E10


title: CRISPRcut_Day12_TR4_B4_R1

tag: genotype

tag: group

tag: perturbation

value: CRISPRcut

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


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

description:
Library name: DSP-1001660020083-C-D08
Nanostring GeoMx DSP

value: GeoMx Seq Code C D08


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

description:
Library name: DSP-1001660020083-C-D07
Nanostring GeoMx DSP

value: GeoMx Seq Code C D07


title: CRISPRcut_Day12_TR4_B3_R2


title: CRISPRcut_Day12_TR4_B3_R1


title: SL470560

value: hippocampus

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

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


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

description:
Library name: DSP-1001660020083-C-D05
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

tag: primer used

value: GeoMx Seq Code C D05


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

description:
Library name: DSP-1001660020083-C-D06
Nanostring GeoMx DSP

value: GeoMx Seq Code C D06


title: SL470559

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

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: loco box

tag: dob

tag: dod


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

description:
Library name: DSP-1001660020083-C-D03
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 C D03


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

description:
Library name: DSP-1001660020083-C-D04
Nanostring GeoMx DSP

value: Cisplaitn and BVT948. Similar regimes to the single-treated groups

value: GeoMx Seq Code C D04


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

description:
Library name: DSP-1001660020083-C-D02
Nanostring GeoMx DSP

value: GeoMx Seq Code C D02


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

description:
Library name: DSP-1001660020083-C-C12
Nanostring GeoMx DSP

value: GeoMx Seq Code C C12


title: SL470558

tag: hippocampal siide used

value: left

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 percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

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


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

description:
Library name: DSP-1001660020083-C-C11
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C C11


title: CRISPRcut_Day12_TR4_B2_R1

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 and Cisplatin, PanCK+, Pros1+ area, replicate 1

description:
Library name: DSP-1001660020083-C-D01
Nanostring GeoMx DSP

value: Melanoma primary tumor

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

value: GeoMx Seq Code C D01


title: CRISPRcut_Day12_TR4_B1_R2


title: SL470557

value: hippocampus

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

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 box

tag: dob

tag: dod


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

description:
Library name: DSP-1001660020083-C-C10
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

value: Melanoma murine cells

tag: treatment

value: Cisplaitn and BVT948. Similar regimes to the single-treated groups

tag: primer used

value: GeoMx Seq Code C C10


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

description:
Library name: DSP-1001660020083-C-C09
Nanostring GeoMx DSP

value: GeoMx Seq Code C C09


title: CRISPRcut_Day12_TR4_B1_R1

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


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

description:
Library name: DSP-1001660020083-C-D09
Nanostring GeoMx DSP

value: GeoMx Seq Code C D09


title: SL470556

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: 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


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

description:
Library name: DSP-1001660020083-C-C08
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C C08


title: SL470555

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: loco box

tag: dob

tag: dod


title: SL470561

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

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: 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


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

description:
Library name: DSP-1001660020083-C-C07
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: Cisplatin, 5mg/kg, ip, once daily for three days

tag: primer used

value: GeoMx Seq Code C C07


title: CRISPRcut_Day12_TR3_B4_R2

description:
SCF pilot gRNA-barcode library
pilot_count_table.csv

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: CRISPRcut_Day12_TR3_B4_R1


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

description:
Library name: DSP-1001660020083-C-C05
Nanostring GeoMx DSP

value: Melanoma murine cells

value: GeoMx Seq Code C C05


title: SL470554

value: hippocampus

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

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 box

tag: dob

tag: dod


title: CRISPRcut_Day12_TR4_B2_R2

tag: cell line

tag: cell type

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: B16F10 cells treated with Cisplatin, PanCK+, Mer-Stat1 PLA+ area, replicate 4

description:
Library name: DSP-1001660020083-C-C04
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: treatment

tag: primer used

value: GeoMx Seq Code C C04


title: SL470553

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: 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


title: B16F10 cells treated with Cisplatin, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 4

description:
Library name: DSP-1001660020083-C-C02
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C C02


title: B16F10 cells treated with Cisplatin, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 4

description:
Library name: DSP-1001660020083-C-C03
Nanostring GeoMx DSP

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

value: Cisplatin, 5mg/kg, ip, once daily for three days

value: GeoMx Seq Code C C03


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

description:
Library name: DSP-1001660020083-C-C01
Nanostring GeoMx DSP

value: GeoMx Seq Code C C01


title: SL470552

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

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: loco box

tag: dob

tag: dod


title: CRISPRcut_Day12_TR3_B3_R1

tag: cell line

tag: cell type

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: SL470551

tag: tissue

value: hippocampus

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

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_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


title: CRISPRcut_Day12_TR3_B2_R2

tag: cell line

tag: cell type

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


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

description:
Library name: DSP-1001660020083-C-B10
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

value: Melanoma murine cells

tag: treatment

tag: primer used

value: GeoMx Seq Code C B10


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

description:
Library name: DSP-1001660020083-C-B09
Nanostring GeoMx DSP

value: Melanoma primary tumor

value: GeoMx Seq Code C B09


title: CRISPRcut_Day12_TR3_B3_R2


title: SL470550

tag: hippocampal siide used

value: right

tag: Sex

value: Female

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: 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 testdate

tag: loco box

tag: dob

tag: dod


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

description:
Library name: DSP-1001660020083-C-B12
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

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

tag: cell line

tag: cell type

tag: treatment

value: Cisplatin, 5mg/kg, ip, once daily for three days

tag: primer used

value: GeoMx Seq Code C B12


title: CRISPRcut_Day12_TR3_B2_R1

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 Cisplatin, PanCK+, gH2Ax+ area, replicate 3

description:
Library name: DSP-1001660020083-C-B07
Nanostring GeoMx DSP

value: GeoMx Seq Code C B07


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

description:
Library name: DSP-1001660020083-C-B11
Nanostring GeoMx DSP

value: GeoMx Seq Code C B11


title: SL470548

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

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: 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


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

description:
Library name: DSP-1001660020083-C-B05
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

tag: cell line

tag: cell type

value: Melanoma murine cells

tag: treatment

tag: primer used

value: GeoMx Seq Code C B05


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

description:
Library name: DSP-1001660020083-C-B04
Nanostring GeoMx DSP

value: GeoMx Seq Code C B04


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

description:
Library name: DSP-1001660020083-C-B06
Nanostring GeoMx DSP

value: GeoMx Seq Code C B06


title: SL470549

tag: hippocampal siide used

value: right

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: 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: loco box

tag: dob

tag: dod


title: CRISPRcut_Day12_TR3_B1_R1

tag: cell line

tag: cell type

value: lymphoblast

tag: genotype

value: Cas9 and rtTA

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


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

description:
Library name: DSP-1001660020083-C-C06
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

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

tag: treatment

value: Cisplatin, 5mg/kg, ip, once daily for three days

tag: primer used

value: GeoMx Seq Code C C06


title: CRISPRcut_Day12_TR2_B4_R2

value: CRISPRcut


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

description:
Library name: DSP-1001660020083-C-B02
Nanostring GeoMx DSP

value: GeoMx Seq Code C B02


title: SL470547

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

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

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: SL470546

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: 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: loco box

tag: dob

tag: dod


title: CRISPRcut_Day12_TR2_B4_R1

tag: cell line

tag: cell type

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


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

description:
Library name: DSP-1001660020083-C-B01
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

value: Melanoma murine cells

tag: treatment

tag: primer used

value: GeoMx Seq Code C B01


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

description:
Library name: DSP-1001660020083-C-A12
Nanostring GeoMx DSP

value: GeoMx Seq Code C A12


title: CRISPRcut_Day12_TR2_B3_R2

description:
SCF pilot gRNA-barcode library
pilot_count_table.csv


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

description:
Library name: DSP-1001660020083-C-A11
Nanostring GeoMx DSP

value: GeoMx Seq Code C A11


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

description:
Library name: DSP-1001660020083-C-B08
Nanostring GeoMx DSP

value: GeoMx Seq Code C B08


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

description:
Library name: DSP-1001660020083-C-A10
Nanostring GeoMx DSP

value: GeoMx Seq Code C A10


title: SL470544

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: 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


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

description:
Library name: DSP-1001660020083-C-A07
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

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

tag: cell line

tag: cell type

tag: treatment

value: Cisplatin, 5mg/kg, ip, once daily for three days

tag: primer used

value: GeoMx Seq Code C A07


title: CRISPRcut_Day12_TR3_B1_R2

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 Cisplatin, CD45+, Pros1+ area, replicate 1

description:
Library name: DSP-1001660020083-C-A08
Nanostring GeoMx DSP

value: Melanoma primary tumor

value: GeoMx Seq Code C A08


title: CRISPRcut_Day12_TR2_B2_R2


title: CRISPRcut_Day12_TR2_B3_R1


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

description:
Library name: DSP-1001660020083-C-A09
Nanostring GeoMx DSP

value: Melanoma murine cells

value: GeoMx Seq Code C A09


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

description:
Library name: DSP-1001660020083-C-A06
Nanostring GeoMx DSP

value: GeoMx Seq Code C A06


title: SL470543

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

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

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: 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 box

tag: dob

tag: dod


title: SL470545

tag: tissue

tag: hippocampal siide used

value: right

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: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: loco testday

tag: loco batch

tag: loco rack


title: CRISPRcut_Day12_TR2_B2_R1

tag: cell line

tag: cell type

value: lymphoblast

tag: genotype

value: Cas9 and rtTA

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


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

description:
Library name: DSP-1001660020083-C-A04
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

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

tag: treatment

value: Cisplatin, 5mg/kg, ip, once daily for three days

tag: primer used

value: GeoMx Seq Code C A04


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

description:
Library name: DSP-1001660020083-C-B03
Nanostring GeoMx DSP

value: Melanoma murine cells

value: GeoMx Seq Code C B03


title: SL470541

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: 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 box

tag: dob

tag: dod


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

description:
Library name: DSP-1001660020083-C-A05
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C A05


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

description:
Library name: DSP-1001660020083-C-A03
Nanostring GeoMx DSP

value: GeoMx Seq Code C A03


title: SL470542

tag: hippocampal siide used

value: right

tag: Sex

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

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: 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: loco testday

tag: loco batch

tag: loco rack


title: No template control plate C

description:
Library name: DSP-1001660020083-C-A01
Nanostring GeoMx DSP

source_name: No template control

tag: tissue

value: No template control

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code C A01


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

description:
Library name: DSP-1001660020083-C-A02
Nanostring GeoMx DSP

value: GeoMx Seq Code C A02


title: CRISPRcut_Day12_TR2_B1_R1

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: SL470540

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

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 box

tag: dob

tag: dod


title: B16F10 cells treated with BVT948, CD45+, Mer-Stat1 PLA+ area, replicate 4

description:
Library name: DSP-1001660020082-D-F05
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 F05


title: B16F10 cells treated with BVT948, PanCK+, Mer-Stat1 PLA+ area, replicate 4

description:
Library name: DSP-1001660020082-D-F04
Nanostring GeoMx DSP

value: GeoMx Seq Code D F04


title: CRISPRcut_Day12_TR1_B4_R2

tag: genotype

tag: group

tag: perturbation

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 4

description:
Library name: DSP-1001660020082-D-F02
Nanostring GeoMx DSP

value: GeoMx Seq Code D F02


title: SL470538

value: hippocampus

tag: hippocampal siide used

value: right

tag: Sex

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

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

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


title: CRISPRcut_Day12_TR1_B4_R1

description:
SCF pilot gRNA-barcode library
pilot_count_table.csv

tag: cell line

tag: cell type

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: SL470537

tag: tissue

tag: hippocampal siide used

value: left

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 percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: epm rawdatafile

tag: epm trial

tag: loco box

tag: dob

tag: dod


title: SL470536

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: rin

tag: percent coding

tag: percent utr

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 testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: CRISPRcut_Day12_TR1_B3_R1

tag: cell line

tag: cell type

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, CD45+, Pros1+ area, replicate 4

description:
Library name: DSP-1001660020082-D-F01
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

tag: treatment

tag: primer used

value: GeoMx Seq Code D F01


title: B16F10 cells treated with BVT948, PanCK+, Pros1+ area, replicate 4

description:
Library name: DSP-1001660020082-D-E12
Nanostring GeoMx DSP

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

value: Melanoma murine cells

value: GeoMx Seq Code D E12


title: SL470535

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

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 box

tag: dob

tag: dod


title: SL470534

tag: tissue

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: 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: loco testday

tag: loco batch

tag: loco rack


title: B16F10 cells treated with BVT948, CD45+, Mer-Stat1 PLA+ area, replicate 3

description:
Library name: DSP-1001660020082-D-E09
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

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

tag: primer used

value: GeoMx Seq Code D E09


title: macrophage, GPR35 knockout 4

city: Cambridge

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

country: United Kingdom

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

description:
macrophage_KO_4
RNAseq_GPR35_macrophages.txt

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

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

value: bone marrow-derived macrophage

tag: genotype

value: GPR35 knockout


title: CRISPRcut_Day12_TR1_B2_R2

value: lymphoblast

value: Cas9 and rtTA

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: B16F10 cells treated with BVT948, PanCK+, Mer-Stat1 PLA+ area, replicate 3

description:
Library name: DSP-1001660020082-D-E08
Nanostring GeoMx DSP

value: Melanoma primary tumor

value: GeoMx Seq Code D E08


title: CRISPRcut_Day12_TR1_B2_R1

value: CRISPRcut


title: B16F10 cells treated with BVT948, PanCK+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 3

description:
Library name: DSP-1001660020082-D-E06
Nanostring GeoMx DSP

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

value: Melanoma murine cells

value: GeoMx Seq Code D E06


title: B16F10 cells treated with BVT948, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 4

description:
Library name: DSP-1001660020082-D-F03
Nanostring GeoMx DSP

value: GeoMx Seq Code D F03


title: SL470533

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: 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 box

tag: dob

tag: dod


title: CRISPRcut_Day12_TR1_B1_R2

tag: cell line

tag: cell type

tag: genotype

tag: group

tag: perturbation

tag: sort day

tag: transfection replicate

tag: facs bin

tag: pcr replicate


title: B16F10 cells treated with BVT948, CD45+, gH2Ax+ area, replicate 4

description:
Library name: DSP-1001660020082-D-E11
Nanostring GeoMx DSP

tag: tissue

tag: mouse strain

tag: treatment

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

tag: primer used

value: GeoMx Seq Code D E11


title: SL470532

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

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 testdate

tag: loco testday

tag: loco batch

tag: loco rack


title: B16F10 cells treated with BVT948, PanCK+, gH2Ax+ area, replicate 4

description:
Library name: DSP-1001660020082-D-E10
Nanostring GeoMx DSP

tag: tissue

value: Melanoma primary tumor

tag: mouse strain

tag: cell line

tag: cell type

tag: treatment

tag: primer used

value: GeoMx Seq Code D E10


title: CRISPRcut_Day12_TR1_B1_R1

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, CD45+, gH2Ax+ area, replicate 3

description:
Library name: DSP-1001660020082-D-E03
Nanostring GeoMx DSP

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

value: Melanoma murine cells

value: GeoMx Seq Code D E03


title: SL470530

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

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: 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 box

tag: dob

tag: dod


title: macrophage, wild type 1

description:
macrophage_WT_1
RNAseq_GPR35_macrophages.txt

tag: tissue

value: bone marrow-derived macrophage

tag: genotype

value: Wild type

tag: treatment


title: B16F10 cells treated with BVT948, CD45+, gH2Ax-/Pros1-/Mer-Stat1 PLA- area, replicate 3

description:
Library name: DSP-1001660020082-D-E07
Nanostring GeoMx DSP

tag: mouse strain

tag: cell line

tag: cell type

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

tag: primer used

value: GeoMx Seq Code D E07


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

description:
Library name: DSP-1001660020082-D-E04
Nanostring GeoMx DSP

value: GeoMx Seq Code D E04


title: B16F10 cells treated with BVT948, PanCK+, gH2Ax+ area, replicate 3

description:
Library name: DSP-1001660020082-D-E02
Nanostring GeoMx DSP

value: GeoMx Seq Code D E02


title: Ileum, GPR35 knockout 4

description:
Ileum_KO_4
RNAseq_GPR35_ileum.txt

source_name: Ileum

value: Ileum

value: GPR35 knockout


title: SL470528

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

value: Female

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: 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


title: SL470529

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

tag: epm percent_time_open_arm

value: IN

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box

tag: dob

tag: dod


title: CRISPRcut_Day12_TR2_B1_R2

tag: cell line

tag: cell type

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: SL470527

tag: tissue

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

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: loco testday

tag: loco batch

tag: loco rack


title: macrophage, wild type 3

description:
macrophage_WT_3
RNAseq_GPR35_macrophages.txt

tag: tissue

value: bone marrow-derived macrophage

tag: genotype

value: Wild type

tag: treatment


title: Ileum, wild type 5

description:
Ileum_WT_5
RNAseq_GPR35_ileum.txt


title: C_HC_Sc0157

type: RNA

city: Brighton

first: Sarah

last: Unterberger

address: Biology Road

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

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: Ileum, GPR35 knockout 2

description:
Ileum_KO_2
RNAseq_GPR35_ileum.txt

value: Ileum

value: GPR35 knockout