title: SL470034

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

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

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: Two

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


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

status: Public on Feb 07 2025

type: SRA

city: Bellaterra, Barcelona

first: Arnaldo

last: Parra-Damas

address: Campus UAB, Edifici M, M2-003

department: Biochemistry and molecular biology

country: Spain

institute: Universitat Autònoma de Barcelona

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

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

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

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

tag: tissue

value: Hippocampus

tag: cell line

value: Female

tag: cell type

value: Bulk

tag: genotype

tag: treatment

value: Naïve


title: Hepatoblastoma sample 34

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

description:
Library name: H679
10X Genomics, Chromium Next GEM Single Cell Fixed RNA, Multiplex

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism: Homo sapiens

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


title: SL470033

city: Ann Arbor

first: Elaine

last: Hebda-Bauer

state: Michigan

address: 205 Zina Pitcher Place

department: Michigan Neuroscience Institute

country: USA

institute: University of Michigan

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

organism: Rattus norvegicus

source_name: hippocampus

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

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

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

value: hippocampus

tag: hippocampal siide used

value: left

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: One

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


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

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Hepatoblastoma sample 33

description:
Library name: H678
10X Genomics, Chromium Next GEM Single Cell Fixed RNA, Multiplex


title: Fetal Membrane, Buprenorphine, 12

city: New Haven

first: Hanah

last: Georges

state: Connecticut

address: 333 Cedar St

institute: Yale University

description: Library name: Sample 12

data_processing:
Base calling by illumina real time analysis software. De-multiplexing and alignment performed using illumina's CASAVA 1.8.2 software
Assembly: hg19
Supplementary files format and content: txt file with comparisons of media vs buprenorphine treated fetal membranes (log2fold change and p values)

source_name: Term, non-labor, fetal membrane

growth_protocol: Day 0: Fetal membranes collected from patients, biopsied, and placed into 10% FBS media with 0.4um inserts. Day 1: media was replaced with serum free media, membranes were rested for 3 hours then treated for 48 hours.

extract_protocol:
TRIzol
Kapa RNA hyperprep kit with riboerase, samples fragmented, first strand sythesis by random priming, adapters ligated and lirary amplified.

treatment_protocol: Fetal membranes were treated with buprenorphine (40ug/ml)

value: Term, non-labor, fetal membrane

value: Buprenorphine

tag: batch


title: SL470032

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: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: HP, APP/Tau, 9months, Naïve, sample2

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HP, Tau, 6months, Naïve, sample4

growth_protocol: APP/Tau Tg mice were obtained by crossing heterozygous APP (Sw,Ind, J9 line; genetic background C57BL/6; Hsia et al., 1999; Mucke et al., 2000) and Tau P301S mice (PS19 line, JAX #008169; background C57BL/6). We further generated WT;PV_Cre, APP;PV_Cre, Tau;PV_Cre and APP/Tau;PV_Cre mice by crossing APP/Tau and Pvalb-IRES-Cre Tg mice (JAX #017320; background C57BL/6). Heterozygous APP/Tau;PV_Cre mice were bred with the RiboTag mouse line (Sanz et al., 2009; Sanz et al., 2019) to generate WT;PV_Cre;RiboTag, APP;PV_Cre;RiboTag, Tau;PV_Cre;RiboTag and APP/Tau;PV_Cre;RiboTag mice expressing HA-tagged ribosome-bound mRNAs specifically in Cre-recombinase-expressing parvalbumin (PV) neurons. In this study, only input fractions were analyzed (Bulk RNA-seq).

extract_protocol:
Both hippocampi were dissected and placed in an ice-cold Dounce homogenizer (D8938-1SET, Sigma-Aldrich) vessel containing 1000 μl of chilled homogenization buffer (50mM Tris pH 7.5, 100mM KCl, 12mM MgCl2, 1% Nonidet P-40, protease inhibitor, 1mM dl-Dithiothreitol (DTT), 1mg/ml heparin, 100ug/ml cycloheximide, 200U/ml RNAse Out in H2O RNAse free) to a 2-10% w/v ratio. Tissue was homogenized using 40 strokes with a large pestle (A) and 40 strokes more with a small pestle (B) to form the final homogenate. The lysate was centrifugated at 10,000 x g for 10 min at 4ºC to obtain a post-mitochondrial supernatant. 80 μl of lysate (input fraction) was taken and stored at -80ºC for subsequent input analysis.
cDNA libraries were prepared using the NEBNext® Poly(A) mRNA magnetic isolation module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. cDNA libraries were prepared from from 100 ng of RNA. Libraries were sequenced on an Illumina NextSeq 6000 instrument with 40 million reads per sample. Each fragment was sequenced paired-end 2 x 150 bp.

treatment_protocol: All mice (naïve and trained) were handled during 3 minutes for 3 consecutive days prior the beginning of the experiment to reduce stress and anxiety. WT;PV_Cre;RiboTag, APP;PV_Cre;RiboTag, Tau;PV_Cre;RiboTag and APP/Tau;PV_Cre;RiboTag mice were kept in their home cages (naïve) or trained in the MWM during 5 consecutive days (6 trials/day) to find a hidden platform (11 cm diameter) located in a circular pool containing white-colored water (1.2 m diameter). 24 hours after last training trial on day 5, mice were tested for memory retention (probe trial). 2 hours after the probe trial, mice were euthanized by cervical dislocation and brains were immediately dissected.

tag: Sex

tag: group

value: Naive


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

city: Birmingham

first: Nestor

last: Prieto-Dominguez

state: AL

department: Microbiology

institute: The University of Alabama at Birmingham (UAB)

description:
Library name: DSP-1001660020082-D-A02
Nanostring GeoMx DSP

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

source_name: Melanoma primary tumor

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

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

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

value: Melanoma primary tumor

tag: mouse strain

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

value: Melanoma murine cells

value: PBS, ip, qd

tag: primer used

value: GeoMx Seq Code D A02


title: HP, APP, 6months, Naïve, sample5

value: Hippocampus

value: Female


title: HP, Tau, 6months, Naïve, sample3

value: Bulk


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

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

description:
Library name: B_1A
Column name in BART_GeneCount.txt: B_Control_rep1_count

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

source_name: BAR-T

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

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

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

value: BAR-T

value: esophageal epithelium

value: pH 7.0 HBSS


title: SL470031

value: hippocampus

tag: hippocampal siide used

value: left

value: Male

tag: age(days)

tag: animal strain

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

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

value: 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: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: HP, Control, 9months, Trained, sample4

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Trained


title: SL470035

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: HP, Tau, 6months, Naïve, sample2

tag: tissue

tag: Sex

tag: cell type

tag: genotype

tag: group

value: Naive


title: Fetal Membrane, Buprenorphine, 11

description: Library name: Sample 11

value: Term, non-labor, fetal membrane

tag: treatment

value: Buprenorphine

tag: batch


title: Fetal Membrane, Buprenorphine, 10

description: Library name: Sample 10


title: HP, APP/Tau, 6months, Naïve, sample6

value: Hippocampus


title: HP, APP/Tau, 9months, Trained, sample2

tag: cell line

value: Female


title: SL470029

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: Fetal Membrane, Buprenorphine, 8

description: Library name: Sample 8

tag: tissue

tag: treatment

tag: batch


title: HP, Control, 9months, Naïve, sample4

tag: cell line

tag: cell type

value: Bulk

tag: genotype

value: Naïve


title: HP, APP/Tau, 6months, Naïve, sample5

tag: Sex

tag: group


title: SL470028

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

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: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: Fetal Membrane, Buprenorphine, 7

description: Library name: Sample 7

tag: tissue

tag: treatment

tag: batch


title: HP, Control, 9months, Naïve, sample3

tag: cell line

tag: cell type

tag: genotype


title: HP, APP, 6months, Trained, sample3

tag: Sex

tag: group


title: SL470030

value: hippocampus

tag: hippocampal siide used

value: right

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: HP, APP/Tau, 9months, Naïve, sample1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SL470026

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: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: HP, Control, 9months, Trained, sample3

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SL470027

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: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: Fetal Membrane, Media Control, 6

description: Library name: Sample 6

tag: tissue

tag: treatment

value: Media

tag: batch


title: HP, APP, 6months, Naïve, sample4

tag: Sex

tag: cell type

tag: genotype

tag: group


title: Fetal Membrane, Media Control, 5

description: Library name: Sample5


title: HP, Control, 6months, Naïve, sample6


title: SL470024

tag: hippocampal siide used

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: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: Fetal Membrane, Media Control, 2

description: Library name: Sample 2

tag: tissue

tag: treatment

tag: batch


title: HP, Control, 9months, Naïve, sample2

tag: cell line

tag: cell type

tag: genotype


title: HP, Control, 6months, Trained, sample5

tag: Sex

tag: group

value: Trained


title: Fetal Membrane, Media Control, 4

description: Library name: Sample 4

value: Term, non-labor, fetal membrane


title: SL470025

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: HP, Control, 6months, Naïve, sample5

tag: tissue

value: Hippocampus

tag: Sex

tag: cell type

tag: genotype

tag: group

value: Naive


title: Fetal Membrane, Media Control, 1

description: Library name: Sample 1

tag: treatment

tag: batch


title: HP, APP, 6months, Naïve, sample3

value: Female

value: Bulk


title: SL470023

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

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: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL470022

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: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: HP, APP, 6months, Naïve, sample2

tag: tissue

tag: Sex

tag: cell type

tag: genotype

tag: group


title: SeAx_HDAC10_5

city: Poznań

first: Katarzyna

last: Iżykowska

state: Great Poland

address: Strzeszyńska 32

country: Poland

institute: Institute of Human Genetics PAS

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 (hg38) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM), Transcripts Per Million (TPM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files include FPKM values, TPM, read counts for each Sample

source_name: SeAx

growth_protocol: cells were maintained in RPMI1640 supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Qiuck- RNA MiniPrep Kit (Zymo Research)
TruSeq Stranded mRNA protocol

tag: cell line

value: SeAx

value: lymphoid

value: HDAC10 overexpression

tag: treatment

value: no treatment


title: HP, Control, 9months, Trained, sample1


title: SeAx_HDAC10_3


title: SL470021

value: hippocampus

tag: hippocampal siide used

value: right

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: IN

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: HP, Control, 9months, Trained, sample2

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HP, APP/Tau, 6months, Naïve, sample4

tag: Sex

tag: group


title: HP, APP/Tau, 9months, Trained, sample1


title: SL470020

tag: hippocampal siide used

value: Male

tag: age(days)

tag: animal strain

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

tag: generation

value: F2 cross

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

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: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SL470019

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: latency score_day7

tag: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: HP, APP/Tau, 6months, Naïve, sample3

tag: tissue

tag: Sex

tag: cell type

tag: genotype

tag: group


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

source_name: Basolateral amygdala

value: Basolateral amygdala

tag: cell line

tag: treatment

value: Trained


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


title: SL470018

tag: hippocampal siide used

value: left

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: pca index_day7only

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SeAx_GFP_5

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: HP, APP, 6months, Naïve, sample1

tag: tissue

value: Hippocampus

tag: Sex

value: Female

value: Bulk

tag: group

value: Naive


title: SL470017

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

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: response bias_day6

tag: prob diff_day6

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


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

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SeAx_GFP_3

value: SeAx

value: lymphoid

value: no treatment


title: HP, APP, 6months, Trained, sample2

tag: Sex

tag: group


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

value: Naïve


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


title: Hut78_HDAC10_2

value: HDAC10 overexpression


title: Hut78_HDAC10_5


title: SL470016

value: hippocampus

tag: hippocampal siide used

value: right

tag: age(days)

tag: animal strain

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

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

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: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: HP, Control, 6months, Trained, sample4

tag: tissue

tag: Sex

tag: cell type

tag: genotype

tag: group

value: Trained


title: Maternal Prdm10 knockout GV oocyte RNA-seq biol rep1

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description: Library name: MatKO_GV_1_RME622

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

source_name: oocyte

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

value: GV oocyte

value: knock out


title: SL470015

tag: hippocampal siide used

value: left

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: learningclassification

value: GT

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SeAx_GFP_2

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: HP, APP/Tau, 6months, Trained, sample3

tag: tissue

value: Hippocampus

tag: Sex

value: Female

value: Bulk

tag: group


title: BLA, APP/Tau, 9months, Naïve, sample3

value: Basolateral amygdala

value: Naïve


title: HP, Control, 9months, Naïve, sample1


title: Hut78_HDAC10_1

value: lymphoid

value: HDAC10 overexpression

value: no treatment


title: SL470014

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

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: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: BLA, APP/Tau, 9months, Naïve, sample2

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SeAx_HDAC10_2

value: SeAx


title: HP, Control, 6months, Naïve, sample4

tag: Sex

tag: group

value: Naive


title: Hut78_GFP_5


title: BLA, Control, 9months, Naïve, sample5


title: HP, APP/Tau, 6months, Naïve, sample2


title: SL470013

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: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL470012

tag: tissue

tag: hippocampal siide used

value: left

tag: Sex

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: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: Hut78_GFP_2

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: BLA, Control, 9months, Trained, sample4

tag: tissue

value: Trained


title: SL470011

tag: hippocampal siide used

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

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 testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: BLA, APP/Tau, 9months, Trained, sample2

tag: tissue

value: Basolateral amygdala

tag: cell line

value: Female

tag: cell type

value: Bulk

tag: genotype

tag: treatment


title: HP, APP/Tau, 6months, Trained, sample2

value: Hippocampus

tag: Sex

tag: group


title: HP, APP/Tau, 6months, Naïve, sample1


title: SL470010

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

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: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: Hut78_GFP_1

tag: cell line

tag: cell type

value: lymphoid

tag: genotype

tag: treatment

value: no treatment


title: SeAxsh253

value: HDAC10 knock-down


title: SeAxsh252

value: SeAx


title: BLA, APP/Tau, 9months, Naïve, sample1

tag: tissue

value: Naïve


title: SL470009

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

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: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: HP, Tau, 6months, Naïve, sample1

tag: tissue

tag: Sex

tag: cell type

tag: genotype

tag: group

value: Naive


title: BLA, Control, 9months, Naïve, sample4

tag: cell line

tag: treatment


title: SeAxsh251


title: HP, Control, 6months, Naïve, sample2


title: SL470007

tag: hippocampal siide used

value: left

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: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: BLA, Control, 9months, Naïve, sample3

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SL470008

tag: hippocampal siide used

value: right

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SeAxNT23

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: HP, Tau, 6months, Trained, sample4

tag: tissue

tag: Sex

value: Female

value: Bulk

tag: group

value: Trained


title: SL470006

tag: hippocampal siide used

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

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: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: BLA, Control, 9months, Trained, sample3

tag: tissue

value: Basolateral amygdala

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SeAxNT22

value: lymphoid

value: no treatment


title: BLA, Control, 9months, Trained, sample2


title: HP, Control, 6months, Trained, sample3

value: Hippocampus

tag: Sex

tag: group


title: HP, Tau, 6months, Trained, sample3


title: HP, Control, 6months, Naïve, sample3


title: HP, Control, 6months, Naïve, sample1


title: BLA, Control, 9months, Naïve, sample1

value: Naïve


title: BLA, Control, 9months, Trained, sample1


title: Hut78sh252

value: HDAC10 knock-down


title: Hut78sh253


title: HP, Control, 6months, Trained, sample2


title: HP, APP, 6months, Trained, sample1


title: SL470005

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

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: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL470002

tag: tissue

tag: hippocampal siide used

value: right

tag: Sex

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

value: GT

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: Hut78sh251

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SL470001

tag: tissue

tag: hippocampal siide used

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: 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: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: BLA, APP/Tau, 9months, Trained, sample1

tag: tissue

tag: cell line

value: Female

tag: cell type

value: Bulk

tag: genotype

tag: treatment


title: Hut78NT23

value: WT


title: Hut78NT22


title: HP, Tau, 6months, Trained, sample1

tag: Sex

tag: group

value: Trained


title: SL470000

tag: hippocampal siide used

value: left

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: SeAxNT21

tag: cell line

value: SeAx

tag: cell type

value: lymphoid

tag: genotype

tag: treatment

value: no treatment


title: SL469999

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: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: BLA, Control, 9months, Naïve, sample2

tag: tissue

value: Basolateral amygdala

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Naïve


title: SL470004

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

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

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: epm rawdatafile

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: Hut78NT21

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HP, APP/Tau, 6months, Trained, sample1

tag: tissue

value: Hippocampus

tag: Sex

tag: group


title: 14dpi_heart2

city: Jena

first: Dennis

middle: de

last: de Bakker

address: Beutenbergstraße 11

institute: FLI

description: Section 1-43 contains cardiac sample

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters.
The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
processed data files contain transcript read counts normalized against spike-in read count and total read count per section
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file containing transcript counts per gene (rows) and section (columns)

source_name: injured mouse heart

extract_protocol:
Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)  see also: Junker et al., 2014, Cell
CEL-seq protocol (Hashimshony et al., Cell Reports, 2012); also  see: Junker et al., 2014, Cell

treatment_protocol: Unfixed adult mouse hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned, and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. (2014) Cell.

value: heart

tag: developmental stage

value: adult

tag: section direction

value: from injured area into the remote myocardium

tag: transgenic background

tag: gender

tag: section thickness

value: Took 20µm section, then skipped 80µm, took the next 20µm section, etc


title: 14dpi_heart1

description: Section 1-33 contains cardiac sample

value: Male


title: SL469998

tag: hippocampal siide used

value: right

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: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL470003

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: GT

tag: pca index_days6and_7

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: 7dpi_heart1

description: Section 1-48 contains cardiac sample, section 1 is (nearly) empty

tag: tissue

tag: developmental stage

tag: section direction

tag: transgenic background

tag: gender

tag: section thickness


title: HP, Tau, 6months, Trained, sample2

tag: Sex

tag: cell type

value: Bulk

tag: genotype

tag: group

value: Trained


title: AG09270_XO_6

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

description:
d470; GSE264742_counts.csv.gz
DEG.csv.gz

data_processing:
Read pairs were trimmed using fastp
Read pairs were aligned to the human reference genome (hg38) using hisat2 for allele-specific analysis of phased variants using phaser, or quantified against GENCODE version (v36) using salmon.
DESEQ2 output (log2FoldChange, Wald statistic, p.adjust-value by contrast)
Assembly: hg38
Supplementary files format and content: raw counts per sample
Supplementary files format and content: DEG.csv listing DESEQ2 output (log2FoldChange, Wald statistic, p.adjust-value in multiple experimental and control contrasts):
Supplementary files format and content: fXO = female 45,X vs. euploid samples
Supplementary files format and content: mXO1 = male1 45,X vs. euploid samples
Supplementary files format and content: mXO2 = male2 45,X vs. euploid samples
Supplementary files format and content: fmE1 = female vs. male1 euploid samples
Supplementary files format and content: fmE2 =female vs. male2 euploid samples
Supplementary files format and content: m1m2O = male1 vs. male2 45,X samples
Supplementary files format and content: more details in https://www.biorxiv.org/content/10.1101/2023.03.08.531747v2.full

growth_protocol: Human iPSCs were cultured in feeder-free conditions on GelTrex-coated plates (ThermoFisher Scientific) in mTeSR-1 media (Stem Cell Technologies) in 5% CO2 at 37°C. iPSCs were passaged with 0.5M EDTA at least weekly in small aggregates.

extract_protocol:
RNA was extracted from NCCs using the PureLink RNA Mini Kit (ThermoFisher Scientific).
Libraries were prepared at the UConn Center for Genome Innovation using the Illumina Strand mRNA Kit and 100bp paired-ends reads were sequenced to an average depth of 40 million reads/replicate on the NovaSeq (Illumina).

treatment_protocol: Confluent wells of iPSCs cultured on Geltrex-coated plates in mTeSR-1 medium were singularized with Accutase (ThermoFisher Scientific) and plated on Geltrex coated plates at 4.5-6 x104 cells/cm2 in DMEM/F-12, 1x N2, 1% Glutamax, 1% Non-essential Amino Acids, 1 µM CHIR99021 (StemCell Technologies), 2 µM SB431542 (StemCell Technologies), 1 µM DMH1 (Tocris Bioscience), 20 ng/mL BMP4 (Peprotech), and 10 µM Y-27632 (Tocris Bioscience), for the first two days only. Media was changed daily until day 4 and 5 when the cells were harvested. Round of differentiation indicated in the "differentiation round" field.

tag: cell line

value: NCC

tag: differentiation round

value: G


title: AG09270_XO_7

description:
d471; GSE264742_counts.csv.gz
DEG.csv.gz

value: H


title: advanced liver tumour AlbR26Met_1

city: Marseille

first: Abdessamad

last: EL KAOUTARI

state: France

address: 27 boulevard Lei Roure

country: France

institute: INSERM

description: 679906 T2-E20

data_processing:
EdgeR for differerential expression after normalization
Assembly: Reads were aligned to mouse reference genome GRCm38 (mm10) and generated counts were pre-processed and normalized.
Supplementary files format and content: txt matrix of normalized abundance of genes in all samples

source_name: Liver

extract_protocol:
mRNA was extracted with Qiagen kit from the indicated samples, following manufacturer instructions. 500 ng total RNA per sample was diluted in RNase- DNase- and protease- free molecular grade water (maximum volume 20 µL). RNA quality was verified with Agilent bioanalyzer Tapestation with RIN and/or Dv200 values; and purity evaluated with Nanodrop considered as valid when OD260/280 was between 1.8 and 2.2. Samples were submitted to ICM platform for sequencing with Illumina NovaSeq X technology (purification of poly-A containing mRNA molecules; 40 million reads/sample, 100 bases each, paired end).
Random primed cDNA library, purification of poly-A containing mRNA molecules, mRNA fragmentation, random primed cDNA synthesis, adapter ligation and adapter specific PCR, amplification

value: Liver

value: tumour


title: advanced liver tumour AlbR26Met_10

description: 678766 T2-E19


title: advanced liver tumour AlbR26Met_11

description: 679109 T7-E19


title: 3dpi_heart1

description: Section 1-48 contains cardiac sample, sections 1, 2 and 25 are (nearly) empty

value: heart

value: adult

value: from injured area into the remote myocardium


title: SL469997

value: hippocampus

tag: hippocampal siide used

value: right

value: Male

tag: age(days)

tag: animal strain

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

tag: generation

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: loco testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: SL469996

tag: tissue

tag: hippocampal siide used

value: left

tag: Sex

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

tag: pca index_days6and_7

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco box


title: AG09270_XY_9

description:
d468; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: genotype

tag: differentiation round

value: I


title: UK1268_HC

city: Cambridge

first: Matthew

last: Leventhal

state: MA

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

institute: Massachusetts Institute of Technology

data_processing:
Data was aligned to hg19 using TopHat and CuffLinks. The data were then TPM normalized and filtered based on the number of mapped reads and percent mappability
Assembly: hg19
Supplementary files format and content: tab-delimited text file indicates the raw counts per patient

source_name: Temporal cortex

extract_protocol:
We used the laser-capture RNA-seq method to profile total RNA of brain neurons similar to what we reported in previous studies. In brief, laser-capture microdissection was performed on human autopsy brain samples to extract neurons. For each temporal cortex (middle gyrus) about 300 pyramidal neurons were outlined in layers V/VI by their characteristic size, shape, and location in HistoGene-stained frozen sections and laser-captured using the Arcturus Veritas Microdissection System (Applied Biosystems) as in previous studies. Total RNA was isolated and extracted with DNase using the Arcturus Picopure method
Libraries were constructed using the TruSeq RNA Library Prep Kit v2

tag: tissue

value: Temporal cortex

value: Pyramidal neurons

value: HC


title: advanced liver tumour AlbR26Met_12

description: 679109 T11-E20

value: Liver

tag: group


title: SL469995

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

value: GT

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 testdate

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: 7dpi_heart2

description: Section 1-48 contains cardiac sample, sections 1, 2 and 13 are (nearly) empty

tag: tissue

value: heart

tag: developmental stage

tag: section direction

tag: transgenic background

tag: gender

tag: section thickness

value: Took 20µm section, then skipped 80µm, took the next 20µm section, etc


title: UK1263_HC

tag: cell type

tag: genotype


title: advanced liver tumour AlbR26Met_2

description: 678837 T3-E20

tag: group

value: tumour


title: AG09270_XY_7

description:
d466; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

value: NCC

tag: differentiation round

value: G


title: UK1261_HC


title: SL469993

value: hippocampus

tag: hippocampal siide used

value: right

tag: Sex

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

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


title: advanced liver tumour AlbR26Met_3

description: 679980 T8-E19

tag: tissue

tag: group

tag: genotype


title: SL469992

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

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: advanced liver tumour AlbR26Met_4

description: 679909 T6-E19

tag: tissue

tag: group

tag: genotype


title: UK1260_HC

tag: cell type


title: UK1271_HC


title: AG09270_XY_5

description:
d464; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: differentiation round

value: E


title: UK1247_HC

value: Temporal cortex


title: HP, Control, 6months, Trained, sample1

value: Hippocampus

tag: Sex

value: Bulk

value: Trained


title: AG09270_XO_5

description:
d469; GSE264742_counts.csv.gz
DEG.csv.gz

value: F


title: AG09270_XY_6

description:
d465; GSE264742_counts.csv.gz
DEG.csv.gz


title: SL469990

tag: hippocampal siide used

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

value: IN

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


title: AG04381_C15XO_4

description:
d463; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

value: NCC

tag: genotype

tag: differentiation round

value: I


title: advanced liver tumour AlbR26Met_5

description: 680002 T2-E19

tag: tissue

value: Liver

tag: group

value: tumour


title: AG09270_XY_8

description:
d467; GSE264742_counts.csv.gz
DEG.csv.gz

value: H


title: SL469994

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: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: advanced liver tumour AlbR26Met_6

description: 679916 T3-E20

tag: tissue

tag: group

tag: genotype


title: UK1245_HC

value: Temporal cortex

tag: cell type

value: Pyramidal neurons

value: HC


title: advanced liver tumour AlbR26Met_7

description: 678632 T4-E19


title: SL469988

tag: hippocampal siide used

tag: Sex

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

value: GT

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


title: AG04381_C15XO_3

description:
d462; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: genotype

tag: differentiation round

value: G


title: UK1244_HC

tag: tissue


title: UK1224_HC


title: AG04381_C15XO_2

description:
d461; GSE264742_counts.csv.gz
DEG.csv.gz

value: F


title: SL469987

tag: hippocampal siide used

tag: Sex

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: 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: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: advanced liver tumour AlbR26Met_8

description: 679959 T3-E20

tag: tissue

tag: group

tag: genotype


title: UK1217_HC

tag: cell type


title: AG04381_C15XO_1

description:
d460; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

value: NCC

tag: differentiation round

value: E


title: advanced liver tumour AlbR26Met_9

description: 679664 T1-E19

value: Liver


title: AG04381_C7XO_4

description:
d459; GSE264742_counts.csv.gz
DEG.csv.gz


title: SL469986

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: 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


title: SL469991

tag: tissue

value: hippocampus

tag: hippocampal siide used

tag: Sex

value: Male

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

value: ST

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: AG04381_C7XO_3

description:
d458; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: genotype

tag: differentiation round


title: SL469989

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: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

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


title: SL469984

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: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: UK1211_HC

tag: tissue

value: Temporal cortex

tag: cell type

value: Pyramidal neurons

tag: genotype


title: AG04381_C7XO_2

description:
d457; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: differentiation round


title: UK1165_HC

value: HC


title: SL469985

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: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

tag: pca index_days6and_7

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


title: mutant liver healty AlbR26Met_3

description: 680505 HL-E20

tag: tissue

tag: group

value: healty

tag: genotype


title: SL469983

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: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: AG04381_C7XO_1

description:
d456; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: genotype

tag: differentiation round


title: AG04381_C70XY_4

description:
d455; GSE264742_counts.csv.gz
DEG.csv.gz

value: I


title: UK1161_HC

tag: tissue


title: mutant liver healty AlbR26Met_5

description: 680004 HL-E19

tag: group


title: SL469981

tag: hippocampal siide used

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

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: 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


title: AG04381_C70XY_3

description:
d454; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

value: NCC

tag: genotype

tag: differentiation round

value: G


title: UK1095_HC

tag: tissue


title: SL469980

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

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: AO24

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description: 10x Genomics

data_processing:
cellranger mkfastq
cellranger count
cellbender
scrublet
doubletFinder
seurat
Assembly: mm10
Supplementary files format and content: barcodes.tsv' a tab-delimited text files include list of cell-barcodes and 'features.tsv' a tab-delimited text file include list of genes and 'matrix.mtx' file in a sparse matrix format containing raw counts per gene per cell-barcode.

source_name: NEOCORTEX

extract_protocol:
Single nuclei were obtained from cortex samples in 1 ml ice cold Nuclei EZ lysis buffer (Sigma, #EZ PREP NUC-101), homogenized using 2 ml glass dounce tissue grinders on ice; 15 times with pestle A and then 15 times with pestle B. The solution was then transferred to a new 2 mL microcentrifuge tube, 1mL nuclei EZ lysis buffer was added, followed by 5-minute incubation on ice, and then centrifuged at 500xg for 5 minutes at 4°C. Supernatants were removed, pellets were resuspended in 1mL nuclei EZ lysis buffer, followed by an additional 5-minute incubation on ice, and centrifuged at 500xg for 5 minutes at 4°C. The supernatant was then discarded, the pellet resuspended in NSB (1X PBS w/ 0.2U/ul RNase inhibitors /1% Ultra-pure BSA) and filtered through a 40um Flowmi Cell strainer (Bel-Art, H13680-0040). Nuclei were then counted on a hemocytometer (iChip) in a 10ul of suspension with 1:1 0.4% Trypan Blue. Nuclei concentration was adjusted for targeted sequencing of 10,000 cells/sample using the 10X Genomics Single Cell 3′ Reagent Kits v3 protocol to prepare libraries. 4 mice/genotype and timepoint were used, using both males and females. Libraries were sequenced using the McDermott Sequencing Core at UT Southwestern.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 10x Genomics). Isolated nuclei were mixed with the 10X  master mix and loaded with partitioning oil and gel beads onto the provided chip. This results in generation of gel bead-in-emulsion (GEMs).  GEMs were then retrotranscripted to cDNA; these contained  Ilumina R1 primer sequence, Unique Molecular Identifier (UMIs) and the 10x Barcode. Silane DynaBeads were used to purify cDNA which were then amplified by PCR. SPRIselect beads were used to select proper sized fragments. Samples were cleaned with 80% ethanol after every amplification step as well. Finally, libraries were constructed and an Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during these final steps.

tag: tissue

value: NEOCORTEX

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

tag: genotype

value: FLX


title: UK1092_HC

tag: cell type


title: SL469979

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: IN

tag: pca index_days6and_7

tag: response bias_day7

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


title: mutant liver healty AlbR26Met_1

description: 679904 HL-E20

tag: tissue

value: Liver

tag: group

tag: genotype


title: AG04381_C70XY_1

description:
d452; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: differentiation round

value: E


title: UK1057_HC

value: Temporal cortex

value: Pyramidal neurons


title: UK1187_HC

value: HC


title: AG04381_C69XY_4

description:
d451; GSE264742_counts.csv.gz
DEG.csv.gz

value: H


title: AO23

description: 10x Genomics

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative


title: SL469977

tag: hippocampal siide used

value: left

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

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: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: mutant liver healty AlbR26Met_4

description: 679950 HL-E19

tag: tissue

tag: group

value: healty

tag: genotype


title: AG04381_C69XY_3

description:
d450; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

value: NCC

tag: differentiation round

value: G


title: MGH1722_HC


title: UK1026_HC


title: SL469978

tag: hippocampal siide used

tag: Sex

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: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box


title: AO21

description: 10x Genomics

tag: tissue

value: NEOCORTEX

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

tag: genotype

value: CKO


title: UK1103_HC

tag: cell type


title: AG04381_C69XY_2

description:
d449; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: differentiation round

value: F


title: SL469982

value: hippocampus

tag: hippocampal siide used

tag: Sex

value: Female

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm 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: response bias_day6

tag: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: AO22

description: 10x Genomics

tag: tissue

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

tag: genotype


title: MGH1703_HC

value: Temporal cortex

tag: cell type

value: Pyramidal neurons


title: SL469975

tag: hippocampal siide used

tag: Sex

tag: age(days)

tag: animal strain

tag: generation

tag: rat number

tag: family

tag: hpc dissection_date

tag: hpc dissection_day

tag: dissector

tag: rnaconc

tag: pf reads

tag: ribosomeperc

tag: mrnaperc

tag: rin

tag: percent coding

tag: percent utr

tag: percent intronic

tag: percent intergenic

tag: pct usable_bases

tag: median cv_coverage

tag: lateral locoscore

tag: rearing locoscore

tag: total locoscore

tag: epm percent_time_open_arm

tag: epm boli

tag: epm distancetraveled

tag: epm time_immobile

tag: learningclassification

value: ST

tag: pca index_days6and_7

tag: response bias_day7

tag: prob diff_day7

tag: latency score_day7

tag: pca index_day7only

tag: response bias_day6

tag: epm trial

tag: epm testdate

tag: epm testday

tag: epm testorderbyday

tag: loco testdate

tag: loco box


title: AO20

description: 10x Genomics

tag: tissue

tag: strain

tag: age

tag: batch prep

tag: sequencing batch_cumulative

tag: genotype

value: FLX


title: AG04381_C70XY_2

description:
d453; GSE264742_counts.csv.gz
DEG.csv.gz

tag: cell line

tag: cell type

tag: differentiation round


title: AO19

description: 10x Genomics


title: AG05278_C8XO_4

description:
d295; GSE264742_counts.csv.gz
DEG.csv.gz

value: D


title: SL469976

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

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: prob diff_day6

tag: latency score_day6

tag: pca index_day6only

tag: epm rawdatafile

tag: loco testday

tag: loco batch

tag: loco rack

tag: dob

tag: dod


title: mutant liver healty AlbR26Met_2

description: 680502 HL-E20

tag: tissue

value: Liver

tag: group

value: healty

tag: genotype


title: MGH1688_HC

tag: cell type

value: HC