title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030280LR01-Day1-GC6-3]

description: Valproate, 500 mg/kg, Day 1, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027079LR01-GD4-1]

status: Public on Dec 13 2023

type: SRA

city: Houston

first: yi

last: chai

address: pgpr

country: USA

institute: Biostate AI

description: Tetracyclin, 15 mg/kg, Day 8, Repeat 1

library_source: transcriptomic

data_processing:
Raw data from Illumina sequencer
illumina Adaptor Trim
HISAT2 Alignment
Assembly: NCBI GCF_015227675.2, Genome assembly mRatBN7.2
Supplementary files format and content: csv

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Blood

growth_protocol: Animals were kept under a standard condition with room temperature at 21-23 ºC, 40-70% relative humidity, and a 12/12h light: dark cycle. Chow and water are available ad libitum.

extract_protocol:
Trizol based total RNA extraction method
RNA libraries for RNA-Seq were prepared by using mRNA capture based standard library preparation kit (Vazyme) following manufacturer's protocol.

tag: age

value: 6 wks

tag: Sex

value: male

tag: tissue

value: whole blood

tag: treatment

value: Tetracyclin, 15 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027078LR01-GD3-3]

description: Isoniazid, 30 mg/kg, Day 6, Repeat 2

value: Isoniazid, 30 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_1-2-K15-I15

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: OF1A human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027076LR01-GD3-1]

description: Isoniazid, 10 mg/kg, Day 6, Repeat 3

value: Isoniazid, 10 mg/kg, Day 6, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027074LR01-GD2-2]

description: Isoniazid, 10 mg/kg, Day 6, Repeat 1

value: Isoniazid, 10 mg/kg, Day 6, Repeat 1


title: 3543_OF1A_1-2-K15-F4


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027075LR01-GD2-3]

description: Isoniazid, 10 mg/kg, Day 6, Repeat 2

value: Isoniazid, 10 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_1-2-K15-F16


title: 3543_OF1A_1-2-K15-F15


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030275LR01-Day1-GC5-3]

description: Valproate, 500 mg/kg, Day 1, Repeat 3

value: 3-4 wks

value: Valproate, 500 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_1-2-K15-E4


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027073LR01-GD2-1]

description: Tetracyclin, 4 mg/kg, Day 8, Repeat 3

value: Tetracyclin, 4 mg/kg, Day 8, Repeat 3


title: 3543_OF1A_1-2-K15-E3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027072LR01-GD1-3]

description: Tetracyclin, 200 mg/kg, Day 10, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027071LR01-GD1-2]

description: Tetracyclin, 4 mg/kg, Day 8, Repeat 2

value: Tetracyclin, 4 mg/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027068LR01-GB8-2]

description: Tetracyclin, 200 mg/kg, Day 5, Repeat 2

value: Tetracyclin, 200 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027070LR01-GD1-1]

description: Tetracyclin, 50 mg/kg, Day 10, Repeat 3

value: Tetracyclin, 50 mg/kg, Day 10, Repeat 3


title: 3543_OF1A_1-2-K15-E16


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027069LR01-GB8-3]

description: Tetracyclin, 200 mg/kg, Day 5, Repeat 3

value: 6 wks

value: Tetracyclin, 200 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-2-K15-D16


title: 3543_OF1A_1-2-K15-E15


title: 3543_OF1A_1-2-K15-D4


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027067LR01-GB8-1]

description: Tetracyclin, 200 mg/kg, Day 5, Repeat 1

value: male

value: whole blood

value: Tetracyclin, 200 mg/kg, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027065LR01-GB7-2]

description: Tetracyclin, 50 mg/kg, Day 5, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027077LR01-GD3-2]

description: Isoniazid, 30 mg/kg, Day 6, Repeat 1

value: Isoniazid, 30 mg/kg, Day 6, Repeat 1


title: 3543_OF1A_1-2-K15-D15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027066LR01-GB7-3]

description: Tetracyclin, 50 mg/kg, Day 5, Repeat 3

value: Tetracyclin, 50 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-2-K15-C4


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027064LR01-GB7-1]

description: Tetracyclin, 50 mg/kg, Day 5, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 5, Repeat 1


title: 3543_OF1A_1-2-K15-C3


title: 3543_OF1A_1-2-K15-F3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027063LR01-GB6-3]

description: Tetracyclin, 50 mg/kg, Day 10, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_1-2-K15-C16


title: 3543_OF1A_1-2-K15-C15


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027062LR01-GB6-2]

description: Tetracyclin, 15 mg/kg, Day 5, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 5, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027061LR01-GB6-1]

description: Tetracyclin, 15 mg/kg, Day 5, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 5, Repeat 2


title: 3543_OF1A_1-2-K15-B4


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027060LR01-GB5-3]

description: Tetracyclin, 4 mg/kg, Day 8, Repeat 1

value: Tetracyclin, 4 mg/kg, Day 8, Repeat 1


title: 3543_OF1A_1-2-K15-B16


title: 3543_OF1A_1-2-K15-B3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027059LR01-GB5-2]

description: Tetracyclin, 15 mg/kg, Day 5, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027058LR01-GB5-1]

description: Tetracyclin, 4 mg/kg, Day 5, Repeat 3

value: 6 wks

value: Tetracyclin, 4 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-2-K15-D3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027012LR01-GD4-3-2023-09-08]

description: Tetracyclin, 4 mg/kg, Day 5, Repeat 2

value: male

value: Tetracyclin, 4 mg/kg, Day 5, Repeat 2


title: 3543_OF1A_1-2-K15-B15


title: 3543_OF1A_1-2-K15-A4


title: 3543_OF1A_1-2-K15-A3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027010LR01-GD4-1-2023-09-08]

description: Tetracyclin, 4 mg/kg, Day 5, Repeat 1

value: whole blood

value: Tetracyclin, 4 mg/kg, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027009LR01-GD3-3-2023-09-08]

description: Isoniazid, 300 mg/kg, Day 5, Repeat 3

value: Isoniazid, 300 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-2-K15-A16

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027011LR01-GD4-2-2023-09-08]

description: Tetracyclin, 50 mg/kg, Day 10, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 10, Repeat 1


title: 3543_OF1A_1-1-K15-P1

value: Female

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027008LR01-GD3-2-2023-09-08]

description: Isoniazid, 300 mg/kg, Day 8, Repeat 3

value: Isoniazid, 300 mg/kg, Day 8, Repeat 3


title: 3543_OF1A_1-1-K15-P2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027006LR01-GD2-3-2023-09-08]

description: Isoniazid, 300 mg/kg, Day 5, Repeat 2

value: Isoniazid, 300 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027007LR01-GD3-1-2023-09-08]

description: Isoniazid, 300 mg/kg, Day 8, Repeat 2

value: Isoniazid, 300 mg/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027005LR01-GD2-2-2023-09-08]

description: Tetracyclin, 15 mg/kg, Day 10, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 10, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027003LR01-GD1-3-2023-09-08]

description: Isoniazid, 300 mg/kg, Day 8, Repeat 1

value: Isoniazid, 300 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027004LR01-GD2-1-2023-09-08]

description: Isoniazid, 300 mg/kg, Day 5, Repeat 1

value: Isoniazid, 300 mg/kg, Day 5, Repeat 1


title: 3543_OF1A_1-1-K15-P13


title: 3543_OF1A_1-1-K15-P14


title: 3543_OF1A_1-1-K15-O2


title: 3543_OF1A_1-1-K15-O1


title: 3543_OF1A_1-1-K15-O14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027002LR01-GD1-2-2023-09-08]

description: Isoniazid, 100 mg/kg, Day 5, Repeat 3

value: 6 wks

value: Isoniazid, 100 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-1-K15-O13


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027001LR01-GD1-1-2023-09-08]

description: Isoniazid, 100 mg/kg, Day 8, Repeat 3

value: male

value: Isoniazid, 100 mg/kg, Day 8, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026999LR01-GB8-2-2023-09-08]

description: Isoniazid, 100 mg/kg, Day 8, Repeat 2

value: whole blood

value: Isoniazid, 100 mg/kg, Day 8, Repeat 2


title: 3543_OF1A_1-1-K15-N2


title: 3543_OF1A_1-1-K15-N1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026998LR01-GB8-1-2023-09-08]

description: Isoniazid, 100 mg/kg, Day 5, Repeat 1

value: Isoniazid, 100 mg/kg, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026997LR01-GB7-3-2023-09-08]

description: Tetracyclin, 15 mg/kg, Day 10, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_1-2-K15-A15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-1-K15-N13

value: Female


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026996LR01-GB7-2-2023-09-08]

description: Isoniazid, 30 mg/kg, Day 5, Repeat 3

value: Isoniazid, 30 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-1-K15-M2

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026994LR01-GB6-3-2023-09-08]

description: Isoniazid, 30 mg/kg, Day 5, Repeat 2

value: Isoniazid, 30 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026995LR01-GB7-1-2023-09-08]

description: Tetracyclin, 15 mg/kg, Day 10, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 10, Repeat 1


title: 3543_OF1A_1-1-K15-M1


title: 3543_OF1A_1-1-K15-M14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026993LR01-GB6-2-2023-09-08]

description: Tetracyclin, 4 mg/kg, Day 10, Repeat 3

value: Tetracyclin, 4 mg/kg, Day 10, Repeat 3


title: 3543_OF1A_1-1-K15-L2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026989LR01-GB5-1-2023-09-08]

description: Isoniazid, 100 mg/kg, Day 8, Repeat 1

value: Isoniazid, 100 mg/kg, Day 8, Repeat 1


title: 3543_OF1A_1-1-K15-L13


title: 3543_OF1A_1-1-K15-L14


title: 3543_OF1A_1-1-K15-L1


title: 3543_OF1A_1-1-K15-K2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026990LR01-GB5-2-2023-09-08]

description: Isoniazid, 10 mg/kg, Day 5, Repeat 3

value: Isoniazid, 10 mg/kg, Day 5, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027000LR01-GB8-3-2023-09-08]

description: Isoniazid, 100 mg/kg, Day 5, Repeat 2

value: 6 wks

value: Isoniazid, 100 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026959LR01-GD4-2-20230907]

description: Tetracyclin, 4 mg/kg, Day 10, Repeat 1

value: male

value: Tetracyclin, 4 mg/kg, Day 10, Repeat 1


title: 3543_OF1A_1-1-K15-N14


title: 3543_OF1A_1-1-K15-K1


title: 3543_OF1A_1-1-K15-K14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026957LR01-GD3-3-20230907]

description: Tetracyclin, 200 mg/kg, Day 4, Repeat 3

value: whole blood

value: Tetracyclin, 200 mg/kg, Day 4, Repeat 3


title: 3543_OF1A_1-1-K15-K13


title: 3543_OF1A_1-1-K15-M13


title: 3543_OF1A_1-1-K15-J2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026992LR01-GB6-1-2023-09-08]

description: Isoniazid, 30 mg/kg, Day 5, Repeat 1

value: Isoniazid, 30 mg/kg, Day 5, Repeat 1


title: 3543_OF1A_1-1-K15-J14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026954LR01-GD2-3-20230907]

description: Isoniazid, 300 mg/kg, Day 10, Repeat 3

value: Isoniazid, 300 mg/kg, Day 10, Repeat 3


title: 3543_OF1A_1-1-K15-J1

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026955LR01-GD3-1-20230907]

description: Tetracyclin, 200 mg/kg, Day 4, Repeat 2

value: Tetracyclin, 200 mg/kg, Day 4, Repeat 2


title: 3543_OF1A_1-1-K15-J13

value: Female


title: 3543_OF1A_1-1-K15-I2

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026952LR01-GD2-1-20230907]

description: Tetracyclin, 200 mg/kg, Day 4, Repeat 1

value: Tetracyclin, 200 mg/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026956LR01-GD3-2-20230907]

description: Isoniazid, 30 mg/kg, Day 8, Repeat 3

value: Isoniazid, 30 mg/kg, Day 8, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026991LR01-GB5-3-2023-09-08]

description: Tetracyclin, 4 mg/kg, Day 10, Repeat 2

value: Tetracyclin, 4 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_1-1-K15-I1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026951LR01-GD1-3-20230907]

description: Isoniazid, 300 mg/kg, Day 10, Repeat 1

value: Isoniazid, 300 mg/kg, Day 10, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026960LR01-GD4-3-20230907]

description: Isoniazid, 10 mg/kg, Day 5, Repeat 2

value: Isoniazid, 10 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026958LR01-GD4-1-20230907]

description: Isoniazid, 10 mg/kg, Day 5, Repeat 1

value: 6 wks

value: Isoniazid, 10 mg/kg, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026950LR01-GD1-2-20230907]

description: Tetracyclin, 50 mg/kg, Day 4, Repeat 3

value: male

value: Tetracyclin, 50 mg/kg, Day 4, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026948LR01-GB8-3-20230907]

description: Tetracyclin, 50 mg/kg, Day 4, Repeat 1

value: whole blood

value: Tetracyclin, 50 mg/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026947LR01-GB8-2-20230907]

description: Isoniazid, 30 mg/kg, Day 8, Repeat 2

value: Isoniazid, 30 mg/kg, Day 8, Repeat 2


title: 3543_OF1A_1-1-K15-I13


title: 3543_OF1A_1-1-K15-I14


title: 3543_OF1A_1-1-K15-H2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026946LR01-GB8-1-20230907]

description: Isoniazid, 100 mg/kg, Day 10, Repeat 3

value: Isoniazid, 100 mg/kg, Day 10, Repeat 3


title: 3543_OF1A_1-1-K15-H14

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-1-K15-H13


title: 3543_OF1A_1-1-K15-G1


title: 3543_OF1A_1-1-K15-G2


title: 3543_OF1A_1-1-K15-G14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026953LR01-GD2-2-20230907]

description: Isoniazid, 300 mg/kg, Day 10, Repeat 2

value: Isoniazid, 300 mg/kg, Day 10, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026943LR01-GB7-1-20230907]

description: Isoniazid, 30 mg/kg, Day 8, Repeat 1

value: Isoniazid, 30 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026944LR01-GB7-2-20230907]

description: Isoniazid, 100 mg/kg, Day 10, Repeat 2

value: Isoniazid, 100 mg/kg, Day 10, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026941LR01-GB6-2-20230907]

description: Isoniazid, 10 mg/kg, Day 8, Repeat 3

value: Isoniazid, 10 mg/kg, Day 8, Repeat 3


title: 3543_OF1A_1-1-K15-F2

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-1-K15-G13


title: 3543_OF1A_1-1-K15-F1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026940LR01-GB6-1-20230907]

description: Tetracyclin, 15 mg/kg, Day 4, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026939LR01-GB5-3-20230907]

description: Isoniazid, 10 mg/kg, Day 8, Repeat 2

value: Isoniazid, 10 mg/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026938LR01-GB5-2-20230907]

description: Tetracyclin, 4 mg/kg, Day 4, Repeat 3

value: 6 wks

value: Tetracyclin, 4 mg/kg, Day 4, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026942LR01-GB6-3-20230907]

description: Tetracyclin, 15 mg/kg, Day 4, Repeat 2

value: male

value: Tetracyclin, 15 mg/kg, Day 4, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026937LR01-GB5-1-20230907]

description: Isoniazid, 100 mg/kg, Day 10, Repeat 1

value: whole blood

value: Isoniazid, 100 mg/kg, Day 10, Repeat 1


title: 3543_OF1A_1-1-K15-F13


title: 3543_OF1A_1-1-K15-F14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026949LR01-GD1-1-20230907]

description: Tetracyclin, 50 mg/kg, Day 4, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 4, Repeat 2


title: 3543_OF1A_1-1-K15-H1


title: 3543_OF1A_1-1-K15-E2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026936LR01-GD4-3-20230906]

description: Tetracyclin, 4 mg/kg, Day 4, Repeat 2

value: Tetracyclin, 4 mg/kg, Day 4, Repeat 2


title: 3543_OF1A_1-1-K15-E1

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-1-K15-E14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026935LR01-GD4-2-20230906]

description: Isoniazid, 10 mg/kg, Day 8, Repeat 1

value: Isoniazid, 10 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026945LR01-GB7-3-20230907]

description: Tetracyclin, 15 mg/kg, Day 4, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 4, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026934LR01-GD4-1-20230906]

description: Tetracyclin, 4 mg/kg, Day 4, Repeat 1

value: Tetracyclin, 4 mg/kg, Day 4, Repeat 1


title: 3543_OF1A_1-1-K15-E13


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026933LR01-GD3-3-20230906]

description: Isoniazid, 30 mg/kg, Day 10, Repeat 3

value: Isoniazid, 30 mg/kg, Day 10, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026932LR01-GD3-2-20230906]

description: Isoniazid, 300 mg/kg, Day 4, Repeat 3

value: Isoniazid, 300 mg/kg, Day 4, Repeat 3


title: 3543_OF1A_1-1-K15-D2

value: Female

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026929LR01-GD2-2-20230906]

description: Isoniazid, 300 mg/kg, Day 4, Repeat 1

value: Isoniazid, 300 mg/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026928LR01-GD2-1-20230906]

description: Tetracyclin, 200 mg/kg, Day 7, Repeat 2

value: 6 wks

value: Tetracyclin, 200 mg/kg, Day 7, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026931LR01-GD3-1-20230906]

description: Tetracyclin, 200 mg/kg, Day 7, Repeat 3

value: male

value: Tetracyclin, 200 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_1-1-K15-D13


title: 3543_OF1A_1-1-K15-C2


title: 3543_OF1A_1-1-K15-D1


title: 3543_OF1A_1-1-K15-D14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026927LR01-GD1-3-20230906]

description: Isoniazid, 100 mg/kg, Day 4, Repeat 3

value: whole blood

value: Isoniazid, 100 mg/kg, Day 4, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026926LR01-GD1-2-20230906]

description: Isoniazid, 30 mg/kg, Day 10, Repeat 2

value: Isoniazid, 30 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_1-1-K15-C13


title: 3543_OF1A_1-1-K15-C14


title: 3543_OF1A_1-1-K15-C1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026925LR01-GD1-1-20230906]

description: Isoniazid, 100 mg/kg, Day 4, Repeat 2

value: Isoniazid, 100 mg/kg, Day 4, Repeat 2


title: 3543_OF1A_1-1-K15-B2

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-1-K15-B13


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026921LR01-GB7-3-20230906]

description: Tetracyclin, 50 mg/kg, Day 7, Repeat 3

value: Tetracyclin, 50 mg/kg, Day 7, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026922LR01-GB8-1-20230906]

description: Tetracyclin, 200 mg/kg, Day 7, Repeat 1

value: Tetracyclin, 200 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_1-1-K15-A2


title: 3543_OF1A_1-1-K15-B14


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026923LR01-GB8-2-20230906]

description: Isoniazid, 30 mg/kg, Day 4, Repeat 3

value: Isoniazid, 30 mg/kg, Day 4, Repeat 3


title: 3543_OF1A_1-1-K15-B1


title: 3543_OF1A_1-1-K15-A14


title: 3543_OF1A_1-1-K15-A1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026919LR01-GB7-1-20230906]

description: Isoniazid, 30 mg/kg, Day 10, Repeat 1

value: Isoniazid, 30 mg/kg, Day 10, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026920LR01-GB7-2-20230906]

description: Isoniazid, 30 mg/kg, Day 4, Repeat 2

value: Isoniazid, 30 mg/kg, Day 4, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026918LR01-GB6-3-20230906]

description: Isoniazid, 30 mg/kg, Day 4, Repeat 1

value: Isoniazid, 30 mg/kg, Day 4, Repeat 1


title: 3543_OF1A_1-1-K15-A13

value: Female

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026916LR01-GB6-1-20230906]

description: Isoniazid, 10 mg/kg, Day 4, Repeat 3

value: 6 wks

value: Isoniazid, 10 mg/kg, Day 4, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026930LR01-GD2-3-20230906]

description: Isoniazid, 300 mg/kg, Day 4, Repeat 2

value: male

value: Isoniazid, 300 mg/kg, Day 4, Repeat 2


title: 3543_OF1A_2-6-M1-P24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026915LR01-GB5-3-20230906]

description: Isoniazid, 10 mg/kg, Day 10, Repeat 2

value: whole blood

value: Isoniazid, 10 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_2-6-M1-P12


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026914LR01-GB5-2-20230906]

description: Isoniazid, 10 mg/kg, Day 4, Repeat 2

value: Isoniazid, 10 mg/kg, Day 4, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026913LR01-GB5-1-20230906]

description: Isoniazid, 10 mg/kg, Day 4, Repeat 1

value: Isoniazid, 10 mg/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026924LR01-GB8-3-20230906]

description: Isoniazid, 100 mg/kg, Day 4, Repeat 1

value: Isoniazid, 100 mg/kg, Day 4, Repeat 1


title: 3543_OF1A_2-6-M1-O23

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026912LR01-GD4-3-20230905]

description: Tetracyclin, 50 mg/kg, Day 7, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_2-6-M1-P11


title: 3543_OF1A_2-6-M1-O12


title: 3543_OF1A_2-6-M1-N23


title: 3543_OF1A_2-6-M1-N24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026908LR01-GD3-2-20230905]

description: Tetracyclin, 50 mg/kg, Day 7, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 7, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026917LR01-GB6-2-20230906]

description: Isoniazid, 10 mg/kg, Day 10, Repeat 3

value: Isoniazid, 10 mg/kg, Day 10, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026910LR01-GD4-1-20230905]

description: Isoniazid, 10 mg/kg, Day 10, Repeat 1

value: Isoniazid, 10 mg/kg, Day 10, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026909LR01-GD3-3-20230905]

description: Tetracyclin, 200 mg/kg, Day 3, Repeat 2

value: Tetracyclin, 200 mg/kg, Day 3, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026907LR01-GD3-1-20230905]

description: Tetracyclin, 200 mg/kg, Day 3, Repeat 1

value: Tetracyclin, 200 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_2-6-M1-M23

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-6-M1-N11


title: 3543_OF1A_2-6-M1-N12


title: 3543_OF1A_2-6-M1-M12


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026906LR01-GD2-3-20230905]

description: Tetracyclin, 200 mg/kg, Day 9, Repeat 3

value: 6 wks

value: Tetracyclin, 200 mg/kg, Day 9, Repeat 3


title: 3543_OF1A_2-6-M1-M11


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026904LR01-GD2-1-20230905]

description: Tetracyclin, 15 mg/kg, Day 7, Repeat 3

value: male

value: Tetracyclin, 15 mg/kg, Day 7, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026903LR01-GD1-3-20230905]

description: Tetracyclin, 200 mg/kg, Day 9, Repeat 2

value: whole blood

value: Tetracyclin, 200 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_2-6-M1-P23


title: 3543_OF1A_2-6-M1-L24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026902LR01-GD1-2-20230905]

description: Tetracyclin, 50 mg/kg, Day 3, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_2-6-M1-L11


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026901LR01-GD1-1-20230905]

description: Tetracyclin, 15 mg/kg, Day 7, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_2-6-M1-K24

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026911LR01-GD4-2-20230905]

description: Tetracyclin, 200 mg/kg, Day 3, Repeat 3

value: Tetracyclin, 200 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_2-6-M1-K12


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026900LR01-GB8-3-20230905]

description: Tetracyclin, 200 mg/kg, Day 9, Repeat 1

value: Tetracyclin, 200 mg/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026898LR01-GB8-1-20230905]

description: Tetracyclin, 50 mg/kg, Day 3, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 3, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026899LR01-GB8-2-20230905]

description: Tetracyclin, 15 mg/kg, Day 7, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_2-6-M1-K11


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026897LR01-GB7-3-20230905]

description: Tetracyclin, 15 mg/kg, Day 3, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026905LR01-GD2-2-20230905]

description: Tetracyclin, 50 mg/kg, Day 3, Repeat 3

value: Tetracyclin, 50 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026896LR01-GB7-2-20230905]

description: Tetracyclin, 50 mg/kg, Day 9, Repeat 3

value: Tetracyclin, 50 mg/kg, Day 9, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026895LR01-GB7-1-20230905]

description: Tetracyclin, 15 mg/kg, Day 3, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_2-6-M1-J23

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-6-M1-K23


title: 3543_OF1A_2-6-M1-J12


title: 3543_OF1A_2-6-M1-J24


title: 3543_OF1A_2-6-M1-I12


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026891LR01-GB5-3-20230905]

description: Tetracyclin, 4 mg/kg, Day 7, Repeat 1

value: 6 wks

value: male

value: Tetracyclin, 4 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_2-6-M1-I11


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026894LR01-GB6-3-20230905]

description: Tetracyclin, 4 mg/kg, Day 7, Repeat 3

value: whole blood

value: Tetracyclin, 4 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_2-6-M1-J11


title: 3543_OF1A_2-6-M1-I23


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026893LR01-GB6-2-20230905]

description: Tetracyclin, 4 mg/kg, Day 7, Repeat 2

value: Tetracyclin, 4 mg/kg, Day 7, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026892LR01-GB6-1-20230905]

description: Tetracyclin, 15 mg/kg, Day 3, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 3, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026890LR01-GB5-2-20230905]

description: Tetracyclin, 4 mg/kg, Day 3, Repeat 3

value: Tetracyclin, 4 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_2-6-M1-H24

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_2-6-M1-H11


title: 3543_OF1A_2-6-M1-H23


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026887LR01-GD4-2-20230904]

description: Tetracyclin, 4 mg/kg, Day 3, Repeat 1

value: Tetracyclin, 4 mg/kg, Day 3, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026889LR01-GB5-1-20230905]

description: Tetracyclin, 4 mg/kg, Day 3, Repeat 2

value: Tetracyclin, 4 mg/kg, Day 3, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026888LR01-GD4-3-20230904]

description: Tetracyclin, 50 mg/kg, Day 9, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_2-6-M1-G24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026886LR02-GD4-1-20230904]

description: Isoniazid, 300 mg/kg, Day 7, Repeat 3

value: Isoniazid, 300 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_2-6-M1-G23


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026884LR01-GD3-2-20230904]

description: Isoniazid, 300 mg/kg, Day 3, Repeat 3

value: Isoniazid, 300 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026883LR01-GD3-1-20230904]

description: Isoniazid, 300 mg/kg, Day 3, Repeat 2

value: Isoniazid, 300 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_2-6-M1-G12

value: Female


title: 3543_OF1A_2-6-M1-G11

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026882LR01-GD2-3-20230904]

description: Tetracyclin, 50 mg/kg, Day 9, Repeat 1

value: 6 wks

value: Tetracyclin, 50 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_2-6-M1-F24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026881LR01-GD2-2-20230904]

description: Isoniazid, 300 mg/kg, Day 3, Repeat 1

value: male

value: Isoniazid, 300 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_2-6-M1-F23


title: 3543_OF1A_2-6-M1-E23


title: 3543_OF1A_2-6-M1-F11


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026880LR01-GD2-1-20230904]

description: Isoniazid, 300 mg/kg, Day 7, Repeat 1

value: whole blood

value: Isoniazid, 300 mg/kg, Day 7, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026879LR01-GD1-3-20230904]

description: Isoniazid, 100 mg/kg, Day 3, Repeat 3

value: Isoniazid, 100 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026878LR01-GD1-2-20230904]

description: Tetracyclin, 15 mg/kg, Day 9, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 9, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026876LR01-GB8-3-20230904]

description: Isoniazid, 100 mg/kg, Day 3, Repeat 1

value: Isoniazid, 100 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_2-6-M1-F12

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_2-6-M1-H12


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026875LR01-GB8-2-20230904]

description: Tetracyclin, 15 mg/kg, Day 9, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_2-6-M1-E12


title: 3543_OF1A_2-6-M1-E11


title: 3543_OF1A_2-6-M1-E24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026877LR01-GD1-1-20230904]

description: Isoniazid, 100 mg/kg, Day 3, Repeat 2

value: Isoniazid, 100 mg/kg, Day 3, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026873LR01-GB7-3-20230904]

description: Isoniazid, 100 mg/kg, Day 7, Repeat 3

value: Isoniazid, 100 mg/kg, Day 7, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026874LR01-GB8-1-20230904]

description: Isoniazid, 30 mg/kg, Day 3, Repeat 3

value: Isoniazid, 30 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026871LR01-GB7-1-20230904]

description: Tetracyclin, 15 mg/kg, Day 9, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_2-6-M1-D23

value: Female


title: 3543_OF1A_2-6-M1-D12

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026872LR01-GB7-2-20230904]

description: Isoniazid, 30 mg/kg, Day 3, Repeat 2

value: 6 wks

value: Isoniazid, 30 mg/kg, Day 3, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026885LR01-GD3-3-20230904]

description: Isoniazid, 300 mg/kg, Day 7, Repeat 2

value: male

value: Isoniazid, 300 mg/kg, Day 7, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026870LR01-GB6-3-20230904]

description: Isoniazid, 30 mg/kg, Day 3, Repeat 1

value: whole blood

value: Isoniazid, 30 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_2-6-M1-C24


title: 3543_OF1A_2-6-M1-C12


title: 3543_OF1A_2-6-M1-C23


title: 3543_OF1A_2-6-M1-C11


title: 3543_OF1A_2-6-M1-B24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026866LR01-GB5-2-20230904]

description: Isoniazid, 100 mg/kg, Day 7, Repeat 2

value: Isoniazid, 100 mg/kg, Day 7, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026869LR01-GB6-2-20230904]

description: Isoniazid, 10 mg/kg, Day 3, Repeat 3

value: Isoniazid, 10 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_2-6-M1-B23


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026868LR01-GB6-1-20230904]

description: Tetracyclin, 4 mg/kg, Day 9, Repeat 3

value: Tetracyclin, 4 mg/kg, Day 9, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026865LR01-GB5-1-20230904]

description: Isoniazid, 10 mg/kg, Day 3, Repeat 1

value: Isoniazid, 10 mg/kg, Day 3, Repeat 1


title: 3543_OF1A_2-6-M1-D24

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026863LR01-GD4-2-20230903]

description: Tetracyclin, 200 mg/kg, Day 2, Repeat 2

value: Tetracyclin, 200 mg/kg, Day 2, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026867LR01-GB5-3-20230904]

description: Isoniazid, 10 mg/kg, Day 3, Repeat 2

value: Isoniazid, 10 mg/kg, Day 3, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026861LR01-GD3-3-20230903]

description: Isoniazid, 30 mg/kg, Day 7, Repeat 3

value: Isoniazid, 30 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_2-6-M1-B11


title: 3543_OF1A_2-6-M1-A23


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026864LR01-GD4-3-20230903]

description: Tetracyclin, 200 mg/kg, Day 2, Repeat 3

value: Tetracyclin, 200 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_2-6-M1-B12

value: Female


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026862LR01-GD4-1-20230903]

description: Isoniazid, 100 mg/kg, Day 7, Repeat 1

value: Isoniazid, 100 mg/kg, Day 7, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026860LR01-GD3-2-20230903]

description: Tetracyclin, 200 mg/kg, Day 2, Repeat 1

value: 6 wks

value: Tetracyclin, 200 mg/kg, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026858LR01-GD2-3-20230903]

description: Tetracyclin, 50 mg/kg, Day 2, Repeat 3

value: male

value: Tetracyclin, 50 mg/kg, Day 2, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026859LR01-GD3-1-20230903]

description: Tetracyclin, 4 mg/kg, Day 9, Repeat 2

value: whole blood

value: Tetracyclin, 4 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_2-6-M1-D11

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-5-M1-P22


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026857LR01-GD2-2-20230903]

description: Tetracyclin, 4 mg/kg, Day 9, Repeat 1

value: Tetracyclin, 4 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_2-6-M1-A12


title: 3543_OF1A_2-6-M1-A11


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026856LR01-GD2-1-20230903]

description: Tetracyclin, 50 mg/kg, Day 2, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_2-5-M1-P21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026855LR01-GD1-3-20230903]

description: Isoniazid, 300 mg/kg, Day 9, Repeat 3

value: Isoniazid, 300 mg/kg, Day 9, Repeat 3


title: 3543_OF1A_2-5-M1-P10

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_2-5-M1-O9


title: 3543_OF1A_2-5-M1-O21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026854LR01-GD1-2-20230903]

description: Tetracyclin, 50 mg/kg, Day 2, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 2, Repeat 1


title: 3543_OF1A_2-6-M1-A24


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026853LR01-GD1-1-20230903]

description: Tetracyclin, 15 mg/kg, Day 2, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_2-5-M1-O10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026852LR01-GB8-3-20230903]

description: Tetracyclin, 15 mg/kg, Day 2, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 2, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026851LR01-GB8-2-20230903]

description: Isoniazid, 300 mg/kg, Day 9, Repeat 2

value: Isoniazid, 300 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_2-5-M1-N22

value: Female


title: 3543_OF1A_2-5-M1-P9


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026848LR01-GB7-2-20230903]

description: Tetracyclin, 4 mg/kg, Day 2, Repeat 3

value: Tetracyclin, 4 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_2-5-M1-N21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026850LR01-GB8-1-20230903]

description: Tetracyclin, 15 mg/kg, Day 2, Repeat 1

value: 6 wks

value: Tetracyclin, 15 mg/kg, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026847LR01-GB7-1-20230903]

description: Isoniazid, 30 mg/kg, Day 7, Repeat 2

value: male

value: Isoniazid, 30 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_2-5-M1-N9


title: 3543_OF1A_2-5-M1-N10


title: 3543_OF1A_2-5-M1-M21


title: 3543_OF1A_2-5-M1-M22


title: 3543_OF1A_2-5-M1-M10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026844LR01-GB6-1-20230903]

description: Tetracyclin, 4 mg/kg, Day 2, Repeat 1

value: whole blood

value: Tetracyclin, 4 mg/kg, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026843LR01-GB5-3-20230903]

description: Isoniazid, 300 mg/kg, Day 2, Repeat 3

value: Isoniazid, 300 mg/kg, Day 2, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026845LR01-GB6-2-20230903]

description: Isoniazid, 30 mg/kg, Day 7, Repeat 1

value: Isoniazid, 30 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_2-5-M1-L9

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-5-M1-L22


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026842LR01-GB5-2-20230903]

description: Isoniazid, 10 mg/kg, Day 7, Repeat 3

value: Isoniazid, 10 mg/kg, Day 7, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026841LR01-GB5-1-20230903]

description: Isoniazid, 300 mg/kg, Day 2, Repeat 2

value: Isoniazid, 300 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_2-5-M1-L21

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026849LR01-GB7-3-20230903]

description: Isoniazid, 300 mg/kg, Day 9, Repeat 1

value: Isoniazid, 300 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_2-5-M1-M9


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026840LR01-GD4-3-20230902]

description: Isoniazid, 10 mg/kg, Day 7, Repeat 2

value: Isoniazid, 10 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_2-5-M1-K9


title: 3543_OF1A_2-5-M1-K22


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026837LR01-GD3-3-20230902]

description: Isoniazid, 100 mg/kg, Day 9, Repeat 2

value: Isoniazid, 100 mg/kg, Day 9, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026846LR01-GB6-3-20230903]

description: Tetracyclin, 4 mg/kg, Day 2, Repeat 2

value: Tetracyclin, 4 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_2-5-M1-L10

value: Female


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026839LR01-GD4-2-20230902]

description: Isoniazid, 10 mg/kg, Day 7, Repeat 1

value: 6 wks

value: Isoniazid, 10 mg/kg, Day 7, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026836LR01-GD3-2-20230902]

description: Isoniazid, 300 mg/kg, Day 2, Repeat 1

value: male

value: Isoniazid, 300 mg/kg, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026834LR01-GD2-3-20230902]

description: Isoniazid, 100 mg/kg, Day 2, Repeat 3

value: whole blood

value: Isoniazid, 100 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_2-5-M1-K10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026833LR01-GD2-2-20230902]

description: Isoniazid, 100 mg/kg, Day 2, Repeat 2

value: Isoniazid, 100 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_2-5-M1-K21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026831LR01-GD1-3-20230902]

description: Isoniazid, 100 mg/kg, Day 2, Repeat 1

value: Isoniazid, 100 mg/kg, Day 2, Repeat 1


title: 3543_OF1A_2-5-M1-J21

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-5-M1-J9


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026830LR01-GD1-2-20230902]

description: Tetracyclin, 200 mg/kg, Day 6, Repeat 2

value: Tetracyclin, 200 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_2-5-M1-J10


title: 3543_OF1A_2-5-M1-I22


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026835LR01-GD3-1-20230902]

description: Tetracyclin, 200 mg/kg, Day 6, Repeat 3

value: Tetracyclin, 200 mg/kg, Day 6, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026832LR01-GD2-1-20230902]

description: Isoniazid, 100 mg/kg, Day 9, Repeat 1

value: Isoniazid, 100 mg/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026828LR01-GB8-3-20230902]

description: Isoniazid, 30 mg/kg, Day 9, Repeat 3

value: Isoniazid, 30 mg/kg, Day 9, Repeat 3


title: 3543_OF1A_2-5-M1-I9

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026829LR01-GD1-1-20230902]

description: Tetracyclin, 200 mg/kg, Day 6, Repeat 1

value: Tetracyclin, 200 mg/kg, Day 6, Repeat 1


title: 3543_OF1A_2-5-M1-I10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026838LR01-GD4-1-20230902]

description: Isoniazid, 100 mg/kg, Day 9, Repeat 3

value: Isoniazid, 100 mg/kg, Day 9, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026827LR01-GB8-2-20230902]

description: Isoniazid, 30 mg/kg, Day 2, Repeat 3

value: Isoniazid, 30 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_2-5-M1-H9

value: Female


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026826LR01-GB8-1-20230902]

description: Tetracyclin, 50 mg/kg, Day 6, Repeat 3

value: 6 wks

value: Tetracyclin, 50 mg/kg, Day 6, Repeat 3


title: 3543_OF1A_2-5-M1-H22


title: 3543_OF1A_2-5-M1-J22


title: 3543_OF1A_2-5-M1-H10


title: 3543_OF1A_2-5-M1-H21


title: 3543_OF1A_2-5-M1-G9


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026822LR01-GB6-3-20230902]

description: Isoniazid, 30 mg/kg, Day 9, Repeat 2

value: male

value: Isoniazid, 30 mg/kg, Day 9, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026825LR01-GB7-3-20230902]

description: Tetracyclin, 50 mg/kg, Day 6, Repeat 2

value: whole blood

value: Tetracyclin, 50 mg/kg, Day 6, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026823LR01-GB7-1-20230902]

description: Isoniazid, 30 mg/kg, Day 2, Repeat 1

value: Isoniazid, 30 mg/kg, Day 2, Repeat 1


title: 3543_OF1A_2-5-M1-G21

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-5-M1-G22


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026819LR01-GB5-3-20230902]

description: Isoniazid, 10 mg/kg, Day 2, Repeat 2

value: Isoniazid, 10 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_2-5-M1-G10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026818LR01-GB5-2-20230902]

description: Isoniazid, 30 mg/kg, Day 9, Repeat 1

value: Isoniazid, 30 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_2-5-M1-F9


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026824LR01-GB7-2-20230902]

description: Isoniazid, 30 mg/kg, Day 2, Repeat 2

value: Isoniazid, 30 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_2-5-M1-I21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026821LR01-GB6-2-20230902]

description: Isoniazid, 10 mg/kg, Day 2, Repeat 3

value: Isoniazid, 10 mg/kg, Day 2, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026820LR01-GB6-1-20230902]

description: Tetracyclin, 50 mg/kg, Day 6, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026816LR01-GD4-3-20230901]

description: Tetracyclin, 15 mg/kg, Day 6, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 6, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026817LR01-GB5-1-20230902]

description: Isoniazid, 10 mg/kg, Day 2, Repeat 1

value: Isoniazid, 10 mg/kg, Day 2, Repeat 1


title: 3543_OF1A_2-5-M1-F21

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_2-5-M1-F22

value: Female


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026815LR01-GD4-2-20230901]

description: Tetracyclin, 200 mg/kg, Day 1, Repeat 3

value: 6 wks

value: Tetracyclin, 200 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_2-5-M1-E21


title: 3543_OF1A_2-5-M1-E22


title: 3543_OF1A_2-5-M1-F10


title: 3543_OF1A_2-5-M1-E9


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026814LR01-GD4-1-20230901]

description: Isoniazid, 10 mg/kg, Day 9, Repeat 3

value: male

value: Isoniazid, 10 mg/kg, Day 9, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026811LR01-GD3-1-20230901]

description: Tetracyclin, 200 mg/kg, Day 1, Repeat 1

value: whole blood

value: Tetracyclin, 200 mg/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026813LR01-GD3-3-20230901]

description: Tetracyclin, 200 mg/kg, Day 1, Repeat 2

value: Tetracyclin, 200 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_2-5-M1-D9

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026810LR01-GD2-3-20230901]

description: Tetracyclin, 15 mg/kg, Day 6, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 6, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026812LR01-GD3-2-20230901]

description: Isoniazid, 10 mg/kg, Day 9, Repeat 2

value: Isoniazid, 10 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_2-5-M1-E10


title: 3543_OF1A_2-5-M1-D21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026809LR01-GD2-2-20230901]

description: Isoniazid, 10 mg/kg, Day 9, Repeat 1

value: Isoniazid, 10 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_2-5-M1-D10


title: 3543_OF1A_2-5-M1-D22


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026806LR01-GD1-2-20230901]

description: Tetracyclin, 50 mg/kg, Day 1, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026804LR01-GB8-3-20230901]

description: Tetracyclin, 200 mg/kg, Day 8, Repeat 2

value: Tetracyclin, 200 mg/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026807LR01-GD1-3-20230901]

description: Tetracyclin, 200 mg/kg, Day 8, Repeat 3

value: Tetracyclin, 200 mg/kg, Day 8, Repeat 3


title: 3543_OF1A_2-5-M1-C21


title: 3543_OF1A_2-5-M1-C10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026805LR01-GD1-1-20230901]

description: Tetracyclin, 15 mg/kg, Day 6, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026801LR01-GB7-3-20230901]

description: Tetracyclin, 15 mg/kg, Day 1, Repeat 3

value: Tetracyclin, 15 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_2-5-M1-B9

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: 3543_OF1A_2-5-M1-B21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026803LR01-GB8-2-20230901]

description: Tetracyclin, 200 mg/kg, Day 8, Repeat 1

value: 6 wks

value: Tetracyclin, 200 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026800LR01-GB7-2-20230901]

description: Tetracyclin, 4 mg/kg, Day 6, Repeat 3

value: male

value: Tetracyclin, 4 mg/kg, Day 6, Repeat 3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026799LR01-GB7-1-20230901]

description: Tetracyclin, 15 mg/kg, Day 1, Repeat 2

value: whole blood

value: Tetracyclin, 15 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_2-5-M1-A9

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-5-M1-B10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026798LR01-GB6-3-20230901]

description: Tetracyclin, 4 mg/kg, Day 6, Repeat 2

value: Tetracyclin, 4 mg/kg, Day 6, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026808LR01-GD2-1-20230901]

description: Tetracyclin, 50 mg/kg, Day 1, Repeat 3

value: Tetracyclin, 50 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_2-5-M1-A22


title: 3543_OF1A_2-5-M1-A21


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026797LR01-GB6-2-20230901]

description: Tetracyclin, 15 mg/kg, Day 1, Repeat 1

value: Tetracyclin, 15 mg/kg, Day 1, Repeat 1


title: 3543_OF1A_2-5-M1-C22


title: 3543_OF1A_2-5-M1-C9


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026795LR01-GB5-3-20230901]

description: Tetracyclin, 4 mg/kg, Day 1, Repeat 3

value: Tetracyclin, 4 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_2-5-M1-A10


title: 3543_OF1A_2-4-M1-P8


title: 3543_OF1A_2-5-M1-B22


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026802LR01-GB8-1-20230901]

description: Tetracyclin, 50 mg/kg, Day 1, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 1, Repeat 1


title: 3543_OF1A_2-4-M1-P7


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026794LR01-GB5-2-20230901]

description: Tetracyclin, 4 mg/kg, Day 6, Repeat 1

value: Tetracyclin, 4 mg/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026793LR01-GB5-1-20230901]

description: Tetracyclin, 50 mg/kg, Day 8, Repeat 2

value: Tetracyclin, 50 mg/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026791LR01-GD4-2-20230831]

description: Tetracyclin, 50 mg/kg, Day 8, Repeat 1

value: Tetracyclin, 50 mg/kg, Day 8, Repeat 1


title: 3543_OF1A_2-4-M1-P20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026790LR01-GD4-1-20230831]

description: Tetracyclin, 4 mg/kg, Day 1, Repeat 1

value: Tetracyclin, 4 mg/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026792LR01-GD4-3-20230831]

description: Tetracyclin, 4 mg/kg, Day 1, Repeat 2

value: 6 wks

value: Tetracyclin, 4 mg/kg, Day 1, Repeat 2


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026788LR01-GD3-2-20230831]

description: Isoniazid, 300 mg/kg, Day 1, Repeat 3

value: male

value: Isoniazid, 300 mg/kg, Day 1, Repeat 3


title: pgEpiSC_low

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

country: China

institute: China Agricultural University

data_processing:
Raw reads from scRNA-seq were split by 8 bp cell barcodes located on the Read 2 allowed 2 mismatches, besides, the 8pb unique molecular identifiers(UMIs) located on the Read 2 were switched to the identifier line of paired Read 1.
Then the Read 1 were processed to remove the template switch oligo (TSO) primer, low quality bases and polyA sequence. The trimmed reads were aligned against Ensembl Sus scrofa reference genome (Sscrofa11.1, GCA_000003025.6) using STAR software (version 2.7.1a) with default parameters.
The aligned reads were further assigned to the ensemble gene annotations (Sus_scrofa.Sscrofa11.1.98) using  featureCounts (version 1.6.4). Gene expression levels were estimated by counting the UMIs located the genes after deduplication by UMI-tools, next yielded an expression matrix consisting of UMI counts for each cell and gene.
Genome_build: Suscrofa.11.1
Supplementary_files_format_and_content: tab-delimited text files include the mean values of CPM values for each cell type.
Supplementary_files_format_and_content: tab-delimited text files include the variance of CPM values for each cell type.
Supplementary_files_format_and_content: Barcode information for single cell libraries
Supplementary_files_format_and_content: cell-level raw counts

organism: Sus scrofa

source_name: Pig pre-gastrulation epiblast stem cells (pig pgEpiSCs)

extract_protocol:
A modified Smart-seq2 protocol (Gao et al., 2018; Wang et al., 2018)
Single cell was transferred into prepared lysis buffer contained an 8bp barcode. Then, the first-strand cDNA was reversed-synthesized and amplified in a reverse transcription (RT) mixture containing 4U RNase inhibitor, 100U SuperScript II reverse transcriptase (Invitrogen, Cat. 18064071), 1 mM dNTPs (TAKARA, Cat. 4019), 60 mM MgCl2, 3 µM RT primer with 10 µM TSO primer. After PCR incubation, the product was purified by 0.8×AMPure XP beads (Beckman, Cat. A63882). Biotin PCR was carried out and enriched. The single cell RNA-seq library was constructed according to the KAPA Hyper Prep Kits with PCR Library Amplication/Illumina series (KAPA, KK8054).

tag: developmental stage

value: E10 embryonic epiblast

value: Embryonic epiblast


title: 3543_OF1A_2-4-M1-N20

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-4-M1-N8


title: P20

source_name: Pig pre-implantation embryos

value: Pig pre-implantation embryos (E0-E14)

value: Embryos


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026789LR01-GD3-3-20230831]

description: Tetracyclin, 15 mg/kg, Day 8, Repeat 3

value: whole blood

value: Tetracyclin, 15 mg/kg, Day 8, Repeat 3


title: 3543_OF1A_2-4-M1-O20


title: 3543_OF1A_2-4-M1-O7


title: 3543_OF1A_2-4-M1-O19


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026785LR01-GD2-2-20230831]

description: Isoniazid, 300 mg/kg, Day 6, Repeat 2

value: Isoniazid, 300 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_2-4-M1-O8


title: 3543_OF1A_2-4-M1-M7


title: 3543_OF1A_2-4-M1-M19


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026796LR01-GB6-1-20230901]

description: Tetracyclin, 50 mg/kg, Day 8, Repeat 3

value: Tetracyclin, 50 mg/kg, Day 8, Repeat 3


title: 3543_OF1A_2-4-M1-N7


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026787LR01-GD3-1-20230831]

description: Isoniazid, 300 mg/kg, Day 6, Repeat 3

value: Isoniazid, 300 mg/kg, Day 6, Repeat 3


title: 3543_OF1A_2-4-M1-N19

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: pgEpiSC_high


title: 3543_OF1A_2-4-M1-M8


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026786LR01-GD2-3-20230831]

description: Isoniazid, 300 mg/kg, Day 1, Repeat 2

value: Isoniazid, 300 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_2-4-M1-M20


title: 3543_OF1A_2-4-M1-L7


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026783LR01-GD1-3-20230831]

description: Isoniazid, 100 mg/kg, Day 1, Repeat 3

value: 6 wks

value: Isoniazid, 100 mg/kg, Day 1, Repeat 3


title: P18


title: 3543_OF1A_2-4-M1-L19


title: 3543_OF1A_2-4-M1-K8


title: P16


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026782LR01-GD1-2-20230831]

description: Isoniazid, 300 mg/kg, Day 6, Repeat 1

value: male

value: Isoniazid, 300 mg/kg, Day 6, Repeat 1


title: P19


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026781LR01-GD1-1-20230831]

description: Isoniazid, 100 mg/kg, Day 1, Repeat 2

value: Isoniazid, 100 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_2-4-M1-K7


title: 3543_OF1A_2-4-M1-K19


title: P15


title: P14


title: 3543_OF1A_2-4-M1-J7


title: 3543_OF1A_2-4-M1-J20


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026780LR01-GB8-3-20230831]

description: Isoniazid, 100 mg/kg, Day 1, Repeat 1

value: Isoniazid, 100 mg/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026784LR01-GD2-1-20230831]

description: Isoniazid, 300 mg/kg, Day 1, Repeat 1

value: Isoniazid, 300 mg/kg, Day 1, Repeat 1


title: 3543_OF1A_2-4-M1-J8

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-4-M1-L20


title: 3543_OF1A_2-4-M1-K20


title: P13

value: Pig pre-implantation embryos (E0-E14)

value: Embryos


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026779LR01-GB8-2-20230831]

description: Isoniazid, 100 mg/kg, Day 6, Repeat 3

value: whole blood

value: Isoniazid, 100 mg/kg, Day 6, Repeat 3


title: P17


title: P12


title: 3543_OF1A_2-4-M1-J19


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026778LR01-GB8-1-20230831]

description: Isoniazid, 30 mg/kg, Day 1, Repeat 3

value: Isoniazid, 30 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_2-4-M1-I20


title: 3543_OF1A_2-4-M1-I8


title: 3543_OF1A_2-4-M1-I7


title: 3543_OF1A_2-4-M1-H8


title: P11


title: 3543_OF1A_2-4-M1-I19


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026777LR01-GB7-3-20230831]

description: Isoniazid, 30 mg/kg, Day 1, Repeat 2

value: Isoniazid, 30 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_2-4-M1-H7

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: P8


title: P7


title: P9


title: 3543_OF1A_2-4-M1-F8


title: 3543_OF1A_2-4-M1-G8


title: 3543_OF1A_2-4-M1-G20


title: 3543_OF1A_2-4-M1-H19


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026775LR01-GB7-1-20230831]

description: Isoniazid, 30 mg/kg, Day 1, Repeat 1

value: Isoniazid, 30 mg/kg, Day 1, Repeat 1


title: 3543_OF1A_2-4-M1-G19


title: P6


title: 3543_OF1A_2-4-M1-G7


title: P5


title: P4


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026773LR01-GB6-2-20230831]

description: Isoniazid, 100 mg/kg, Day 6, Repeat 1

value: 6 wks

value: Isoniazid, 100 mg/kg, Day 6, Repeat 1


title: 3543_OF1A_2-4-M1-E7


title: 3543_OF1A_2-4-M1-F7


title: 3543_OF1A_2-4-M1-E20


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026774LR01-GB6-3-20230831]

description: Isoniazid, 100 mg/kg, Day 6, Repeat 2

value: male

value: Isoniazid, 100 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_2-4-M1-F20


title: 3543_OF1A_2-4-M1-E19


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026772LR01-GB6-1-20230831]

description: Isoniazid, 10 mg/kg, Day 1, Repeat 3

value: Isoniazid, 10 mg/kg, Day 1, Repeat 3


title: 3543_OF1A_2-4-M1-F19


title: 3543_OF1A_2-4-M1-E8


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026776LR01-GB7-2-20230831]

description: Tetracyclin, 15 mg/kg, Day 8, Repeat 2

value: Tetracyclin, 15 mg/kg, Day 8, Repeat 2


title: 3543_OF1A_2-4-M1-H20


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026769LR01-GB5-1-20230831]

description: Isoniazid, 10 mg/kg, Day 1, Repeat 1

value: Isoniazid, 10 mg/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026771LR01-GB5-3-20230831]

description: Isoniazid, 30 mg/kg, Day 6, Repeat 3

value: Isoniazid, 30 mg/kg, Day 6, Repeat 3


title: P10


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23026770LR01-GB5-2-20230831]

description: Isoniazid, 10 mg/kg, Day 1, Repeat 2

value: Isoniazid, 10 mg/kg, Day 1, Repeat 2


title: P3

value: Pig pre-implantation embryos (E0-E14)


title: 3543_OF1A_2-4-M1-D8

value: Female

value: nuclear RNA + genomic DNA


title: P2

value: Embryos


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026679LR01-GC4-1-9-4]

description: Valproate, 1000 mg/kg, Day 10, Repeat 1

value: 8 wks

value: whole blood

value: Valproate, 1000 mg/kg, Day 10, Repeat 1


title: P1


title: 3543_OF1A_2-4-M1-D20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026678LR01-GC2-2-9-4]

description: Valproate, 500 mg/kg, Day 10, Repeat 2

value: Valproate, 500 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_2-4-M1-D7


title: pEF-2-input

data_processing:
The cleaned reads were aligned to the pig genome (Sscrofa 11.1) using the BWA (version 0.7.15) with parameters: bwa mem -k 32 -M
The biological replicates of each cell type were pooled together using SAMtools (version 0.1.19).
Peak calling was performed using SICER (version 1.1) with parameters: --effGenomeSize 0.95 --windowSize 200 --gapSize 3 --mapq 0 --fragSize 264
Genome_build: Suscrofa.11.1
Supplementary_files_format_and_content: peak text files

source_name: Porcine embryonic fibroblast

extract_protocol:
Cells were lysed with lysis buffer supplemented with protease inhibitor cocktail and 1 mM PMSF (1x final each) and then sonicated to fragments about 200-500 bp using a Bioruptor. Immunoprecipitated DNA was isolated with H3K27ac antibodies (Abcam, Cat.N: ab4729)
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the NEXTflex™ ChIP-Seq Kit (Bioo Scientific, Cat.N: NOVA-5143-02). All libraries were sequenced on HiSeq X Ten (Illumina) platform to produce an average of ~120.62 million 150-bp paired-end raw reads and ~115.78 million high-quality reads for each library.

value: E30 fetal

value: Embryonic fibroblast

tag: chip antibody


title: 3543_OF1A_2-4-M1-C7


title: 3543_OF1A_2-4-M1-C8


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026677LR01-GC2-1-9-4]

description: Valproate, 500 mg/kg, Day 10, Repeat 1

value: male

value: Valproate, 500 mg/kg, Day 10, Repeat 1


title: 3543_OF1A_2-4-M1-C20


title: pEF-1-input


title: pEF-2-H3K27ac


title: 3543_OF1A_2-4-M1-B7


title: 3543_OF1A_2-4-M1-C19


title: 3543_OF1A_2-4-M1-B8


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026675LR01-GC1-2-9-4]

description: Valproate, 250 mg/kg, Day 10, Repeat 2

value: Valproate, 250 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_2-4-M1-B19


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026676LR01-GC1-3-9-4]

description: Valproate, 250 mg/kg, Day 10, Repeat 3

value: Valproate, 250 mg/kg, Day 10, Repeat 3


title: pEF-1-H3K27ac


title: 3543_OF1A_2-4-M1-A8


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026673LR01-GA4-3-9-4]

description: Carbon tetrachloride, 2 ml/kg, Day 10, Repeat 3


title: 3543_OF1A_2-4-M1-A20


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026674LR01-GC1-1-9-4]

description: Valproate, 250 mg/kg, Day 10, Repeat 1

value: Valproate, 250 mg/kg, Day 10, Repeat 1


title: pgEpiSC-4-input

value: E10 embryonic epiblast

value: Embryonic epiblast


title: 3543_OF1A_2-4-M1-A19

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026672LR01-GA4-2-9-4]

description: Carbon tetrachloride, 2 ml/kg, Day 10, Repeat 2


title: pgEpiSC-4-H3K27ac


title: 3543_OF1A_2-3-M1-P6

value: nuclear RNA + genomic DNA


title: pgEpiSC-1-input


title: 3543_OF1A_2-4-M1-D19


title: 3543_OF1A_2-3-M1-P5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026671LR01-GA4-1-9-4]

description: Carbon tetrachloride, 2 ml/kg, Day 10, Repeat 1


title: pgEpiSC-1-H3K27ac


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026670LR01-GA3-3-9-4]

description: Carbon tetrachloride, 1.5 ml/kg, Day 10, Repeat 3


title: 3543_OF1A_2-3-M1-P17


title: 3543_OF1A_2-3-M1-O6


title: 3543_OF1A_2-3-M1-P18


title: 3543_OF1A_2-4-M1-B20


title: RPUV

city: ithaca

first: Luye

last: An

address: 618 tower road

department: biomedical sciences

institute: cornell university

description: 10x genomics, sample ID in multiplexed raw files is "166159_AAC55GWM5_3_RP-2_11July22"

library_source: transcriptomic single cell

data_processing:
raw data were demultplexing, barcoding and gene count using Cellranger software
Assembly: mm10
Supplementary files format and content: matrix files, barcoding files and features files were provided following standard cellranger procedure.

molecule: total RNA

organism: Mus musculus

source_name: dorsal skin

extract_protocol:
Fresh collected tissue was digested and immune cells were enriched by CD45+ magnetic beads.
Single cell suspension were submitted to sequencing core of BRC at Cornell University for cell viability check and sequencing.

treatment_protocol: mouse dorsal skin were irradiated with UVB for 3times, once per two days. Detailed procedures were provided in methods.

value: dorsal skin

tag: condition

value: 8weeks, telogen

tag: genotype

value: RP

tag: strain

value: UVB


title: 3543_OF1A_2-3-M1-O5

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_2-3-M1-O17


title: 3543_OF1A_2-4-M1-A7


title: WTUV

description: 10x genomics, sample ID in the multiplexed faw file is "Sample_163739_AAC2T5GM5_1_1June2022"

value: WT


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026669LR01-GA3-2-9-4]

description: Carbon tetrachloride, 1.5 ml/kg, Day 10, Repeat 2

value: 8 wks

value: whole blood


title: 3543_OF1A_2-3-M1-O18


title: WTctrl

description: 10x genomics, sample ID in multiplexed raw files is "166160_AAC55GWM5_4_WF2_11July22"

value: male

value: no-UVB


title: 3543_OF1A_2-3-M1-N5


title: 3543_OF1A_2-3-M1-N18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026667LR01-GA2-3-9-4]

description: Carbon tetrachloride, 1 ml/kg, Day 10, Repeat 3


title: 3543_OF1A_2-3-M1-N17


title: 3543_OF1A_2-3-M1-N6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026666LR01-GA2-2-9-4]

description: Carbon tetrachloride, 1 ml/kg, Day 10, Repeat 2


title: 3543_OF1A_2-3-M1-M5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026665LR01-GA2-1-9-4]

description: Carbon tetrachloride, 1 ml/kg, Day 10, Repeat 1


title: 3543_OF1A_2-3-M1-M17


title: 3543_OF1A_2-3-M1-L6


title: 3543_OF1A_2-3-M1-M6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026664LR01-GA1-3-9-4]

description: Carbon tetrachloride, 0.5 ml/kg, Day 10, Repeat 3


title: 3543_OF1A_2-3-M1-L5


title: 3543_OF1A_2-3-M1-L17


title: M_UV_4

data_processing:
Raw data were aligned to genome using package STAR with default parameters
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include reads per gene

extract_protocol:
Fresh collected tissue was homogenized using liquid nitrogen and total RNA was extracted using Trizol standard protocol
0.5ug of total RNA was used for initital prep. mRNA was enriched using Poly A enrichment method. Library was preped using NEBNext Ultra II directional RNA library prep kit

value: WT C57Bl/6


title: M_Ctrl_1


title: M_Ctrl_3


title: 3543_OF1A_2-3-M1-K6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026663LR01-GA1-2-9-4]

description: Carbon tetrachloride, 0.5 ml/kg, Day 10, Repeat 2


title: M_Ctrl_2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026668LR01-GA3-1-9-4]

description: Carbon tetrachloride, 1.5 ml/kg, Day 10, Repeat 1


title: M_Ctrl_4


title: M_UV_3


title: 3543_OF1A_2-3-M1-K18


title: 3543_OF1A_2-3-M1-K5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026661LR01-1-3-9-4]

description: Sodium chloride, 0.9%, Day 10, Repeat 3

value: Sodium chloride, 0.9%, Day 10, Repeat 3


title: M_UV_2


title: 3543_OF1A_2-3-M1-J6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026662LR01-GA1-1-9-4]

description: Carbon tetrachloride, 0.5 ml/kg, Day 10, Repeat 1


title: 3543_OF1A_2-3-M1-K17


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026660LR01-1-2-9-4]

description: Sodium chloride, 0.9%, Day 10, Repeat 2

value: Sodium chloride, 0.9%, Day 10, Repeat 2


title: 3543_OF1A_2-3-M1-J5


title: M_UV_1


title: 3543_OF1A_2-3-M1-J18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026659LR01-1-1-9-4]

description: Sodium chloride, 0.9%, Day 10, Repeat 1

value: Sodium chloride, 0.9%, Day 10, Repeat 1


title: F_Ctrl_4

value: female


title: 3543_OF1A_2-3-M1-L18

value: Female


title: F_Ctrl_3


title: 3543_OF1A_2-3-M1-I6

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-3-M1-I5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026657LR01-GC2-2-9-3]

description: Valproate, 500 mg/kg, Day 9, Repeat 2

value: Valproate, 500 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_2-3-M1-I18


title: F_Ctrl_2

value: dorsal skin

value: 8weeks, telogen


title: 3543_OF1A_2-3-M1-I17


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026656LR01-GC2-1-9-3]

description: Valproate, 500 mg/kg, Day 9, Repeat 1

value: Valproate, 500 mg/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026655LR01-GC1-3-9-3]

description: Valproate, 250 mg/kg, Day 9, Repeat 3

value: Valproate, 250 mg/kg, Day 9, Repeat 3


title: 3543_OF1A_2-3-M1-H6

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: F_UV_4

value: UVB


title: 3543_OF1A_2-3-M1-H5


title: 3543_OF1A_2-3-M1-H17


title: 3543_OF1A_2-3-M1-H18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026654LR01-GC1-2-9-3]

description: Valproate, 250 mg/kg, Day 9, Repeat 2

value: 8 wks

value: whole blood

value: Valproate, 250 mg/kg, Day 9, Repeat 2


title: F_Ctrl_1

value: WT C57Bl/6


title: F_UV_2


title: 3543_OF1A_2-3-M1-G6


title: 3543_OF1A_2-3-M1-F6


title: 3543_OF1A_2-3-M1-G5


title: 3543_OF1A_2-3-M1-J17


title: F_UV_3


title: 3543_OF1A_2-3-M1-G17


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026652LR01-GA4-3-9-3]

description: Carbon tetrachloride, 2 ml/kg, Day 9, Repeat 3

value: male


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026658LR01-GC4-1-9-3]

description: Valproate, 1000 mg/kg, Day 9, Repeat 1

value: Valproate, 1000 mg/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026653LR01-GC1-1-9-3]

description: Valproate, 250 mg/kg, Day 9, Repeat 1

value: Valproate, 250 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_2-3-M1-F5


title: F_UV_1

value: female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026651LR01-GA4-2-9-3]

description: Carbon tetrachloride, 2 ml/kg, Day 9, Repeat 2


title: 3543_OF1A_2-3-M1-F18

value: Female


title: 3543_OF1A_2-3-M1-F17

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-3-M1-E6


title: 3543_OF1A_2-3-M1-G18


title: 3543_OF1A_2-3-M1-E17


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026649LR01-GA3-3-9-3]

description: Carbon tetrachloride, 1.5 ml/kg, Day 9, Repeat 3


title: 3543_OF1A_2-3-M1-D6


title: 3543_OF1A_2-3-M1-E18


title: 3543_OF1A_2-3-M1-E5


title: iMos, Doxycycline+MCC950, NLRP3 WT 1

city: Murcia

first: Pablo

middle: Pelegrin

last: Vivancos

state: Murcia

address: Av. Buenavista, 32

country: Spain

institute: IMIB-Arrixaca Pascual Parrilla

data_processing:
DRAGEN RNA v. 3.10.12
DRAGEN FASTQ was used to manipulation of FASTQ files, including:  adapter trimming, quality trimming, length filtering, format conversions and down-sampling for  each samples
Sequences reads were mapped to  mm10 using DRAGEN RNA Aligner
To normalization the rawCounts and differential expression  DRAGEN Quant Module /DESeq2 were used
Assembly: Mus musculus (UCSC) mm10
Supplementary files format and content: Excel file of raw-counts includes the reads for each samples

source_name: bone marrow

growth_protocol: DMEM high glucose + 10% FBS suplemmented with Atb (G418 and puromicyn)

extract_protocol:
Total RNA was extracted from Nlrp3−/− immortalized mouse macrophages expressing NLRP3 wild type or NLRP3 p.D303N using the RNeasy kit (74104, Qiagen) following manufacturer instructions
cDNA synthesis and library generation were performed using Stranded mRNA Prep Kit (Illumina) following the manufacturer’s instructions

treatment_protocol: Nlrp3−/− immortalized macrophages were treated for 16 h with or without doxycycline (1 µg/ml) to induce the expression of the human NLRP3 wild-type or  p.D303N variant, in the absence or presence of MCC950 (10 µM) from Sigma

value: bone marrow

tag: cell line

value: transformed cells

tag: cell type

value: immortalized macrophages

value: NLRP3 Wild-type


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026647LR01-GA3-1-9-3]

description: Carbon tetrachloride, 1.5 ml/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026648LR01-GA3-2-9-3]

description: Carbon tetrachloride, 1.5 ml/kg, Day 9, Repeat 2


title: 3543_OF1A_2-3-M1-D5


title: 3543_OF1A_2-3-M1-D18


title: 3543_OF1A_2-3-M1-C6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026646LR01-GA2-3-9-3]

description: Carbon tetrachloride, 1 ml/kg, Day 9, Repeat 3


title: 3543_OF1A_2-3-M1-C5


title: iMos, Doxycycline+MCC950, NLRP3 WT 2


title: iMos, Doxycycline, NLRP3 WT 2

value: Doxycyline


title: iMos, Doxycycline, NLRP3 WT 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026645LR01-GA2-2-9-3]

description: Carbon tetrachloride, 1 ml/kg, Day 9, Repeat 2


title: 3543_OF1A_2-3-M1-C18

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: iMos, Doxycycline, NLRP3 WT 1


title: 3543_OF1A_2-3-M1-C17


title: iMos, Doxycycline+MCC950, NLRP3 WT 3


title: 3543_OF1A_2-3-M1-B6


title: 3543_OF1A_2-3-M1-B5


title: iMos, Untreated, NLRP3 WT,3

value: Untreated


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026650LR01-GA4-1-9-3]

description: Carbon tetrachloride, 2 ml/kg, Day 9, Repeat 1

value: 8 wks


title: iMos, Doxycycline, NLRP3 WT 4


title: 3543_OF1A_2-3-M1-B18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026643LR01-GA1-3-9-3]

description: Carbon tetrachloride, 0.5 ml/kg, Day 9, Repeat 3

value: whole blood


title: 3543_OF1A_2-3-M1-B17


title: 3543_OF1A_2-3-M1-A5


title: iMos, Untreated, NLRP3 WT,2


title: iMos, Untreated, NLRP3 WT,1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026641LR01-GA1-1-9-3]

description: Carbon tetrachloride, 0.5 ml/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026642LR01-GA1-2-9-3]

description: Carbon tetrachloride, 0.5 ml/kg, Day 9, Repeat 2


title: 3543_OF1A_2-3-M1-A17


title: 3543_OF1A_2-3-M1-D17


title: 3543_OF1A_2-3-M1-A18


title: iMos, Doxycycline+MCC950, NLRP3 p.D303N 3

value: NLRP3 p.D303N


title: iMos, Doxycycline+MCC950, NLRP3 p.D303N 2


title: 3543_OF1A_2-2-M1-P4


title: iMos, Doxycycline+MCC950, NLRP3 p.D303N 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026639LR01-1-2-9-3]

description: Sodium chloride, 0.9%, Day 9, Repeat 2

value: Sodium chloride, 0.9%, Day 9, Repeat 2


title: 3543_OF1A_2-2-M1-P15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026640LR01-1-3-9-3]

description: Sodium chloride, 0.9%, Day 9, Repeat 3

value: male

value: Sodium chloride, 0.9%, Day 9, Repeat 3


title: 3543_OF1A_2-2-M1-P3


title: 3543_OF1A_2-2-M1-P16


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026644LR01-GA2-1-9-3]

description: Carbon tetrachloride, 1 ml/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026638LR01-1-1-9-3]

description: Sodium chloride, 0.9%, Day 9, Repeat 1

value: Sodium chloride, 0.9%, Day 9, Repeat 1


title: 3543_OF1A_2-2-M1-O3


title: iMos, Doxycycline+MCC950, NLRP3 p.D303N 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026637LR01-GC4-1-9-2]

description: Valproate, 1000 mg/kg, Day 8, Repeat 1

value: Valproate, 1000 mg/kg, Day 8, Repeat 1


title: 3543_OF1A_2-2-M1-O15

value: Female


title: 3543_OF1A_2-2-M1-O16

value: nuclear RNA + genomic DNA


title: iMos, Doxycycline, NLRP3 p.D303N 4

value: bone marrow


title: 3543_OF1A_2-3-M1-A6


title: 3543_OF1A_2-2-M1-N4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026636LR01-GC2-2-9-2]

description: Valproate, 500 mg/kg, Day 8, Repeat 2

value: Valproate, 500 mg/kg, Day 8, Repeat 2


title: 3543_OF1A_2-2-M1-N3


title: iMos, Doxycycline, NLRP3 p.D303N 3

value: transformed cells

value: immortalized macrophages


title: 3543_OF1A_2-2-M1-N16


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026635LR01-GC2-1-9-2]

description: Valproate, 500 mg/kg, Day 8, Repeat 1

value: Valproate, 500 mg/kg, Day 8, Repeat 1


title: 3543_OF1A_2-2-M1-N15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: iMos, Doxycycline, NLRP3 p.D303N 1

value: Doxycyline


title: 3543_OF1A_2-2-M1-O4


title: 3543_OF1A_2-2-M1-M4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026634LR01-GC1-3-9-2]

description: Valproate, 250 mg/kg, Day 8, Repeat 3

value: 8 wks

value: Valproate, 250 mg/kg, Day 8, Repeat 3


title: iMos, Doxycycline, NLRP3 p.D303N 2

value: NLRP3 p.D303N


title: 3543_OF1A_2-2-M1-M16


title: 3543_OF1A_2-2-M1-M3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026632LR01-GC1-1-9-2]

description: Valproate, 250 mg/kg, Day 8, Repeat 1

value: whole blood

value: Valproate, 250 mg/kg, Day 8, Repeat 1


title: 3543_OF1A_2-2-M1-L4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026633LR01-GC1-2-9-2]

description: Valproate, 250 mg/kg, Day 8, Repeat 2

value: male

value: Valproate, 250 mg/kg, Day 8, Repeat 2


title: 3543_OF1A_2-2-M1-M15


title: iMos, Untreated, NLRP3 p.D303N 3

value: Untreated


title: iMos, Untreated, NLRP3 p.D303N 4


title: iMos, Untreated, NLRP3 p.D303N 2


title: 3543_OF1A_2-2-M1-L3

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026631LR01-GA4-3-9-2]

description: Carbon tetrachloride, 2 ml/kg, Day 8, Repeat 3


title: 3543_OF1A_2-2-M1-L16

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026630LR01-GA4-2-9-2]

description: Carbon tetrachloride, 2 ml/kg, Day 8, Repeat 2


title: 3543_OF1A_2-2-M1-L15


title: iMos, Untreated, NLRP3 p.D303N,1

value: bone marrow


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026629LR01-GA4-1-9-2]

description: Carbon tetrachloride, 2 ml/kg, Day 8, Repeat 1


title: 3543_OF1A_2-2-M1-K16


title: 3543_OF1A_2-2-M1-K3


title: 3543_OF1A_2-2-M1-K15


title: LPSEff_n2

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

country: Germany

institute: Goethe University Frankfurt

data_processing:
adapter trimming: cutadapt
rRNA removal with bowtie2
alignment to the mouse genome (mm39): STAR
Transcript counts were determined using htseq-count with default parameters.
Differentially expressed genes were determined using DESeq2 in R. P-values were adjusted by Benjamini-Hochberg FDR correction.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized read counts for each sample

source_name: mouse primary macrophages

growth_protocol: Bone marrow-derived macrophages (BMDM) were derived from femurs of adult male and female C57BL/6 mice and were differentiated with 20 ng/mL macrophage colony-stimulating factor (M-CSF) and 20 ng/mL granulocyte macrophage colony-stimulating factor (GM-CSF)  in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 U/mL penicillin and 100 µg/mL streptomycin over a period of 7 days.

extract_protocol:
RNA was isolated using the RNA Clean & Concentrator-25 kit according to the manufacturer’s instructions.
rRNA was depleted from total RNA using RiboCop rRNA depletion kit according to the manufacturer’s instructions. The sequencing libraries were prepared using the TruSeq Ribo Profile (Mammalian) Library Prep Kit according to the protocol.

treatment_protocol: BMDM after 6 days of differentiation were then co-cultured with apoptotic NIH-3T3 cells at a ratio of 1:5 for 16 h in the presence of dimerizer (10 nM) stimulation. After washing with PBS for two times, cells were stimulated for 6 h with 100 ng/mL LPS and 100 U/mL murine IFNg. For cell harvest, CD45+ cells were isolated with CD45 MicroBeads  according to manufacturer’s instructions.

value: mouse primary macrophages

value: C57BL/6 wildtype

value: co-culture with apoptotic NIH-3T3 cells in a ratio of 1:5 for 16 h, PBS wash, 100 ng/mL LPS and 100 U/mL murine IFNg for 6 h


title: 3543_OF1A_2-2-M1-J4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026628LR01-GA3-3-9-2]

description: Carbon tetrachloride, 1.5 ml/kg, Day 8, Repeat 3


title: 3543_OF1A_2-2-M1-J3


title: 3543_OF1A_2-2-M1-J16


title: Eff_n2

value: co-culture with apoptotic NIH-3T3 cells in a ratio of 1:5 for 16 h


title: LPSEff_n1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026627LR01-GA3-2-9-2]

description: Carbon tetrachloride, 1.5 ml/kg, Day 8, Repeat 2


title: 3543_OF1A_2-2-M1-J15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Eff_n1


title: 3543_OF1A_2-2-M1-I3


title: 3543_OF1A_2-2-M1-I16


title: 3543_OF1A_2-2-M1-I15


title: 3543_OF1A_2-2-M1-K4


title: LPS_n2

value: 100 ng/mL LPS and 100 U/mL murine IFNg for 6 h


title: 3543_OF1A_2-2-M1-H3


title: 3543_OF1A_2-2-M1-H4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026624LR01-GA2-2-9-2]

description: Carbon tetrachloride, 1 ml/kg, Day 8, Repeat 2

value: 8 wks


title: LPS_n1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026623LR01-GA2-1-9-2]

description: Carbon tetrachloride, 1 ml/kg, Day 8, Repeat 1


title: Ctrl_n2

value: Control


title: 3543_OF1A_2-2-M1-H15


title: 3543_OF1A_2-2-M1-H16


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026622LR01-GA1-3-9-2]

description: Carbon tetrachloride, 0.5 ml/kg, Day 8, Repeat 3


title: 3543_OF1A_2-2-M1-G4


title: Ctrl_n1


title: 3543_OF1A_2-2-M1-G3


title: 3543_OF1A_2-2-M1-I4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026626LR01-GA3-1-9-2]

description: Carbon tetrachloride, 1.5 ml/kg, Day 8, Repeat 1


title: 3543_OF1A_2-2-M1-F4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026621LR01-GA1-2-9-2]

description: Carbon tetrachloride, 0.5 ml/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026625LR01-GA2-3-9-2]

description: Carbon tetrachloride, 1 ml/kg, Day 8, Repeat 3


title: 3543_OF1A_2-2-M1-F15


title: 3543_OF1A_2-2-M1-F16


title: 3543_OF1A_2-2-M1-F3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026619LR01-1-3-9-2]

description: Sodium chloride, 0.9%, Day 8, Repeat 3

value: Sodium chloride, 0.9%, Day 8, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026620LR01-GA1-1-9-2]

description: Carbon tetrachloride, 0.5 ml/kg, Day 8, Repeat 1

value: whole blood


title: 3543_OF1A_2-2-M1-E4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026618LR01-1-2-9-2]

description: Sodium chloride, 0.9%, Day 8, Repeat 2

value: Sodium chloride, 0.9%, Day 8, Repeat 2


title: 3543_OF1A_2-2-M1-E16


title: 3543_OF1A_2-2-M1-E15


title: 3543_OF1A_2-2-M1-E3


title: 3543_OF1A_2-2-M1-D4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026616LR01-GC4-1-9-1]

description: Valproate, 1000 mg/kg, Day 7, Repeat 1

value: male

value: Valproate, 1000 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_2-2-M1-D3


title: 3543_OF1A_2-2-M1-G16


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026615LR01-GC2-2-9-1]

description: Valproate, 500 mg/kg, Day 7, Repeat 2

value: Valproate, 500 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_2-2-M1-G15

value: Female


title: 3543_OF1A_2-2-M1-D15

value: nuclear RNA + genomic DNA


title: 3543_OF1A_2-2-M1-C4


title: S16, NEIL2_KO, rep 8

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
The clean reads were aligned to human genome GRCh38/hg38 by HISAT2. Sam filles were sorted as bam files and indexed by samtools.
The processing data of transcript count (number of reads per gene) were extract using featureCounts (v2.0.1) tool in default setting.
The processing data was further normalized and used to identify the differentially expressed genes in knockout compared to wild type by DEseq2 tool.
Assembly: hg38
Supplementary files format and content: The processed file is  in GTF format . The first 5 columns are the gene coordination annotation in the order as: 1.the gene ID;  2. chromosome name; 3.the start coordinate; 4.the end coordinate; 5.strand.  Columns after 5 represent the number of reads per gene in individual sample.

extract_protocol:
RNA extracted by NAxtra magnetic nanoparticles.
total RNA libraries were prepared using Qiagen Stranded RNA library kit (cat #180743) .


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026614LR01-GC2-1-9-1]

description: Valproate, 500 mg/kg, Day 7, Repeat 1

value: Valproate, 500 mg/kg, Day 7, Repeat 1


title: S15, NEIL2_KO, rep 7


title: high glucose, replicate 2

type: RNA

city: Guangzhou

first: Yanhua

last: Sha

address: 111 Dade Road

institute: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: exosomes isolated from cell supernatant of HG group

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total exosomal RNA was extracted by TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The extracted RNAs was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Scientific) and quality was monitored using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The HK-2 cells were cultured in RPMI 1640 medium supplemented with 10% exosome depleted FBS under standard culture conditions (5% CO2 , 37°C). For glucose stimulation experiments, the cells were cultured in high glucose medium containing 30 mmol/L glucose for 30h at 37°C. For the control group, HK2 cells were cultured in normal glucose medium containing 5.5 mmol/L glucose for 30h at 37°C.

tag: specimen

value: cell supernatant

value: 30 mmol/L glucose


title: high glucose, replicate 1


title: normal glucose, replicate 2

source_name: exosomes isolated from cell supernatant of NG group

value: 5.5 mmol/L glucose


title: 3543_OF1A_2-2-M1-C16


title: S14, NEIL2_KO, rep 6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026613LR01-GC1-3-9-1]

description: Valproate, 250 mg/kg, Day 7, Repeat 3

value: Valproate, 250 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_2-2-M1-C15

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: high glucos, replicate 3


title: 3543_OF1A_2-2-M1-B4


title: normal glucose, replicate 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026617LR01-1-1-9-2]

description: Sodium chloride, 0.9%, Day 8, Repeat 1

value: Sodium chloride, 0.9%, Day 8, Repeat 1


title: 3543_OF1A_2-2-M1-D16


title: 3543_OF1A_2-2-M1-A4


title: S12, NEIL2_KO, rep 4


title: 3543_OF1A_2-2-M1-A3


title: normal glucose, replicate 3


title: 3543_OF1A_2-2-M1-B16


title: S10, NEIL2_KO, rep 2


title: 3543_OF1A_2-2-M1-A15


title: 3543_OF1A_2-1-M1-P2


title: 3543_OF1A_2-1-M1-P1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026608LR01-GA4-1-9-1]

description: Carbon tetrachloride, 2 ml/kg, Day 7, Repeat 1

value: 8 wks


title: S09, NEIL2_KO, rep 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026607LR01-GA3-3-9-1]

description: Carbon tetrachloride, 1.5 ml/kg, Day 7, Repeat 3


title: 3543_OF1A_2-1-M1-P13


title: S08, WT, rep 8

value: wild type


title: 3543_OF1A_2-1-M1-O2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026606LR01-GA3-2-9-1]

description: Carbon tetrachloride, 1.5 ml/kg, Day 7, Repeat 2


title: 3543_OF1A_2-1-M1-O1


title: S07, WT, rep 7


title: S06, WT, rep 6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026605LR01-GA3-1-9-1]

description: Carbon tetrachloride, 1.5 ml/kg, Day 7, Repeat 1


title: 3543_OF1A_2-1-M1-O14


title: 3543_OF1A_2-1-M1-O13


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026612LR01-GC1-2-9-1]

description: Valproate, 250 mg/kg, Day 7, Repeat 2

value: Valproate, 250 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_2-1-M1-N2


title: 3543_OF1A_2-1-M1-N1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026604LR01-GA2-3-9-1]

description: Carbon tetrachloride, 1 ml/kg, Day 7, Repeat 3

value: whole blood


title: 3543_OF1A_2-2-M1-A16


title: S11, NEIL2_KO, rep 3


title: 3543_OF1A_2-2-M1-B3


title: S05, WT, rep 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026611LR01-GC1-1-9-1]

description: Valproate, 250 mg/kg, Day 7, Repeat 1

value: Valproate, 250 mg/kg, Day 7, Repeat 1


title: S13, NEIL2_KO, rep 5


title: 3543_OF1A_2-1-M1-P14


title: 3543_OF1A_2-1-M1-N14


title: 3543_OF1A_2-1-M1-N13


title: 3543_OF1A_2-2-M1-C3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026603LR01-GA2-2-9-1]

description: Carbon tetrachloride, 1 ml/kg, Day 7, Repeat 2

value: male


title: 3543_OF1A_2-2-M1-B15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026609LR01-GA4-2-9-1]

description: Carbon tetrachloride, 2 ml/kg, Day 7, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026602LR01-GA2-1-9-1]

description: Carbon tetrachloride, 1 ml/kg, Day 7, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026610LR01-GA4-3-9-1]

description: Carbon tetrachloride, 2 ml/kg, Day 7, Repeat 3


title: S04, WT, rep 4


title: 3543_OF1A_2-1-M1-M1


title: 3543_OF1A_2-1-M1-M2


title: 3543_OF1A_2-1-M1-M14


title: S03, WT, rep 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026601LR01-GA1-3-9-1]

description: Carbon tetrachloride, 0.5 ml/kg, Day 7, Repeat 3


title: 3543_OF1A_2-1-M1-M13


title: S02, WT, rep 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026600LR01-GA1-2-9-1]

description: Carbon tetrachloride, 0.5 ml/kg, Day 7, Repeat 2


title: 3543_OF1A_2-1-M1-L1


title: 3543_OF1A_2-1-M1-L2


title: S01, WT, rep 1


title: 3543_OF1A_2-1-M1-L14


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026598LR01-1-3-9-1]

description: Sodium chloride, 0.9%, Day 7, Repeat 3

value: Sodium chloride, 0.9%, Day 7, Repeat 3


title: 3543_OF1A_2-1-M1-K1


title: 3543_OF1A_2-1-M1-L13


title: 3543_OF1A_2-1-M1-K2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026597LR01-1-2-9-1]

description: Sodium chloride, 0.9%, Day 7, Repeat 2

value: Sodium chloride, 0.9%, Day 7, Repeat 2


title: 3543_OF1A_2-1-M1-K13

value: Female


title: 3543_OF1A_2-1-M1-J1

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026596LR01-1-1-9-1]

description: Sodium chloride, 0.9%, Day 7, Repeat 1

value: Sodium chloride, 0.9%, Day 7, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026595LR01-GC4-1-8-31]

description: Valproate, 1000 mg/kg, Day 6, Repeat 1

value: Valproate, 1000 mg/kg, Day 6, Repeat 1


title: 3543_OF1A_2-1-M1-J2


title: 3543_OF1A_2-1-M1-I2


title: 3543_OF1A_2-1-M1-J13


title: 3543_OF1A_2-1-M1-J14


title: 3543_OF1A_2-1-M1-I1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23026594LR01-GC2-2-8-31]

description: Valproate, 500 mg/kg, Day 6, Repeat 2

value: Valproate, 500 mg/kg, Day 6, Repeat 2


title: AL078604.2_MDAMB468_kd_rep3

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

department: Pathology

country: Canada

institute: Dalhousie University

description: Gene expression from MDA-MB-468 cells with AL078604.2 knockdown

hyb_protocol: The purified RNA samples were then sent to The Centre for Applied Genomics (TCAG), located at The Hospital for Sick Children in Toronto, Canada. The RNA samples underwent reverse transcription into complementary DNA (cDNA) and were subsequently hybridized to the Affymetrix Human Gene 2.0 ST microarray platform.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner#4).

data_processing: Raw CEL files were processed using the Transcriptome Analysis Console (Affymetrix).

label: biotin

source_name: MDA-MB-468 cells

label_protocol: Sample were prepared with the Affymetrix WT PLUS Kit and labeled with Biotin Allonamide Triphosphate.

growth_protocol: Cells were cultured in a humidified incubator at 37C, with 5% CO2 in culture media, supplemented with 10% FBS.

extract_protocol: Cells were collected in TRIzol and RNA purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) following the manufacturer’s instructions.

treatment_protocol: Cells were treated for 48 hours with 15nM screening-grade modified antisense oligonucleotices GapmeRs, (Qiagen) admixed with TransIT-BrCa (MS Biolnyx) as per the manufacturer’s instructions.

value: anti-AL078604.2 ASO


title: 3543_OF1A_2-1-M1-I14


title: 3543_OF1A_2-1-M1-H2


title: 3543_OF1A_2-1-M1-I13