title: rRNA Depleted total RNA from liver from untreated SS rats (replicate 3.1, sequencing batch 9)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: SS_3_batch9
SS_3.1


title: rRNA Depleted total RNA from liver from untreated SS rats (replicate 1, sequencing batch 8)

status: Public on Apr 01 2022

type: SRA

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SS_1_batch8
HRDPv5 Sample Name: SS-JrHsd_1_batch8
SS_1

library_source: transcriptomic

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Filter transcripts/genes from RSEM filtered transcriptome results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: Rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome

molecule: total RNA

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA was collected from liver using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded total RNA Kit (Illumina, San Diego, CA, USA).
rRNA depleted stranded total RNA

treatment_protocol: Tissue frozen in RNA later.

tag: tissue

value: liver

tag: strain

value: SS/JrHsdMcwi

tag: batch

tag: treatment

tag: Sex

value: male


title: peripheral blood (3999840163_R01C02)

status: Public on Apr 22 2022

type: genomic

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

country: Germany

institute: Max-Planck-Institute Psychiatry

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing:
The Bioconductor R package minfi was used for the quality control of DNAm data. Failed probes based on a detection P-value larger than 0.01 in >50% of the samples as well and non-specific binding probes a nd probes on X and Y chromosome were removed.
We also excluded probes if single nucleotide polymorphisms (SNPs) were documented in the interval for which the Illumina probe is designed to hybridize. Probes located close (10 bp from query site) to a SNP which had a minor allele frequency of ≥0.05, as reported in the 1,000 Genomes Project, were also removed
The data were then normalized with functional normalization. Batch effects were identified using the Empirical Bayes’ method ComBat . Batch corrected M-values after ComBat were used for all further statistical analyses

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from peripheral blood

tag: panic disorder case (1)-control(0)

tag: age

tag: genetic sex

value: F

tag: weighted life events


title: peripheral blood (9989536096_R01C01)


title: peripheral blood (9989536066_R01C01)


title: peripheral blood (3999840048_R05C02)


title: peripheral blood (9989536129_R01C01)


title: peripheral blood (3999840140_R06C01)


title: rRNA Depleted total RNA from liver from untreated SR rats (replicate 3, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SR_3_batch10
HRDPv5 Sample Name: SR-JrHsd_3_batch10
SR_3

value: SR/JrHsd


title: rRNA Depleted total RNA from liver from untreated SR rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SR_2_batch8
HRDPv5 Sample Name: SR-JrHsd_2_batch8
SR_2


title: rRNA Depleted total RNA from liver from untreated SR rats (replicate 1, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SR_1_batch8
HRDPv5 Sample Name: SR-JrHsd_1_batch8
SR_1


title: rRNA Depleted total RNA from liver from untreated SHRSP rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: SHRSP-Crl_2_batch8
SHRSP_2


title: peripheral blood (3999840061_R02C02)


title: rRNA Depleted total RNA from liver from untreated SHRSP rats (replicate 1, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHRSP_1_batch8
HRDPv5 Sample Name: SHRSP-Crl_1_batch8
SHRSP_1


title: peripheral blood (9989536100_R02C01)

value: M


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 2, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_2_batch1
HRDPv5 Sample Name: SHR_2_batch1
SHR_2

value: SHR/OlaIpcv


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch7
HRDPv5 Sample Name: Excluded
SHR_1_control_7


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 3, sequencing batch 11)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_3_batch11
HRDPv5 Sample Name: SHR_3_batch11
SHR_3


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch4
HRDPv5 Sample Name: Excluded
SHR_1_control_4


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch5
HRDPv5 Sample Name: SHR_1_batch5
SHR_1_control_5


title: rRNA Depleted total RNA from liver from untreated SHRSP rats (replicate 3, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHRSP_3_batch10
HRDPv5 Sample Name: SHRSP-Crl_3_batch10
SHRSP_3


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch2
HRDPv5 Sample Name: Excluded
SHR_1_control_2


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 13)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch13
HRDPv5 Sample Name: SHR_1_batch13
SHR_1_control_13


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch6
HRDPv5 Sample Name: Excluded
SHR_1_control_6


title: peripheral blood (9989536025_R04C02)


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 15)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch15
HRDPv5 Sample Name: Excluded
SHR_1_control_15


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch3
HRDPv5 Sample Name: Excluded
SHR_1_control_3


title: peripheral blood (9989536119_R04C01)


title: peripheral blood (9989536109_R04C02)


title: peripheral blood (3999840070_R05C01)


title: peripheral blood (3999840148_R02C01)


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 11)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch11
HRDPv5 Sample Name: Excluded
SHR_1_control_11


title: rRNA Depleted total RNA from liver from untreated LEW/SsNHsd rats (replicate 1, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEW.SsNHsd_1_batch10
HRDPv5 Sample Name: LEW-SsNHsd_1_batch10
LEW-SsNHsd_1

value: LEW/SsNHsd


title: peripheral blood (9989536137_R03C02)


title: rRNA Depleted total RNA from liver from untreated LEW/Crl rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEW_2_batch8
HRDPv5 Sample Name: LEW-Crl_2_batch8
LEW-Crl_2

value: LEW/Crl


title: rRNA Depleted total RNA from liver from untreated LEW/Crl rats (replicate 1, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEW_1_batch8
HRDPv5 Sample Name: LEW-Crl_1_batch8
LEW-Crl_1


title: rRNA Depleted total RNA from liver from untreated LE/Stm rats (replicate 3.1, sequencing batch 13)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LE.Stm_3_batch13
HRDPv5 Sample Name: LE-Stm_3_batch13
LE-Stm_3.1

value: LE/Stm


title: rRNA Depleted total RNA from liver from untreated LE/Stm rats (replicate 2.1, sequencing batch 13)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LE.Stm_2_batch13
HRDPv5 Sample Name: LE-Stm_2_batch13
LE-Stm_2.1


title: rRNA Depleted total RNA from liver from untreated LE/Stm rats (replicate 1, sequencing batch 13)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LE.Stm_1_batch13
HRDPv5 Sample Name: LE-Stm_1_batch13
LE-Stm_1


title: peripheral blood (3999840095_R05C01)


title: rRNA Depleted total RNA from liver from untreated HXB7 rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB7_1_batch1
HRDPv5 Sample Name: HXB7_1_batch1
HXB7_1


title: rRNA Depleted total RNA from liver from untreated HXB5 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB5_3_batch5
HRDPv5 Sample Name: HXB5_3_batch5
HXB5_3


title: peripheral blood (3999840071_R02C01)


title: rRNA Depleted total RNA from liver from untreated HXB5 rats (replicate 2, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB5_2_batch4
HRDPv5 Sample Name: HXB5_2_batch4
HXB5_2


title: rRNA Depleted total RNA from liver from untreated HXB5 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB5_1_batch2
HRDPv5 Sample Name: HXB5_1_batch2
HXB5_1


title: peripheral blood (9989536110_R02C01)


title: rRNA Depleted total RNA from liver from untreated LEW/SsNHsd rats (replicate 3, sequencing batch 9)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEW.SsNHsd_3_batch9
HRDPv5 Sample Name: LEW-SsNHsd_3_batch9
LEW-SsNHsd_3


title: rRNA Depleted total RNA from liver from untreated LEW/SsNHsd rats (replicate 2, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEW.SsNHsd_2_batch10
HRDPv5 Sample Name: LEW-SsNHsd_2_batch10
LEW-SsNHsd_2


title: rRNA Depleted total RNA from liver from untreated HXB4 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB4_1_batch2
HRDPv5 Sample Name: HXB4_1_batch2
HXB4_1


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: Excluded
SHR_1_control_1


title: rRNA Depleted total RNA from liver from untreated HXB31 rats (replicate 2, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB31_2_batch6
HRDPv5 Sample Name: HXB31_2_batch6
HXB31_2


title: rRNA Depleted total RNA from liver from untreated HXB31 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB31_3_batch6
HRDPv5 Sample Name: HXB31_3_batch6
HXB31_3


title: rRNA Depleted total RNA from liver from untreated HXB31 rats (replicate 1.2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB31_1_batch3
HRDPv5 Sample Name: HXB31_1_batch3
HXB31_1.2


title: rRNA Depleted total RNA from liver from untreated HXB31 rats (replicate 1.1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: HXB31_1_batch2
HXB31_1.1


title: rRNA Depleted total RNA from liver from untreated HXB3 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB3_3_batch5
HRDPv5 Sample Name: HXB3_3_batch5
HXB3_3


title: rRNA Depleted total RNA from liver from untreated HXB7 rats (replicate 3, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB7_3_batch4
HRDPv5 Sample Name: HXB7_3_batch4
HXB7_3


title: peripheral blood (9989536013_R06C02)


title: rRNA Depleted total RNA from liver from untreated HXB3 rats (replicate 1.2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB3_1_batch3
HRDPv5 Sample Name: HXB3_1_batch3
HXB3_1.2


title: rRNA Depleted total RNA from liver from untreated HXB3 rats (replicate 2, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB3_2_batch4
HRDPv5 Sample Name: HXB3_2_batch4
HXB3_2


title: rRNA Depleted total RNA from liver from untreated HXB3 rats (replicate 1.1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: HXB3_1_batch2
HXB3_1.1


title: rRNA Depleted total RNA from liver from untreated HXB29 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB29_1_batch2
HRDPv5 Sample Name: HXB29_1_batch2
HXB29_1


title: rRNA Depleted total RNA from liver from untreated HXB27 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB27_3_batch5
HRDPv5 Sample Name: HXB27_3_batch5
HXB27_3


title: rRNA Depleted total RNA from liver from untreated HXB27 rats (replicate 2, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB27_2_batch1
HRDPv5 Sample Name: HXB27_2_batch1
HXB27_2


title: rRNA Depleted total RNA from liver from untreated HXB29 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB29_3_batch6
HRDPv5 Sample Name: HXB29_3_batch6
HXB29_3


title: rRNA Depleted total RNA from liver from untreated HXB25 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB25_3_batch5
HRDPv5 Sample Name: HXB25_3_batch5
HXB25_3


title: rRNA Depleted total RNA from liver from untreated HXB29 rats (replicate 2, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB29_2_batch6
HRDPv5 Sample Name: HXB29_2_batch6
HXB29_2


title: rRNA Depleted total RNA from liver from untreated HXB4 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB4_3_batch5
HRDPv5 Sample Name: HXB4_3_batch5
HXB4_3


title: rRNA Depleted total RNA from liver from untreated HXB27 rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB27_1_batch1
HRDPv5 Sample Name: HXB27_1_batch1
HXB27_1


title: rRNA Depleted total RNA from liver from untreated HXB23 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB23_3_batch7
HRDPv5 Sample Name: HXB23_3_batch7
HXB23_3


title: rRNA Depleted total RNA from liver from untreated HXB23 rats (replicate 2, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB23_2_batch5
HRDPv5 Sample Name: HXB23_2_batch5
HXB23_2


title: rRNA Depleted total RNA from liver from untreated HXB25 rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB25_1_batch1
HRDPv5 Sample Name: HXB25_1_batch1
HXB25_1


title: rRNA Depleted total RNA from liver from untreated HXB4 rats (replicate 2, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB4_2_batch4
HRDPv5 Sample Name: HXB4_2_batch4
HXB4_2


title: rRNA Depleted total RNA from liver from untreated HXB23 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB23_1_batch3
HRDPv5 Sample Name: HXB23_1_batch3
HXB23_1


title: rRNA Depleted total RNA from liver from untreated HXB24 rats (replicate 2, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB24_2_batch5
HRDPv5 Sample Name: HXB24_2_batch5
HXB24_2


title: rRNA Depleted total RNA from liver from untreated HXB22 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB22_3_batch7
HRDPv5 Sample Name: HXB22_3_batch7
HXB22_3


title: rRNA Depleted total RNA from liver from untreated HXB22 rats (replicate 2, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB22_2_batch5
HRDPv5 Sample Name: HXB22_2_batch5
HXB22_2


title: rRNA Depleted total RNA from liver from untreated HXB22 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB22_1_batch3
HRDPv5 Sample Name: HXB22_1_batch3
HXB22_1


title: rRNA Depleted total RNA from liver from untreated HXB21 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB21_3_batch7
HRDPv5 Sample Name: HXB21_3_batch7
HXB21_3


title: rRNA Depleted total RNA from liver from untreated HXB21 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB21_1_batch2
HRDPv5 Sample Name: HXB21_1_batch2
HXB21_1


title: rRNA Depleted total RNA from liver from untreated HXB20 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB20_3_batch7
HRDPv5 Sample Name: HXB20_3_batch7
HXB20_3


title: rRNA Depleted total RNA from liver from untreated HXB20 rats (replicate 4, sequencing batch 15)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB20_4_batch15
HRDPv5 Sample Name: HXB20_4_batch15
HXB20_4


title: rRNA Depleted total RNA from liver from untreated HXB24 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB24_3_batch7
HRDPv5 Sample Name: HXB24_3_batch7
HXB24_3


title: rRNA Depleted total RNA from liver from untreated HXB20 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB20_1_batch2
HRDPv5 Sample Name: HXB20_1_batch2
HXB20_1


title: rRNA Depleted total RNA from liver from untreated HXB20 rats (replicate 2, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB20_2_batch5
HRDPv5 Sample Name: HXB20_2_batch5
HXB20_2


title: rRNA Depleted total RNA from liver from untreated LEW/Crl rats (replicate 3, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: LEW-Crl_3_batch10
LEW-Crl_3


title: rRNA Depleted total RNA from liver from untreated HXB2 rats (replicate 4, sequencing batch 15)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB2_4_batch15
HRDPv5 Sample Name: HXB2_4_batch15
HXB2_4


title: rRNA Depleted total RNA from liver from untreated HXB18 rats (replicate 2, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB18_2_batch5
HRDPv5 Sample Name: HXB18_2_batch5
HXB18_2


title: rRNA Depleted total RNA from liver from untreated HXB17 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB17_3_batch5
HRDPv5 Sample Name: HXB17_3_batch5
HXB17_3


title: rRNA Depleted total RNA from liver from untreated HXB18 rats (replicate 1.2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB18_1_batch3
HRDPv5 Sample Name: HXB18_1_batch3
HXB18_1.2


title: rRNA Depleted total RNA from liver from untreated HXB17 rats (replicate 2, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB17_2_batch1
HRDPv5 Sample Name: HXB17_2_batch1
HXB17_2


title: rRNA Depleted total RNA from liver from untreated HXB17 rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB17_1_batch1
HRDPv5 Sample Name: HXB17_1_batch1
HXB17_1


title: rRNA Depleted total RNA from liver from untreated HXB2 rats (replicate 3, sequencing batch 11)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB2_3_batch11
HRDPv5 Sample Name: HXB2_3_batch11
HXB2_3


title: rRNA Depleted total RNA from liver from untreated HXB15 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB15_3_batch5
HRDPv5 Sample Name: HXB15_3_batch5
HXB15_3


title: rRNA Depleted total RNA from liver from untreated HXB13 rats (replicate 3, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB13_3_batch4
HRDPv5 Sample Name: HXB13_3_batch4
HXB13_3


title: rRNA Depleted total RNA from liver from untreated HXB2 rats (replicate 2, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB2_2_batch1
HRDPv5 Sample Name: HXB2_2_batch1
HXB2_2


title: rRNA Depleted total RNA from liver from untreated HXB18 rats (replicate 1.1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: HXB18_1_batch2
HXB18_1.1


title: rRNA Depleted total RNA from liver from untreated HXB13 rats (replicate 2, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB13_2_batch1
HRDPv5 Sample Name: HXB13_2_batch1
HXB13_2


title: rRNA Depleted total RNA from liver from untreated HXB13 rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB13_1_batch1
HRDPv5 Sample Name: HXB13_1_batch1
HXB13_1


title: rRNA Depleted total RNA from liver from untreated HXB15 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB15_1_batch2
HRDPv5 Sample Name: HXB15_1_batch2
HXB15_1


title: rRNA Depleted total RNA from liver from untreated HXB10 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB10_3_batch5
HRDPv5 Sample Name: HXB10_3_batch5
HXB10_3


title: rRNA Depleted total RNA from liver from untreated HXB10 rats (replicate 2, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB10_2_batch4
HRDPv5 Sample Name: HXB10_2_batch4
HXB10_2


title: rRNA Depleted total RNA from liver from untreated HXB10 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB10_1_batch3
HRDPv5 Sample Name: HXB10_1_batch3
HXB10_1


title: rRNA Depleted total RNA from liver from untreated HXB21 rats (replicate 2, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB21_2_batch5
HRDPv5 Sample Name: HXB21_2_batch5
HXB21_2


title: rRNA Depleted total RNA from liver from untreated HXB1 rats (replicate 4, sequencing batch 15)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB1_4_batch15
HRDPv5 Sample Name: HXB1_4_batch15
HXB1_4


title: rRNA Depleted total RNA from liver from untreated HXB18 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB18_3_batch7
HRDPv5 Sample Name: HXB18_3_batch7
HXB18_3


title: rRNA Depleted total RNA from liver from untreated HXB1 rats (replicate 2, sequencing batch 11)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB1_2_batch11
HRDPv5 Sample Name: HXB1_2_batch11
HXB1_2


title: rRNA Depleted total RNA from liver from untreated HXB1 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB1_1_batch2
HRDPv5 Sample Name: HXB1_1_batch2
HXB1_1


title: rRNA Depleted total RNA from liver from untreated HXB2 rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB2_1_batch1
HRDPv5 Sample Name: HXB2_1_batch1
HXB2_1


title: peripheral blood (9989536114_R01C02)


title: rRNA Depleted total RNA from liver from untreated HXB15 rats (replicate 2, sequencing batch 4)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB15_2_batch4
HRDPv5 Sample Name: HXB15_2_batch4
HXB15_2


title: rRNA Depleted total RNA from liver from untreated HXB1 rats (replicate 3, sequencing batch 5)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB1_3_batch5
HRDPv5 Sample Name: HXB1_3_batch5
HXB1_3


title: rRNA Depleted total RNA from liver from untreated F344/NHsd rats (replicate 2, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: F344.NHsd_2_batch10
HRDPv5 Sample Name: F344-NHsd_2_batch10
F344-NHsd_2


title: rRNA Depleted total RNA from liver from untreated F344/Stm rats (replicate 3.2, sequencing batch 13)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: F344-Stm_3_batch13
F344-Stm_3.2


title: rRNA Depleted total RNA from liver from untreated F344/Stm rats (replicate 3.1, sequencing batch 12)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: F344-Stm_3_batch12
F344-Stm_3.1


title: rRNA Depleted total RNA from liver from untreated Dark-Agouti rats (replicate 1, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: DA_1_batch8
HRDPv5 Sample Name: Dark-Agouti_1_batch8
DA_1

value: DA/OlaHsd


title: rRNA Depleted total RNA from liver from untreated Cop rats (replicate 3, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: Cop_3_batch8
HRDPv5 Sample Name: Cop-CrCrl_3_batch8
Cop_3

value: Cop/CrCrl


title: rRNA Depleted total RNA from liver from untreated Cop rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: Cop_2_batch8
HRDPv5 Sample Name: Cop-CrCrl_2_batch8
Cop_2


title: rRNA Depleted total RNA from liver from untreated Dark-Agouti rats (replicate 3, sequencing batch 9)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: Dark-Agouti_3_batch10
DA_3


title: rRNA Depleted total RNA from liver from untreated BXH9 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH9_1_batch3
HRDPv5 Sample Name: BXH9_1_batch3
BXH9_1


title: rRNA Depleted total RNA from liver from untreated F344/NCrl rats (replicate 1, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: F344.NCl_1_batch7
HRDPv5 Sample Name: F344-NCl_1_batch7
F344-NCrl_1


title: rRNA Depleted total RNA from liver from untreated F344/NCrl rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: F344.NCl_2_batch8
HRDPv5 Sample Name: F344-NCl_2_batch8
F344-NCrl_2


title: rRNA Depleted total RNA from liver from untreated F344/Stm rats (replicate 2.1, sequencing batch 13)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: F344-Stm_2_batch13
F344-Stm_2.1


title: rRNA Depleted total RNA from liver from untreated F344/NHsd rats (replicate 3, sequencing batch 9)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: F344.NHsd_3_batch9
HRDPv5 Sample Name: F344-NHsd_3_batch9
F344-NHsd_3


title: rRNA Depleted total RNA from liver from untreated BXH9 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH9_3_batch6
HRDPv5 Sample Name: BXH9_3_batch6
BXH9_3


title: rRNA Depleted total RNA from liver from untreated Cop rats (replicate 1, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: Cop_1_batch7
HRDPv5 Sample Name: Cop-CrCrl_1_batch7
Cop_1


title: rRNA Depleted total RNA from liver from untreated Dark-Agouti rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: DA_2_batch8
HRDPv5 Sample Name: Dark-Agouti_2_batch8
DA_2


title: rRNA Depleted total RNA from liver from untreated BXH9 rats (replicate 2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH9_2_batch3
HRDPv5 Sample Name: BXH9_2_batch3
BXH9_2


title: rRNA Depleted total RNA from liver from untreated BXH8 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH8_1_batch3
HRDPv5 Sample Name: BXH8_1_batch3
BXH8_1


title: rRNA Depleted total RNA from liver from untreated F344/NHsd rats (replicate 1, sequencing batch 9)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: F344.NHsd_1_batch9
HRDPv5 Sample Name: F344-NHsd_1_batch9
F344-NHsd_1


title: rRNA Depleted total RNA from liver from untreated F344/NCrl rats (replicate 3, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: F344.NCl_3_batch10
HRDPv5 Sample Name: F344-NCl_3_batch10
F344-NCrl_3


title: rRNA Depleted total RNA from liver from untreated BXH6 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH6_3_batch6
HRDPv5 Sample Name: BXH6_3_batch6
BXH6_3


title: rRNA Depleted total RNA from liver from untreated BXH6 rats (replicate 2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH6_2_batch3
HRDPv5 Sample Name: BXH6_2_batch3
BXH6_2


title: rRNA Depleted total RNA from liver from untreated BXH8 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH8_3_batch6
HRDPv5 Sample Name: BXH8_3_batch6
BXH8_3


title: rRNA Depleted total RNA from liver from untreated BXH6 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH6_1_batch3
HRDPv5 Sample Name: BXH6_1_batch3
BXH6_1


title: rRNA Depleted total RNA from liver from untreated BXH5 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH5_3_batch7
HRDPv5 Sample Name: BXH5_3_batch7
BXH5_3


title: rRNA Depleted total RNA from liver from untreated BXH5 rats (replicate 2, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH5_2_batch6
HRDPv5 Sample Name: BXH5_2_batch6
BXH5_2


title: rRNA Depleted total RNA from liver from untreated BXH3 rats (replicate 2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH3_2_batch3
HRDPv5 Sample Name: BXH3_2_batch3
BXH3_2


title: rRNA Depleted total RNA from liver from untreated BXH3 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH3_1_batch3
HRDPv5 Sample Name: BXH3_1_batch3
BXH3_1


title: rRNA Depleted total RNA from liver from untreated BXH2 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH2_3_batch7
HRDPv5 Sample Name: BXH2_3_batch7
BXH2_3


title: rRNA Depleted total RNA from liver from untreated BXH2 rats (replicate 2, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH2_2_batch6
HRDPv5 Sample Name: BXH2_2_batch6
BXH2_2


title: rRNA Depleted total RNA from liver from untreated BXH2 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH2_1_batch2
HRDPv5 Sample Name: BXH2_1_batch2
BXH2_1


title: rRNA Depleted total RNA from liver from untreated BXH3 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH3_3_batch6
HRDPv5 Sample Name: BXH3_3_batch6
BXH3_3


title: rRNA Depleted total RNA from liver from untreated BXH5 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH5_1_batch3
HRDPv5 Sample Name: BXH5_1_batch3
BXH5_1


title: rRNA Depleted total RNA from liver from untreated BXH8 rats (replicate 2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH8_2_batch3
HRDPv5 Sample Name: BXH8_2_batch3
BXH8_2


title: rRNA Depleted total RNA from liver from untreated BXH13 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH13_1_batch3
HRDPv5 Sample Name: BXH13_1_batch3
BXH13_1


title: rRNA Depleted total RNA from liver from untreated BXH12 rats (replicate 1, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH12_1_batch1
HRDPv5 Sample Name: BXH12_1_batch1
BXH12_1


title: rRNA Depleted total RNA from liver from untreated BXH13 rats (replicate 2, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH13_2_batch6
HRDPv5 Sample Name: BXH13_2_batch6
BXH13_2


title: rRNA Depleted total RNA from liver from untreated BXH11 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH11_3_batch6
HRDPv5 Sample Name: BXH11_3_batch6
BXH11_3


title: rRNA Depleted total RNA from liver from untreated BXH11 rats (replicate 2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH11_2_batch3
HRDPv5 Sample Name: BXH11_2_batch3
BXH11_2


title: rRNA Depleted total RNA from liver from untreated BXH11 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH11_1_batch3
HRDPv5 Sample Name: BXH11_1_batch3
BXH11_1


title: rRNA Depleted total RNA from liver from untreated BXH11 rats (replicate 4, sequencing batch 15)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH11_4_batch15
HRDPv5 Sample Name: BXH11_4_batch15
BXH11_4


title: rRNA Depleted total RNA from liver from untreated F344/Stm rats (replicate 1, sequencing batch 13)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: F344.Stm_1_batch13
HRDPv5 Sample Name: F344-Stm_1_batch13
F344-Stm_1


title: rRNA Depleted total RNA from liver from untreated BXH10 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH10_3_batch6
HRDPv5 Sample Name: BXH10_3_batch6
BXH10_3


title: rRNA Depleted total RNA from liver from untreated BNLx rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BNLx_3_batch6
HRDPv5 Sample Name: BNLx_3_batch6
BNLx_3

value: BN-Lx/Cub


title: rRNA Depleted total RNA from liver from untreated BXH13 rats (replicate 3, sequencing batch 7)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH13_3_batch7
HRDPv5 Sample Name: BXH13_3_batch7
BXH13_3


title: rRNA Depleted total RNA from liver from untreated BXH10 rats (replicate 2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH10_2_batch3
HRDPv5 Sample Name: BXH10_2_batch3
BXH10_2


title: rRNA Depleted total RNA from liver from untreated BNLx rats (replicate 2, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BNLx_2_batch3
HRDPv5 Sample Name: BNLx_2_batch3
BNLx_2


title: rRNA Depleted total RNA from liver from untreated BNLx rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BNLx_1_batch3
HRDPv5 Sample Name: BNLx_1_batch3
BNLx_1


title: rRNA Depleted total RNA from liver from untreated ACI rats (replicate 3, sequencing batch 10)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: ACI_3_batch10
HRDPv5 Sample Name: ACI-SegHsd_3_batch10
ACI_3

value: ACI/SegHsd


title: rRNA Depleted total RNA from liver from untreated ACI rats (replicate 1, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: ACI_1_batch8
HRDPv5 Sample Name: ACI-SegHsd_1_batch8
ACI_1


title: rRNA Depleted total RNA from liver from untreated ACI rats (replicate 2, sequencing batch 8)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: ACI_2_batch8
HRDPv5 Sample Name: ACI-SegHsd_2_batch8
ACI_2


title: rRNA Depleted total RNA from liver from untreated BXH10 rats (replicate 1, sequencing batch 3)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH10_1_batch3
HRDPv5 Sample Name: BXH10_1_batch3
BXH10_1


title: rRNA Depleted total RNA from liver from untreated LE/Stm rats (replicate 2.2, sequencing batch 14)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: LE-Stm_2_batch14
LE-Stm_2.2


title: rRNA Depleted total RNA from liver from untreated BXH12 rats (replicate 3, sequencing batch 6)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH12_3_batch6
HRDPv5 Sample Name: BXH12_3_batch6
BXH12_3


title: rRNA Depleted total RNA from whole brain from untreated LE-Stm rats (replicate 2.2, sequencing batch 14)

description:
LE-Stm_2_batch14
rRNA depleted total RNA

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2 (v2.3.4.3) to rRNA.
Genome alignment Hisat2 (v2.1.0).
Stringtie (v1.3.5) reconstruction.
Merge reconstruction Stringtie (v1.3.5).
Run RSEM (v1.3.1) on reconstruction.
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides.
Run RSEM (v1.3.1) on filtered reconstruction.
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides.
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R).
Remove technical artifacts including batch effects using Removal of Unwanted Variance (RUVg) with empirically-derived controls (RUVSeq package in R).
Assembly: rn6 (Rnor_6.0)
Supplementary files format and content: Tab-delimited text files include batch corrected/normalized expression values.

source_name: whole brain

extract_protocol:
RNA was collected from whole brain using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Kit (Illumina, San Diego, CA, USA).

value: whole brain


title: rRNA Depleted total RNA from liver from untreated F344/Stm rats (replicate 3.3, sequencing batch 14)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: F344-Stm_3_batch14
F344-Stm_3.3


title: rRNA Depleted total RNA from liver from untreated LE/Stm rats (replicate 3.2, sequencing batch 14)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: LE-Stm_3_batch14
LE-Stm_3.2


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 14)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LE-Stm rats (replicate 1.2, sequencing batch 14)

description:
LE-Stm_1_batch14
rRNA depleted total RNA


title: rRNA Depleted total RNA from liver from untreated F344/Stm rats (replicate 2.2, sequencing batch 14)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: F344-Stm_2_batch14
F344-Stm_2.2


title: rRNA Depleted total RNA from liver from untreated BXH12 rats (replicate 2, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BXH12_2_batch1
HRDPv5 Sample Name: BXH12_2_batch1
BXH12_2


title: rRNA Depleted total RNA from whole brain from untreated WKY rats (replicate 3, sequencing batch 11)

description:
WKY-NCrl_3_batch11
WKY_3_batch11
rRNA depleted total RNA

value: WKY/NCrl


title: rRNA Depleted total RNA from whole brain from untreated WKY rats (replicate 1, sequencing batch 8)

description:
WKY-NCrl_1_batch10
WKY_1_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SS rats (replicate 3, sequencing batch 11)

description:
SS-JrHsd_3_batch11
SS_3_batch11
rRNA depleted total RNA

value: SS/JrHsd


title: rRNA Depleted total RNA from whole brain from untreated SS rats (replicate 2, sequencing batch 8)

description:
SS-JrHsd_2_batch8
SS_2_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SR rats (replicate 3, sequencing batch 11)

description:
SR-JrHsd_3_batch11
SR_3_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated WKY rats (replicate 2, sequencing batch 8)

description:
WKY-NCrl_2_batch10
WKY_2_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SS rats (replicate 1, sequencing batch 8)

description:
SS-JrHsd_1_batch11
SS_1_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SR rats (replicate 1, sequencing batch 8)

description:
SR-JrHsd_1_batch8
SR_1_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHRSP rats (replicate 3, sequencing batch 8)

description:
SHRSP-Crl_3_batch8
SHRSP_3_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHRSP rats (replicate 2, sequencing batch 8)

description:
SHRSP-Crl_2_batch10
SHRSP_2_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from liver from untreated SHR rats (replicate 1, sequencing batch 14)

description:
rRNA depleted totalRNA
HRDPv6: Excluded
HRDPv5 Sample Name: Excluded
SHR_1_control_14

value: liver


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 7)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 6)

description:
SHR_1_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 3, sequencing batch 4)

description:
SHR_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 4)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHRSP rats (replicate 1, sequencing batch 9)

description:
SHRSP-Crl_1_batch10
SHRSP_1_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 5)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 11)

description:
SHR_1_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 3)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 10)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LEW-SsNHsd rats (replicate 2, sequencing batch 8)

description:
LEW-SsNHsd_2_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 13)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 2)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LEW-Crl rats (replicate 2, sequencing batch 8)

description:
LEW-Crl_2_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LEW-SsNHsd rats (replicate 1, sequencing batch 9)

description:
LEW-SsNHsd_1_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LEW-Crl rats (replicate 1, sequencing batch 9)

description:
LEW-Crl_1_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from liver from untreated HXB7 rats (replicate 2, sequencing batch 1)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB7_2_batch1
HRDPv5 Sample Name: HXB7_2_batch1
HXB7_2


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 1)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LEW-Crl rats (replicate 3, sequencing batch 8)

description:
LEW-Crl_3_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LE-Stm rats (replicate 3, sequencing batch 13)

description:
LE-Stm_3_batch13
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LE-Stm rats (replicate 1, sequencing batch 13)

description:
LE-Stm_1_batch13
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LE-Stm rats (replicate 2, sequencing batch 13)

description:
LE-Stm_2_batch13
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB7 rats (replicate 3, sequencing batch 5)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SHR rats (replicate 2, sequencing batch 1)

description:
SHR_2_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated SR rats (replicate 2, sequencing batch 8)

description:
SR-JrHsd_2_batch8
SR_2_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB7 rats (replicate 1, sequencing batch 1)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB7 rats (replicate 2, sequencing batch 1)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB5 rats (replicate 3, sequencing batch 5)

description: rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB5 rats (replicate 2, sequencing batch 5)

description:
HXB5_2_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB4 rats (replicate 3, sequencing batch 5)

description:
HXB4_3_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB31 rats (replicate 2, sequencing batch 7)

description:
HXB31_2_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB4 rats (replicate 2, sequencing batch 5)

description:
HXB4_2_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated LEW-SsNHsd rats (replicate 3, sequencing batch 8)

description:
LEW-SsNHsd_3_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB31 rats (replicate 1, sequencing batch 2)

description:
HXB31_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB4 rats (replicate 1, sequencing batch 2)

description:
HXB4_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB5 rats (replicate 1, sequencing batch 2)

description:
HXB5_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB29 rats (replicate 3, sequencing batch 7)

description:
HXB29_3_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB3 rats (replicate 2, sequencing batch 5)

description:
HXB3_2_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB29 rats (replicate 2, sequencing batch 7)

description:
HXB29_2_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB29 rats (replicate 1, sequencing batch 2)

description:
HXB29_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB27 rats (replicate 3, sequencing batch 6)

description:
HXB27_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB3 rats (replicate 1, sequencing batch 2)

description:
HXB3_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB27 rats (replicate 1, sequencing batch 1)

description:
HXB27_1_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB25 rats (replicate 2, sequencing batch 1)

description:
HXB25_2_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB3 rats (replicate 3, sequencing batch 5)

description:
HXB3_3_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB25 rats (replicate 1, sequencing batch 1)

description:
HXB25_1_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB24 rats (replicate 2, sequencing batch 6)

description:
HXB24_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB22 rats (replicate 2, sequencing batch 6)

description:
HXB22_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB23 rats (replicate 3, sequencing batch 6)

description:
HXB23_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB22 rats (replicate 3, sequencing batch 6)

description:
HXB22_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB24 rats (replicate 3, sequencing batch 6)

description:
HXB24_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB24 rats (replicate 1, sequencing batch 2)

description:
HXB24_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB21 rats (replicate 3, sequencing batch 6)

description:
HXB21_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB23 rats (replicate 1, sequencing batch 2)

description:
HXB23_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB23 rats (replicate 2, sequencing batch 6)

description:
HXB23_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB21 rats (replicate 1, sequencing batch 2)

description:
HXB21_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB21 rats (replicate 2, sequencing batch 6)

description:
HXB21_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB20 rats (replicate 2, sequencing batch 6)

description:
HXB20_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB25 rats (replicate 3, sequencing batch 6)

description:
HXB25_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB20 rats (replicate 1, sequencing batch 2)

description:
HXB20_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB27 rats (replicate 2, sequencing batch 1)

description:
HXB27_2_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB2 rats (replicate 2, sequencing batch 1)

description:
HXB2_2_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB20 rats (replicate 3, sequencing batch 6)

description:
HXB20_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB18 rats (replicate 2, sequencing batch 6)

description:
HXB18_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB2 rats (replicate 1, sequencing batch 1)

description:
HXB2_1_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB17 rats (replicate 2, sequencing batch 1)

description:
HXB17_2_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB2 rats (replicate 3, sequencing batch 6)

description:
HXB2_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB18 rats (replicate 1, sequencing batch 2)

description:
HXB18_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB15 rats (replicate 3, sequencing batch 5)

description:
HXB15_3_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB15 rats (replicate 2, sequencing batch 5)

description:
HXB15_2_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB22 rats (replicate 1, sequencing batch 2)

description:
HXB22_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB17 rats (replicate 3, sequencing batch 6)

description:
HXB17_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB13 rats (replicate 3, sequencing batch 5)

description:
HXB13_3_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB10 rats (replicate 3, sequencing batch 5)

description:
HXB10_3_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB1 rats (replicate 3, sequencing batch 5)

description:
HXB1_3_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB31 rats (replicate 3, sequencing batch 7)

description:
HXB31_3_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB10 rats (replicate 2, sequencing batch 5)

description:
HXB10_2_batch5
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB15 rats (replicate 1, sequencing batch 2)

description:
HXB15_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB1 rats (replicate 2, sequencing batch 6)

description:
HXB1_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB10 rats (replicate 1, sequencing batch 2)

description:
HXB10_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB13 rats (replicate 2, sequencing batch 1)

description:
HXB13_2_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB13 rats (replicate 1, sequencing batch 1)

description:
HXB13_1_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-Stm rats (replicate 1, sequencing batch 13)

description:
F344-Stm_1_batch13
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB1 rats (replicate 1, sequencing batch 2)

description:
HXB1_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-NHsd rats (replicate 2, sequencing batch 8)

description:
F344-NHsd_2_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-NHsd rats (replicate 3, sequencing batch 8)

description:
F344-NHsd_3_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-Stm rats (replicate 3, sequencing batch 13)

description:
F344-Stm_3_batch13
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB18 rats (replicate 3, sequencing batch 6)

description:
HXB18_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-NCrl rats (replicate 2, sequencing batch 8)

description:
F344-NCl_2_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated HXB17 rats (replicate 1, sequencing batch 1)

description:
HXB17_1_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-NHsd rats (replicate 1, sequencing batch 9)

description:
F344-NHsd_1_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-NCrl rats (replicate 1, sequencing batch 9)

description:
F344-NCl_1_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-NCrl rats (replicate 3, sequencing batch 8)

description:
F344-NCl_3_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated Dark-Agouti rats (replicate 2, sequencing batch 8)

description:
Dark-Agouti_2_batch10
DA_2_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated Dark-Agouti rats (replicate 3, sequencing batch 8)

description:
Dark-Agouti_3_batch8
DA_3_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated Cop rats (replicate 2, sequencing batch 8)

description:
Cop-CrCrl_2_batch10
rRNA depleted total RNA

value: COP/CrCrl


title: rRNA Depleted total RNA from whole brain from untreated BXH9 rats (replicate 3, sequencing batch 7)

description:
BXH9_3_batch7
rRNA depleted total RNA

value: male


title: rRNA Depleted total RNA from whole brain from untreated BXH9 rats (replicate 2, sequencing batch 3)

description:
BXH9_2_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH9 rats (replicate 1, sequencing batch 3)

description:
BXH9_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated F344-Stm rats (replicate 2, sequencing batch 13)

description:
F344-Stm_2_batch13
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH8 rats (replicate 4, sequencing batch 7)

description:
BXH8_4_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH8 rats (replicate 1, sequencing batch 3)

description:
BXH8_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH6 rats (replicate 2, sequencing batch 3)

description:
BXH6_2_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH5 rats (replicate 3, sequencing batch 7)

description:
BXH5_3_batch10
BXH5_3_batch10
BXH5_3_batch10
BXH5_3_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH8 rats (replicate 3, sequencing batch 7)

description:
BXH8_3_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH6 rats (replicate 3, sequencing batch 7)

description:
BXH6_3_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH5 rats (replicate 2, sequencing batch 7)

description:
BXH5_2_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH5 rats (replicate 1, sequencing batch 3)

description:
BXH5_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH3 rats (replicate 2, sequencing batch 3)

description:
BXH3_2_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH2 rats (replicate 2, sequencing batch 7)

description:
BXH2_2_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH2 rats (replicate 1, sequencing batch 2)

description:
BXH2_1_batch2
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH6 rats (replicate 1, sequencing batch 3)

description:
BXH6_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH3 rats (replicate 1, sequencing batch 3)

description:
BXH3_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH2 rats (replicate 3, sequencing batch 7)

description:
BXH2_3_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated Cop rats (replicate 3, sequencing batch 8)

description:
Cop-CrCrl_3_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH3 rats (replicate 3, sequencing batch 7)

description:
BXH3_3_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH12 rats (replicate 1, sequencing batch 1)

description:
BXH12_1_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH13 rats (replicate 2, sequencing batch 6)

description:
BXH13_2_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH12 rats (replicate 3, sequencing batch 6)

description:
BXH12_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH11 rats (replicate 2, sequencing batch 3)

description:
BXH11_2_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH13 rats (replicate 1, sequencing batch 3)

description:
BXH13_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated Dark-Agouti rats (replicate 1, sequencing batch 8)

description:
Dark-Agouti_1_batch10
DA_1_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH10 rats (replicate 3, sequencing batch 7)

description:
BXH10_3_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH11 rats (replicate 1, sequencing batch 3)

description:
BXH11_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH12 rats (replicate 2, sequencing batch 1)

description:
BXH12_2_batch1
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated Cop rats (replicate 1, sequencing batch 9)

description:
Cop-CrCrl_1_batch9
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH11 rats (replicate 3, sequencing batch 7)

description:
BXH11_3_batch7
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH10 rats (replicate 2, sequencing batch 3)

description:
BXH10_2_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH10 rats (replicate 1, sequencing batch 3)

description:
BXH10_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BNLx rats (replicate 3.1, sequencing batch 6)

description:
BNLx_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BXH13 rats (replicate 3, sequencing batch 6)

description:
BXH13_3_batch6
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BNLx rats (replicate 3.2, sequencing batch 4)

description:
BNLx_3_batch4
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BNLX rats (replicate 1, sequencing batch 3)

description:
BNLx_1_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from whole brain from untreated BNLX rats (replicate 2, sequencing batch 3)

description:
BNLx_2_batch3
rRNA depleted total RNA


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 2B, sequencing batch 6)

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2 (v2.3.4.3) to rRNA.
Genome alignment Hisat2 (v2.1.0).
Stringtie (v1.3.5) reconstruction.
Merge reconstruction Stringtie (v1.3.5).
Run RSEM (v1.3.1) on reconstruction.
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides.
Run RSEM (v1.3.1) on filtered reconstruction.
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides.
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R).
Remove technical artifacts including batch effects using Removal of Unwanted Variance (RUVg) with empirically-derived controls (RUVSeq package in R).

>> updated processing pipeline for new genome version (rn7.2):
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2 (v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie (v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Repeat Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)

Assembly: rn6 (Rnor_6.0) -or- Rn7.2

Supplementary files format and content:
TSV batch corrected/normalized expression values
GTF of the reconstructed transcriptome
PhenoGen.HRDP.v5.totalRNA* files generated with rn6 (Rnor_6.0)
PhenoGen.HRDP.v6.totalRNA* files generated with a new genome version (rn7.2)

source_name: kidney

extract_protocol:
RNA was collected from kidney using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).

value: kidney


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 2, sequencing batch 4)


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 2, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 2, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 3, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 2B, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB7 rats (replicate 1, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 2, sequencing batch 1)


title: rRNA Depleted total RNA from kidney from untreated HXB7 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB4 rats (replicate 2, sequencing batch 2)


title: rRNA Depleted total RNA from whole brain from untreated ACI rats (replicate 2, sequencing batch 8)

description:
ACI-SegHsd_2_batch10
rRNA depleted total RNA


title: rRNA Depleted total RNA from kidney from untreated HXB5 rats (replicate 1, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated HXB31 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB5 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB3 rats (replicate 3, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB31 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB7 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB3 rats (replicate 2, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB31 rats (replicate 2, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated HXB29 rats (replicate 3, sequencing batch 4)


title: rRNA Depleted total RNA from whole brain from untreated ACI rats (replicate 3, sequencing batch 8)

description:
ACI-SegHsd_3_batch8
rRNA depleted total RNA


title: rRNA Depleted total RNA from kidney from untreated HXB29 rats (replicate 1, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB27 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from whole brain from untreated ACI rats (replicate 1, sequencing batch 8)

description:
ACI-SegHsd_1_batch11
rRNA depleted total RNA


title: rRNA Depleted total RNA from kidney from untreated HXB29 rats (replicate 2, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB27 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated SHR rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB27 rats (replicate 2, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated HXB25 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB25 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB24 rats (replicate 4, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated HXB23 rats (replicate 2, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated HXB22 rats (replicate 2, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated HXB24 rats (replicate 2, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB23 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB23 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB25 rats (replicate 2, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated HXB2 rats (replicate 3, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB2 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB3 rats (replicate 1, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated HXB18 rats (replicate 1, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated HXB18 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB17 rats (replicate 1, sequencing batch 1)


title: rRNA Depleted total RNA from kidney from untreated HXB15 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB15 rats (replicate 1, sequencing batch 4)


title: rRNA Depleted total RNA from kidney from untreated HXB17 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB10 rats (replicate 3, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated HXB13 rats (replicate 3, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated HXB10 rats (replicate 2, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB1 rats (replicate 3, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB21 rats (replicate 2, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated BXH9 rats (replicate 1, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated HXB1 rats (replicate 1, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated BXH9 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH9 rats (replicate 2, sequencing batch 4)


title: rRNA Depleted total RNA from kidney from untreated HXB2 rats (replicate 1, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated BXH8 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH8 rats (replicate 1, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated BXH6 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH6 rats (replicate 2, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated BXH6 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated BXH3 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH8 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated BXH3 rats (replicate 1, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated BXH2 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated BXH13 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated BXH2 rats (replicate 2, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH13 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH12 rats (replicate 1, sequencing batch 1)


title: rRNA Depleted total RNA from kidney from untreated BXH12 rats (replicate 2, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH13 rats (replicate 1, sequencing batch 2)


title: rRNA Depleted total RNA from kidney from untreated BXH11 rats (replicate 3, sequencing batch 3)


title: rRNA Depleted total RNA from kidney from untreated BXH11 rats (replicate 3, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated BXH11 rats (replicate 2, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated HXB1 rats (replicate 2, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BXH10 rats (replicate 4, sequencing batch 6)


title: rRNA Depleted total RNA from kidney from untreated BXH10 rats (replicate 3, sequencing batch 5)


title: rRNA Depleted total RNA from kidney from untreated BNLX rats (replicate 2, sequencing batch 1)


title: Shear ATAC-Seq Rep2

status: Public on Mar 14 2022

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

library_source: genomic

data_processing:
Sequencing reads were aligned to hg19 (human) or danRer10 (zebrafish) genomes
RNA-Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow-treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq
ChIP-Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich (https://github.com/jsh58/Genrich) applying the following parameters: genrich -v -e Y,MT -E blacklist.bed -t Sample1ChIP.bam, Sample2ChIP.bam -c Sample1Input.bam, Sample2Input.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis.
ATAC-Seq. Sequencing reads were mapped with Bowtie2, downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC-Seq mode using the following parameters: genrich -j -v -y -r -e Y,MT -E blacklist.bed -t Sample1.bam, Sample2.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis.
ChIP-Seq and ATAC-Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth
Assembly: hg19
Assembly: danRer10
Supplementary files format and content: Control_Lost_ATAC_peaks.txt and Flow_Gained_ATAC_peaks.txt include the peaks with FDR <0.05. DBA_FlowvsControl_ALLPEAKS.csv includes all peaks.

source_name: Human umbilical vein endothelial cells

growth_protocol:
HUVEC were seeded on 6-cm BTF glass plates coated with cross-linked gelatin and cultured to confluence (approximately 105 cells/cm2) in EC growth medium.
Zebrafish were grown and crossed under standard conditions

extract_protocol:
RNA for RNA-Seq was extracted with RNeasy Micro Kit (Qiagen). Cells were cross-linked with formaldehyde (final concentration 1 %) for 5 min, sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI-ATAC after thawing. For zebrafish RNA-Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at -80°C for 2 min. Afterwards, embryos were washed twice with 1x Hanks’Balanced Salt Solution (HBSS, Gibco, # 14185-052)and deyolked with calcium-free Ringer’s solution. Embryos were then dissociated with trypsin-EDTA (0.5 %) and collagenase type IV (50 mg/ml). The reaction was stopped by addition of FCS (5 %) andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. After a final wash, cells were resuspended in 1x HBSS, passed through a 40 m nylon filter to obtain a single cell suspension, which was subjected to fluorescence-activated cell sorting (FACS). EGFP positive ECs were collected in RLT buffer (RNeasy Micro kit, Qiagen).
RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP-Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina). ATAC-Seq libraries were prepared using the protocol by Buenorosto et al (Buenorosto, Nat Met, 2013)

treatment_protocol:
The maximum flow of 18 dyn/cm2 was achieved by computer-controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone (PVP) within ten minutes (ramp function) and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system (BTF system; MOS Technologies) at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator.
48 hpf Tg(kdrl:H2B-EGFP)mu122 zebrafish embryos were dechorionated at 48 hours post fertilization (hpf) using pronase and treated for 4 h with nifedipine (12.5 nM, Biomol, # Cay11106) and tricaine (1.3 mM, Sigma-Aldrich, # A5040) to stop the heart beat or with a corresponding amount of DMSO as a control.

value: Shear stress (18 dyn/cm2 for 6 h)


title: Shear ChIP-Seq Rep2

data_processing:
Sequencing reads were aligned to hg19 (human) or danRer10 (zebrafish) genomes
RNA-Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow-treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq
ChIP-Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich (https://github.com/jsh58/Genrich) applying the following parameters: genrich -v -e Y,MT -E blacklist.bed -t Sample1ChIP.bam, Sample2ChIP.bam -c Sample1Input.bam, Sample2Input.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis.
ATAC-Seq. Sequencing reads were mapped with Bowtie2, downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC-Seq mode using the following parameters: genrich -j -v -y -r -e Y,MT -E blacklist.bed -t Sample1.bam, Sample2.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis.
ChIP-Seq and ATAC-Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth
Assembly: hg19
Assembly: danRer10

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: Control ATAC-Seq Rep2

value: Untreated


title: Control ATAC-Seq Rep1


title: rRNA Depleted total RNA from kidney from untreated BNLX rats (replicate 3, sequencing batch 6)


title: Shear ATAC-Seq Rep1


title: hPGHESC_2_P23_rep1

status: Public on Dec 30 2021

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
[Whole-genome bisulfite sequencing (WGBS)] Raw WGBS data were removed adaptors and low-quality bases using trim_galore (version: 0.1.3) with following parameters (--quality 20 --stringency 3 --length 50 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33). The clean reads were then paired mapped against the human reference genome hg19 using Bismark (version: 0.7.6)(Krueger and Andrews, 2011) with following parameters (--fastq --non_directional --phred33-quals). For improving the number of mapped reads, we re-mapped the unmapped reads with the single-end aligned mode. Only uniquely mapped reads were retained for the downstream analysis.
[RNA sequencing] Raw RNA-seq sequencing data were removed adaptors and low-quality based using the custom script. The clean reads were then mapped against the Ensembl human reference genome hg19 using TopHat (version: 2.0.12)(Trapnell et al., 2009) with the default parameters. Raw read were counted with HTSeq(Anders et al., 2015), and the gene expression level was quantified with the RPKM (reads per kilobase million).
Genome_build: hg19
Supplementary_files_format_and_content: WGBS BED files include the methylation rate information, and each column means the 'chr,start,end,base,strand,all_C,methylated_C,unmethylated_C,methylation_rate,ref,type'; RNA XLS files include the gene expression level of knonw genes, and each column means 'chr,start,end,strand,gene_ID,gene_name,gene_type,count,RPKM'.

source_name: human parthenogenetic haploid embryonic stem cell

extract_protocol:
[RNA extraction] Total RNA was extracted from cell lines used in the WGBS study through a RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. Residual DNA was removed by RNase-free DNase Set (Qiagen)
[Whole-genome bisulfite sequencing (WGBS)] Genomic DNA was extracted from cell lines using the DNeasy Blood & Tissue Kit (Qiagen). There were two repetitions per cell line. For WGBS library construction, the DNA was fragmented into 300 bp by sonication using Covaris S2 instrument (Covaris), following end repair and A-tailing. Cytosine methylated adaptor-ligated DNA was treated with sodium bisulfite through a EZ-96 DNA Methylation-Direct™ MagPrep (Zymo Research). Next, we used KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems) to accomplish 4 cycles of PCR amplification. It should be noted that DNA was treated with sodium bisulfite twice to reach >99% bisulfite conversion rate and lambda DNA was added to assess the rate.
[RNA sequencing] For rRNA-depleted RNA-seq library preparation, total RNA was treated by a NEBNext rRNA Depletion Kit (NEB). The cDNAs were synthesized by a NEBNext RNA First Strand Synthesis Module (NEB) and the second strand was synthesized by a NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB). Final libraries were prepared using a Kapa Hyper Prep Kit (Kapa Biosystems) once again. Both WGBS and bulk RNA-seq libraries were sequenced on the HiSeq 4000 (Novogene).

tag: cell type

tag: passage

value: passage 23

tag: replication

value: technology replication 1


title: hPGHESC_2_P18_rep1

value: human parthenogenetic haploid embryonic stem cell

value: passage 18


title: hPGHESC_1_P15_rep2

value: passage 15

value: technology replication 2


title: rRNA Depleted total RNA from kidney from untreated BXH10 rats (replicate 1, sequencing batch 3)


title: hPGHESC_1_P15_rep1


title: rRNA Depleted total RNA from kidney from untreated BXH3 rats (replicate 4, sequencing batch 6)


title: hPGHESC_2_P18_rep2


title: hPGHESC_2_P23_rep2


title: hAGHESC_2_P7_rep1

source_name: human androgenetic haploid embryonic stem cell

value: passage 7


title: hAGHESC_2_P18_rep2

value: human androgenetic haploid embryonic stem cell


title: hAGHESC_2_P18_rep1


title: hAGHESC_1_P5_rep2

value: passage 5


title: hAGHESC_1_P5_rep1


title: ICA2_P13_rep2

source_name: diploid semi-clone human embryonic stem cell

value: passage 13

value: biology replication 2, technology replication 2


title: hAGHESC_1_P15_rep2


title: hAGHESC_1_P15_rep1


title: hAGHESC_2_P7_rep2


title: ICA1_P13_rep2

value: diploid semi-clone human embryonic stem cell

value: biology replication 1, technology replication 2


title: HUES42_P9_rep2

source_name: diploid human embryonic stem cell

value: diploid human embryonic stem cell

value: passage 9


title: Blood_rep2

source_name: blood

value: blood

value: without culture


title: ICA2_P13_rep1

value: biology replication 2, technology replication 1


title: HUES42_P9_rep1

value: technology replication 1


title: ICA1_P13_rep1

value: biology replication 1, technology replication 1


title: Donor26_Mock_Vehicle

status: Public on Nov 24 2021

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

data_processing:
Sequences were trimmed for adapter sequences and mapped to reference human hg38 genome and gencode v24 transcripts using STAR software. Quantification was carried out with RSEM using transcriptome bam file created by star and gencode v24 transcriptome as index for RSEM.
Genome_build: hg38 with EBV (NC_007605.1)
Supplementary_files_format_and_content: Matrix table with RSEM raw gene counts for every gene and every sample

source_name: human B cells

growth_protocol: Buffy coats obtained from healthy donors were purified by MACSExpress and infected with EBV 2089 strain

extract_protocol:
mRNA was extracted using the Zymo RNA kit with DNAse treatment
NEB ultra II RNA library preparation kit

treatment_protocol: 25HC (H1015; Sigma) was reconstituted in ethanol at 5 mM and stored in single-use aliquots at 20C for no more than 4 weeks. 25HC was diluted in EGM2 media (final: 2.5 uM 25HC) and added 2 hours prior to infection and again after infection and during media renewal at day 5 and day 9 post-infection. De novo infections were carried out with 2089 maxiEBV virus supernatant at MOI = 0.1 green Rajji units and RNA was harvested at 10-12 dpi.

tag: infection status

value: Uninfected

value: ethanol


title: Donor26_Mock_25HC


title: Donor26_EBV_Vehicle

value: EBV de novo infection


title: Donor25_Mock_Veh


title: Donor26_EBV_25HC


title: Donor25_Mock_25HC


title: Donor25_EBV_Vehicle


title: Donor24_EBV_Vehicle


title: Donor24_EBV_25HC


title: Donor22_Mock_Vehicle


title: Donor22_EBV_Vehicle


title: Donor22_Mock_25HC


title: SIMA-ISM-003

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (GRCh38) (STAR v2.7) and then the gene level values were quantified (RSEM v1.31) based on GENCODE annotation (v31) .
After mapping RNA-seq data, rMATS v4.1.0 was used for RNA alternative splicing analysis by using the mapped BAM files as input.
For stranded RNA-seq data, the argument “--libType fr-firststrand” was applied. To process reads with variable lengths, the argument “--variable-read-length” was also used for rMATS.
To select statistically significantly differential splicing events, the following thresholds were used: FDR <0.05 and the absolute value of IncLevelDifference > 0.1.
Genome_build: hg38
Supplementary_files_format_and_content: rMATS tsv tables, gene-level RSEM raw count, TPM, FPKM txt files

source_name: Tumor

growth_protocol: BE2C (100,000 per well) and SKNAS cells (150,000) were plated in 6-well plate in RPMI-1640 media (supplemented with 10% FBS and 1% Pen/strep). SIMA (5 million per flank) and SKNAS cells (5 million per flank) were injected into (4-6 weeks old) NSG mice.

extract_protocol:
RNA was isolated from the cells using RNAeasy mini kit (Qiagen) according to manufacturer’s protocol. Tumor tissues were cut into 1-2mm pieces and sonicated with lysis buffer using RNeasy mini kit (Qiagen) and RNA was isolated according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: Cells were treated either with DMSO (vehicle) or with 250 nM of Indisulam (Cayman chemical, catalog number: 22759) for 72 hours. Tumors were let grown to be palpable and then mice were treated with vehicle or Indisulam (25mg/kg). After termination of the treatment, mice were sacfificed and tumor tissues were isolated.

value: SIMA xenograft

value: indisulam treatment


title: SIMA-ISM-002


title: SIMA-ISM-001


title: Blood_rep1


title: Donor25_EBV_25HC


title: SIMA-Vel-003

value: vehicle treatment


title: SKNAS-ISM-003

value: SKNAS xenograft


title: Donor22_EBV_25HC


title: SKNAS-Vel-002


title: SIMA-Vel-002


title: SKNAS-ISM-001


title: SKNAS-IR2-02

data_processing:
The ATAC-seq raw reads were aligned to the human reference genome (hg19) using BWA (version 0.7.12-r1039) to and then removed duplicated reads with Picard (version 1.65), with only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) .  Reads mapping to mitochondrial DNA were excluded from the analysis. All mapped reads were offset by +4 bp for the + strand and -5 bp for the  – strand.
Nucleosome free reads was used  to generate bigwig files and call eanriched regions. MACS2 (version 2.2.7.1) parameters are  “-q 0.01 –nomodel –extsize 200 –shift 100 -f BEDPE --keep-dup all”.
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

source_name: cell line derived from xenograft tumor

growth_protocol: SKNAS tumor-bearing mice were treated with indisulam or vehicle. Vehicle treated mice were euthanized after reaching tumor volume >2000 mm3. Indisulam-resistant tumor on second relapse were harvested during indisulam treatment (third cycle treatment). Tumor-derived cells were generated by dissecting the tumor into small pieces and digested with 2 mg/ml collagenase type IV and 0.01 mg/ml DNase I dissolved in DMEM at 37 °C for 1 h. Cell suspension from tumors was filtered with 70 µm cell strainer, washed with PBSx1, and resuspended in 100 mm culture dishes. The next day, adherent cells were expanded as Naïve (derived from vehicle treatment), R1 and R2(derived from indisulam treatment, resistant tumors).   ________________________________________

extract_protocol:
Fresh cultured SKNAS-Vel. SKNAS-IR1 and SKNAS-IR2 (100,000 per sample) with or without treatments were harvested and washed with 150ml cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing protease inhibitor (PI). Nuclei were collected by centrifuging at 500g for 10 minutes at 4°C after cell pellets were resuspended in lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 containing 0.1% NP-40 and PI. Nuclei were incubated with Tn5 transposon enzyme in transposase reaction mix buffer (Illumina) for 30 min at 37°C. DNAs were purified from transposition sample by using Min-Elute PCR purification kit (Qiagen, Valencia, CA) and measured by Qubit.
Polymerase chain reaction (PCR) was performed to amplify with High-Fidelity 2X PCR Master Mix [72°C/5mins+ 98 °C /30 s +12 × (98 °C /10 s + 63 °C /30 s + 72 °C /60 s) + 72 °C /5 min]. The libraries were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA). ATAC-seq libraries followed by pair-end sequencing on HiSeq4000 (Illumina) in the Hartwell Center at St Jude Children's Research Hospital.

treatment_protocol: No treatment for these cell line.

tag: cell line

value: SKNAS

value: xenografts were treated with indusilam.


title: SIMA-Vel-001


title: SKNAS-IR2-01


title: SKNAS-Vel-001


title: SKNAS-IR1-01


title: SKNAS-Vel-003


title: SKNAS-ISM-002


title: SKNAS-IR1-02


title: 3MockVehicle

data_processing:
Sequences were trimmed for adapter sequences and mapped to reference human hg38 genome and gencode v24 transcripts using STAR software. Quantification was carried out with RSEM using transcriptome bam file created by star and gencode v24 transcriptome as index for RSEM.
Genome_build: hg19v24 with KSHV(NC_009333.1) and hg38v30 with EBV (NC_007605.1)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were obtained from Lonza and passaged in EGM2 medium (Lonza) for up to 5 passages, with passages 3 to 5 used for experiments.

extract_protocol:
HUVEC mRNA was extracted using the RNeasy kit (Qiagen) with DNAse treatment
Truseq Stranded RNA prep kit RS-122-2201

treatment_protocol: 25HC (H1015; Sigma) was reconstituted in ethanol at 5 mM and stored in single-use aliquots at 20°C for no more than 4 weeks. 25HC was diluted in EGM2 media (final: 5 uM 25HC) and added 2 hours prior to infection and again after infection. De novo infections in HUVECs were carried out by diluting concentrated BCBL-1 supernatant in EGM2 media at a multiplicity of infection (MOI) of 40, as determined by LANA copy number. Polybrene was added at 8 ug/ml. Virus supernatant were washed off after 6 h and replaced with fresh EGM2. HUVECs were harvested 2 days after infection.


title: 4InfectedVehicle

value: KSHV de novo infection


title: 2InfectedVehicle


title: 3Infected25HC


title: 2Mock25HC


title: 2Infected25HC


title: 4Infected25HC


title: Nodular goiters, biological replicate 1

status: Public on Mar 05 2022

city: Hangzhou

first: Lisong

last: Teng

address: Yuhangtang Road

institute: Zhejiang University

description:
Nodular goiters sample
N1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Infnium MethylationEPIC Array using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The raw intensity data were loaded to a biocondutor package “minfi”. The raw data were normalized using the subset-quantile within array normalization (SWAN) method and probes with a detection p-value >= 0.01 in at least one sample were excluded from further analysis. Methylation values, referred to as β-values, were calculated as the ratio of the methylated signal intensity to the sum of the methylated and unmethylated signals after background subtraction. The β-values were reported as a DNA methylation score ranging from 0 (completely unmethylated) to 1 (fully methylated).

label: biotin (C,G), dinitrophenyl (A,T)

source_name: Nodular goiters

growth_protocol: not applicable

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: fixed paraffin-embedded

tag: sample type

value: FFPE

tag: disease state

value: Nodular goiters

value: Thyroid


title: SKNAS-Vel-01

value: xenografts were treated with vehicle.


title: 2MockVehicle


title: ALL-T-4.9_RNA

status: Public on Sep 06 2021

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

country: France

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

data_processing:
The ABI SOLiD system was used to produce sequence files in colour space formats.
For quality filtering, sequencing reads were trimmed for low quality (less than 20) using in house Perl script.
The quality control statistics for the reads before and after trimming were obtained using FastQC.
The trimmed reads were aligned to the human genome version Hg19 using Tophat2 with the -C option for the colour space.
The reads aligned to unique chromosomal positions were retained.
The total numbers of reads that overlap with the transcripts or genes (exonic region only) were obtained using the Cuffdiff function from Cufflinks
Normalization and differential expression were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Log2 transformed counts of genes and their informations according to differential analysis.

source_name: capillary blood

growth_protocol: Sample collection and analyses were obtained with informed consent, in accordance with the Declaration  of Helsinki, with approval from the institutional review boards of participating institutions

extract_protocol:
RNA was harvested using Trizol reagent
Paired-end stranded RNA-seq was performed with ribodepleted Total RNA using ABI SOLiD platform version 4

tag: tissue

value: capillary blood

tag: disease

value: T-cell Acute Lymphocytic Leukemia

tag: subtype

tag: oncogenes


title: rRNA Depleted total RNA from kidney from untreated HXB22 rats (replicate 4, sequencing batch 5)

tag: strain

tag: batch

tag: treatment

value: kidney

tag: Sex

value: male


title: ALL-T-4.6_RNA


title: ALL-T-4.5_RNA


title: 1InfectedVehicle

value: ethanol


title: ALL-T-4.10_RNA

value: Immature


title: 1Infected25HC


title: rRNA Depleted total RNA from kidney from untreated HXB17 rats (replicate 4, sequencing batch 6)


title: ALL-T-4.7_RNA


title: ALL-T-4.8_RNA


title: 4MockVehicle

value: Uninfected


title: ALL-T-4.4_RNA


title: ALL-T-4.2_RNA


title: ALL-T-3.6_RNA


title: ALL-T-4.1_RNA


title: ALL-T-3.5_RNA


title: ALL-T-3.3_RNA


title: ALL-T-3.2_RNA


title: ALL-T-2.22_RNA


title: ALL-T-2.21_RNA


title: ALL-T-3.4_RNA


title: ALL-T-2.19_RNA


title: ALL-T-2.20_RNA


title: Follicular thyroid carcinoma, biological replicate 2

description:
Follicular thyroid carcinoma sample
FTC2

source_name: Follicular thyroid carcinoma

value: Follicular thyroid carcinoma


title: ALL-T-2.18_RNA


title: ALL-T-2.17_RNA


title: ALL-T-3.1_RNA


title: ALL-T-2.16_RNA


title: Nodular goiters, biological replicate 6

description:
Nodular goiters sample
N6


title: ALL-T-2.13_RNA


title: ALL-T-2.14_RNA


title: ALL-T-2.11_RNA


title: SKNAS-Vel-02


title: ALL-T-2.12_RNA


title: ALL-T-2.8_RNA


title: rRNA Depleted total RNA from kidney from untreated HXB18 rats (replicate 4, sequencing batch 6)


title: ALL-T-2.15_RNA


title: ALL-T-2.10_RNA


title: ALL-T-2.6_RNA


title: ALL-T-2.5_RNA


title: ALL-T-2.4_RNA


title: ALL-T-2.3_RNA


title: ALL-T-2.9_RNA


title: ALL-T-2.2_RNA


title: ALL-T-2.7_RNA


title: ALL-T-2.1_RNA


title: ALL-T-1.4_RNA


title: ALL-T-1.3_RNA


title: ALL-T-1.2_RNA


title: ALL-T-1.1_RNA