title: WT Hippocampus 2 months female mRNA rep3 [2_6_12_mo]

description:
Q1300003_02_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months male mRNA rep2 [2_6_12_mo]

status: Public on Jul 14 2020

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

description:
Q1300007_03_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt

library_source: transcriptomic

data_processing:
Libraries for RNA-seq were sequenced using an Illumina HiSeq 2000.
Sequenced reads were trimmed for adaptor sequence using Omitsoft aligner and then mapped to rat genome Rat.B6.0.
a) Trimmed low-quality bases from the reads, aligned reads to the rat reference genome (Ensembl R89) with OmicSoft Aligner and quantitated the reads per gene with OmicSoft Quantitate. b) Fragments Per Kilobase of exon model per million reads mapped were calculated with OmicSoft. c) Generated the QC plots (PCA, Volcano, Bar charts of QC metrics).
Genome_build: Rat.B6.0
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM and Count values for each Sample.

molecule: total RNA

organism: Rattus norvegicus

source_name: Right Hippocampus

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen mRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Hippocampus

tag: genotype

value: Q130 KI Het

tag: age

value: 2 months

tag: Sex

value: Male

tag: batch


title: Q130 KI Hippocampus 2 months male mRNA rep4 [2_6_12_mo]

description:
Q1300008_03_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cortex 2 months female mRNA rep2 [2_6_12_mo]

description:
Q1300003_03_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt

source_name: Right Cortex

value: Cerebral Cortex

value: Wild type

value: Female


title: WT Cortex 2 months female mRNA rep1 [2_6_12_mo]

description:
Q1300003_02_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months male mRNA rep5 [2_6_12_mo]

description:
Q1300006_01_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months male mRNA rep4 [2_6_12_mo]

description:
Q1300006_01_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months male mRNA rep1 [2_6_12_mo]

description:
Q1300006_02_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months female mRNA rep1 [2_6_12_mo]

description:
Q1300004_01_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months female mRNA rep5 [2_6_12_mo]

description:
Q1300002_04_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months female mRNA rep3 [2_6_12_mo]

description:
Q1300004_02_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months female mRNA rep2 [2_6_12_mo]

description:
Q1300002_03_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Striatum 2 months female mRNA rep1 [2_6_12_mo]

description:
Q1300002_04_R_Striatum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt

source_name: Right Striatum

value: Corpus Striatum


title: Q130 KI Cortex 2 months male mRNA rep3 [2_6_12_mo]

description:
Q1300007_03_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months male mRNA rep2 [2_6_12_mo]

description:
Q1300006_02_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months male mRNA rep1 [2_6_12_mo]

description:
Q1300007_02_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months female mRNA rep5 [2_6_12_mo]

description:
Q1300003_01_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months female mRNA rep4 [2_6_12_mo]

description:
Q1300002_03_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cortex 2 months male mRNA rep1 [2_6_12_mo]

description:
Q1300007_01_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months female mRNA rep2 [2_6_12_mo]

description:
Q1300002_04_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months male mRNA rep5 [2_6_12_mo]

description:
Q1300006_04_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt

source_name: Cerebellum

value: Cerebellum


title: WT Cortex 2 months female mRNA rep5 [2_6_12_mo]

description:
Q1300003_04_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months female mRNA rep1 [2_6_12_mo]

description:
Q1300004_01_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cortex 2 months female mRNA rep3 [2_6_12_mo]

description:
Q1300002_01_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cortex 2 months female mRNA rep4 [2_6_12_mo]

description:
Q1300002_02_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months male mRNA rep5 [2_6_12_mo]

description:
Q1300008_03_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cortex 2 months male mRNA rep4 [2_6_12_mo]

description:
Q1300008_02_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months male mRNA rep2 [2_6_12_mo]

description:
Q1300008_02_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cortex 2 months female mRNA rep3 [2_6_12_mo]

description:
Q1300004_02_R_Cortex
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months male mRNA rep4 [2_6_12_mo]

description:
Q1300007_01_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months male mRNA rep3 [2_6_12_mo]

description:
Q1300006_03_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Hippocampus 2 months female mRNA rep4 [2_6_12_mo]

description:
Q1300003_01_R_Hippocampus
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months female mRNA rep3 [2_6_12_mo]

description:
Q1300003_02_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months female mRNA rep1 [2_6_12_mo]

description:
Q1300003_04_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months male mRNA rep2 [2_6_12_mo]

description:
Q1300008_03_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months male mRNA rep1 [2_6_12_mo]

description:
Q1300007_02_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months female mRNA rep5 [2_6_12_mo]

description:
Q1300003_03_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months female mRNA rep4 [2_6_12_mo]

description:
Q1300002_02_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months female mRNA rep2 [2_6_12_mo]

description:
Q1300004_01_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months male mRNA rep5 [2_6_12_mo]

description:
Q1300006_01_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months female mRNA rep2 [2_6_12_mo]

description:
Q1300002_01_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months female mRNA rep1 [2_6_12_mo]

description:
Q1300004_02_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: WT Cerebellum 2 months male mRNA rep1 [2_6_12_mo]

description:
Q1300008_01_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months male mRNA rep4 [2_6_12_mo]

description:
Q1300007_03_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months female mRNA rep5 [2_6_12_mo]

description:
Q1300002_04_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months female mRNA rep4 [2_6_12_mo]

description:
Q1300003_01_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Sample 17_nCoV 9 scRNA-seq [SW119]

status: Public on Jul 06 2020

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Fastq files were generated using cellranger mkfastq (v3.0.2)
From Sample 1 to Sample 20, they have the barcode sequence which end with '-1' to '-20', respectively;
Sample 1 : AAACCCAAGGGCAATC-1 ~ TTTGTTGTCGCCAATA-1
…
Sample 20 : AAACCCACACAGTCGC-20 ~ TTTGTTGTCTGCTTAT-20
The sequenced reads were aligned using cellranger count (v3.0.2; --r1-length 28 --r2-length 91) to cellranger reference GRCh38 (v 3.0.0).
Aligned files were aggregated with cellranger aggr (v3.0.2; --normalize=mapped)
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression matrix, cell barcode information, and gene name list

organism: Homo sapiens

extract_protocol:
The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.
The experimental process was conducted according to manufacturer's instruction without modification. The final libraries were sequenced on Nextseq 550.

tag: subject group

value: COVID-19 patient

tag: subject status

value: severe COVID-19 patient

tag: gender

value: M

tag: cell type

value: PBMC


title: Q130 KI Cerebellum 2 months female mRNA rep3 [2_6_12_mo]

description:
Q1300002_03_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: Q130 KI Cerebellum 2 months male mRNA rep3 [2_6_12_mo]

description:
Q1300006_02_cerebellum
mRNA
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Gene_FPKM.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_Counts.txt
processed data file: WTxQ130_Rat_brain_tissues_2_6_12_mo_Transcript_FPKM.txt


title: biol_rep_88:lop-228:peripheral blood

status: Public on Jun 10 2020

type: RNA

city: São Paulo

first: Levi

middle: Higino

last: Jales Neto

state: SP

address: Dr Arnaldo 455

department: Rheumatology

country: Brazil

institute: FMUSP

description: Gene expression data from SPAH cohort

hyb_protocol: cRNA were hybridized for 16 hr at 40ºC on Affymetrix GeneChip® Human Transcriptome Array HTA 2.0 according to GeneChip® WT PLUS Reagent Kit Affymetrix protoco. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the scanner Gene Chip affymetrix 30007G

data_processing:
After quality control and assessment of the expression signals, CEL files were analyzed using Affymetrix GCOS®. The normalization of the transcriptomic data from 90 samples from the initial SPAH database was performed by the logarithm transformation of the expression signal using Expression Console software. In statistical analysis of the microarray data in studies related to vertebral fractures (characteristics: group_microarrays_VF_study) or Coronary Artery Calcification (characteristics: group_microarrays_CAC_study) binary response variables were adjusted by the logistic regression model with age as a covariate in R to discriminate DE genes.
Log2 RMA signal; signal calculated by Expression Console v 1.1.2800.19935

label: biotin

source_name: peripheral blood

label_protocol: RNA (100ng) from each sample were transcribed using Ambion WT Expression kit (Life Technologies), labeled and hybridized according to to Affymetrix GeneChip® Human Transcriptome Array HTA 2.0 protocol. Affymetrix standard procedure.

extract_protocol: Twenty mL of whole peripheral blood were collected under fasting conditions and stored it at -80°C until performed biochemical tests for bone metabolism (calcium, phosphorus, alkaline phosphatase, 25-hydroxyvitamin D, parathormone [PTH], bone turnover markers [CTX, P1NP]) and collected in PAXgene Blood RNA Tubes for RNA extraction. For RNA extraction, we used fresh blood and RNeasy columns (Qiagen, Germantown, MD) and RNase-Free DNase Set (Qiagen). Purified RNA was evaluated using the Bioanalyzer 2100 System (Agilent, Santa Clara, CA).

value: female

tag: age (years)


title: biol_rep_85:lop-212:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_90:lop-230:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_80:lop-205:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_81:lop-206:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_83:lop-209:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_82:lop-208:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_78:lop-203:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_86:lop-217:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_84:lop-210:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_79:lop-204:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_70:lop-180:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_87:lop-220:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_77:lop-202:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_76:lop-201:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_73:lop-191:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_75:lop-199:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_74:lop-192:peripheral blood

description: Gene expression data from SPAH cohort

tag: height (cm)


title: biol_rep_72:lop-190:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_62:lop-164:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_69:lop-179:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_68:lop-178:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_89:lop-229:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_58:lop-138:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_66:lop-175:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_64:lop-169:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_63:lop-166:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_65:lop-171:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_48:lop-124:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_67:lop-176:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_44:lop-114:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_51:lop-127:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_54:lop-134:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_41:lop-109:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_40:lop-108:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_71:lop-189:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_43:lop-112:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_38:lop-103:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_61:lop-160:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_57:lop-137:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_53:lop-130:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_56:lop-136:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_52:lop-129:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_60:lop-157:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_55:lop-135:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_36:lop-100:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_34:lop-093:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_45:lop-120:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_32:lop-085:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_49:lop-125:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_31:lop-082:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_50:lop-126:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_46:lop-122:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_27:lop-074:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_42:lop-111:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_59:lop-156:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_47:lop-123:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_39:lop-104:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_18:lop-054:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_19:lop-058:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_21:lop-063:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_37:lop-102:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_35:lop-094:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_33:lop-090:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_16:lop-052:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_30:lop-079:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_8:lop-016:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_5:lop-011:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_7:lop-015:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_25:lop-071:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_29:lop-076:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_28:lop-075:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_26:lop-072:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_6:lop-012:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_15:lop-046:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_24:lop-070:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_23:lop-068:peripheral blood

description: Gene expression data from SPAH cohort


title: Col-0_dS_root_rep 3

status: Public on Jun 09 2020

city: Warsaw

first: Anna

middle: Katarzyna

last: Wawrzyńska

address: Pawinskiego 5A

department: Plant Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description: sulfur deficient

hyb_protocol: Hybridization was performed on Gene Atlas array strips (Arabidopsis Gene 1,1 ST Array strip) at 48Â°C for 18 hours on the Affymetrix GeneAtlas Hybridization Station.

scan_protocol: Strips were scanned using the Gene Atlas imaging station.

data_processing: Data were analyzed with Transcriptome Analysis Console (TAC) Software 4.0 following manufacturer’s specifications.

organism: Arabidopsis thaliana

source_name: root

label_protocol: Labeling was performed with Affymetrix GeneChip® WT Terminal Labelling Kit

growth_protocol: Plants were grown hydroponically under short-day conditions (8h light / 16h dark cycles) under full nutrient supply for 5 weeks.

extract_protocol: RNA was isolated from stressed and control plants using TRI Reagent® (Molecular Research Center, Cincinnati, OH, USA) (Chomczynski and Sacchi, 1987) and digested with TURBO™ DNase (Ambion)

treatment_protocol: Plants were either grown under full nutrient conditions or transferred to sulfur deficient nutrients for 5 days


title: biol_rep_20:lop-061:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_22:lop-066:peripheral blood

description: Gene expression data from SPAH cohort


title: rpt2_nS_root_rep 2

description: normal sulfur supply


title: biol_rep_17:lop-053:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_14:lop-041:peripheral blood

description: Gene expression data from SPAH cohort


title: rpt2_nS_root_rep 3

description: normal sulfur supply


title: Col-0_nS_root_rep 3

description: normal sulfur supply


title: rpt2_dS_rosette_rep 2

description: sulfur deficient

source_name: rosette


title: rpt2_dS_rosette_rep 3

description: sulfur deficient


title: biol_rep_12:lop-032:peripheral blood

description: Gene expression data from SPAH cohort


title: Col-0_dS_root_rep 1

description: sulfur deficient


title: biol_rep_11:lop-027:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_13:lop-039:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_10:lop-024:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_9:lop-021:peripheral blood

description: Gene expression data from SPAH cohort


title: CL721

status: Public on Jun 03 2020

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

data_processing:
Clustering was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, USA). After cluster generation, the libraries were sequenced on an Illumina GAIIx and 101-bp single-end reads were generated.
Data was formatted to FASTQ format using CASAVA v1.8 (Illumina). Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
To analyze the sardine and mackerel RNAseq data, an analytical pipeline was developed that starts with the conversion of fastq files to fasta format via a custom PERL script. As comprehensive genomic sequence data for sardine and mackerel is presently not available, we exploited the phylogenetic similarity of sardine and zebrafish and mapped sardine reads to the zebrafish (Danio rerio) Genome Reference Consortium Zebrafish Build 10 (GRCz10) transcriptome. For mackerel, we mapped reads to the reference transcriptome, fugu (Takifugu rubripes) Takifugu rubripes FUGU 4.0  using the Nucleotide-Nucleotide Basic Local Alignment Search Tool (BLAST) nucleotide to nucleotide option (blastn) (Altschul et al. 1990).
After determining the threshold alignment length the reads were assembled into transcript level expression summaries; the number of reads mapped to each gene or transcript, with alignment length greater than the threshold alignment length, were summed, yielding a count as a measure of transcript expression.
In order to infer differential gene expression with robust statistical power, we utilized DEseq2. Transcript count data from DESeq2 analysis was ranked according to adjusted p-value (or q-value), the smallest false discovery rate (FDR) at which a transcript is called significant. FDR was calculated using the Benjamini-Hochberg multiple testing adjustment procedure and the cut-off was set at q ≤ 0.1.
Genome_build: GRCz10 & FUGU 4.0
Supplementary_files_format_and_content: tab-delimited .txt files include the DESEQ2 output for the Control vs EE2 exposed comparison for both fish species.  Columns to the right of the Base Mean column represent DEseq2 output.  baseMean is the mean value of the read counts for that gene across all samples. The log2FoldChange tells us how much the gene's expression has changed due to EE2 exposure. This value is reported on a logarithmic scale to base 2. The lfcSE value is the standard error estimate for the log2 fold change estimate. The p-value and pad-j represent uncorrected and corrected, i.e. Benjamini and Hochberg (False Discovery Rate).     For the sardine data the ID is a zebrafish gene identifier, i.e. the sardine gene mapped to zebrafish NCBI Reference Sequence. The human Ortholog GeneID was determined via Ensembl homology and the corresponding HUMAN ORTHOLOG SYMBOL is provided in addition to aliases and a description of the gene.     For the mackerel data the ID for the JGI Fugu ID (TAKRU4) gene is provided (first two columns), The Fugu_Ensembl_transcript, Fugu_Ensembl_protein and Fugu_Ensembl_gene information are presented. The human ortholog determined via Ensembl homology (Human gene ID), Gene Symbol, NCBI Protein ID (human), REFSEQ: accession (human) and a description of the gene are provided.

organism: Sardinops sagax

source_name: Liver

growth_protocol: Sardine and mackerel were obtained from the live bait receiver operated by Everingham Bros Inc. in Mission Bay, San Diego, California. Fish were allowed to acclimate to research tanks at the NOAA Southwest Fisheries Science Center Experimental Aquarium facility under ambient temperature (~17oC) flow through seawater conditions and fed a pelleted feed (Bio-Oregon) to satiation.

extract_protocol:
Fish were euthanized with an overdose of Tricaine Methanosulfonate (250mg/L) dissolved in seawater. Livers were harvested and flash-frozen in liquid nitrogen at -196oC. These procedures followed an approved institutional IACUC protocol and all animals were treated humanely.  RNA was extracted from liver samples using TRIzol reagent (Invitrogen, CA) and further purified using the RNeasy Mini kit with DNAse to remove DNA (Qiagen, Valencia, CA). RNA concentrations were determined at 260 nm using an ND1000 (Nanodrop, Wilmington, DE). RNA was tested for structural integrity with the 6000 Nano LabChip assay from Agilent, (Santa Clara, CA, USA). Only RNA samples with RIN scores > 7.0 were used for RNA-seq.
Libraries for RNA sequencing (RNAseq) were generated using Illumina TruSeq™ RNA Sample Preparation Kit (Illumina, USA) in accordance with the manufacturer’s recommendations (Figure 2A). The library fragments were purified with AMPure XP system (Beckman Coulter, USA) to select cDNA fragments of approximately 300 bp in length. DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 10-cycle PCR reaction. Products were purified using AMPure XP system and quantified using the Agilent high sensitivity DNA assay on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For exposure experiments (for both species), five males were exposed to 12.5 pM EE2 for five hours (environmentally relevant concentration in the range of surface water levels) and an additional unexposed five males served as controls.

tag: exposure

value: 12.5 pM Ethinylestradiol (EE2)

tag: Stage

value: adult

value: male

value: liver


title: CL723


title: CL70

value: Control


title: CL74


title: Col-0_dS_rosette_rep 2

description: sulfur deficient


title: rpt2_nS_rosette_rep 3

description: normal sulfur supply


title: rpt2_dS_root_rep 3

description: sulfur deficient


title: Col-0_nS_rosette_rep 3

description: normal sulfur supply


title: biol_rep_4:lop-009:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_3:lop-007:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_2:lop-005:peripheral blood

description: Gene expression data from SPAH cohort


title: biol_rep_0:lop-002:peripheral blood

description: Gene expression data from SPAH cohort


title: rpt2_dS_root_rep 2

description: sulfur deficient


title: CL69


title: Brain, 5L

data_processing:
Quality check of the Fastq files using FastQC v0.11.5
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11
The resulting BAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Portions of the analysis was carried out via Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Initial QC and trimming were peroformed on OnRamp then custom Docker instances were created to create a STAR index  based on  the GCF_000826765.1_Fundulus_heteroclitus-3.0.2_genome build. Custom PERL and BASH scripts were used for annnotations.
Genome_build: GCF_000826765.1_Fundulus_heteroclitus-3.0.2_genomic
Supplementary_files_format_and_content: tab-delimited .txt file includes the DESEQ2 output for the I vs L  brains of individual fish.  Column headers are; Name (HGNC Symbol),genename (build geneID),Entrez Geneid,Description,,then 10 Control and 10 treated raw count columns, baseMean, log2 Fold Change,p-Value,p-Adj

organism: Fundulus heteroclitus

source_name: Mummichog brain

growth_protocol: The Furman University Institutional Animal Care and Use Committee (IACUC) approved the use of animals or their tissues in the study (IACUC protocol # 01-19-06). Adult mummichogs were obtained from Aquatic Research Organisms (Hampton, NH). Mummichogs were housed in glass aquarium tanks at room temperature (22oC) each containing 40L of dechlorinated water at 10ppt marine salt (Instant Ocean®) on a 12:12 light/dark cycle. Fish were fed daily with fish flakes and blood worms (Tetra®).

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Fish were anesthetized with 2-phenoxyethanol diluted in tank water (1:500). Fish remained in the anesthetic until they could no longer move or right themselves (≈ 5min). They were then placed in a paper towel soaked from the 2-phenoxyethanol in tank water. Under dissecting microscope, fish were held upright for direct illumination of the head, which allowed visualization of the pigmented meninges overlying the tectal hemispheres of the dorsal midbrain. A sterile 23G syringe needle was placed directly over one tectal hemisphere of the midbrain and slowly rotated back and forth while gently pushing down. This needle was inserted to the depth of its bevel (≈ 2mm) which allowed the lesion to penetrate the optic tectum, tegmental regions of the midbrain and underlying hypothalamic tissue of the diencephalon. After injury, fish were placed in tank water (10ppt saline) for recovery and were swimming under their own power within 5min. They were then placed into a separate tank until sacrifice, which was 1hr post-lesion. For sacrifice, mummichogs were placed in tank water containing 2-phenoxyethanol (1:1000). Fish remained in the anesthetic until they could no longer move or right themselves (≈ 2min). Fish were sacrificed by rapid decapitation and midbrain/diencephalic tissue was isolated, and the left and right hemispheres were separated, weighed, and immediately homogenized in QIAzol® Reagent (QIAGEN) for total RNA isolation using the QIAzol® RNeasy Lipid Tissue Mini Kit (QIAGEN) along with the RNase-Free DNase Set (QIAGEN) to remove genomic DNA.

tag: subject

value: Brain (right hemisphere)

tag: treatment

value: Lesioned (L)


title: rpt2_dS_rosette_rep 1

description: sulfur deficient


title: rpt2_dS_root_rep 1

description: sulfur deficient


title: Brain, 4L


title: Brain, 7L


title: Col-0_nS_root_rep 2

description: normal sulfur supply


title: Brain, 10I

value: Brain (left hemisphere)

value: contralateral Intact (I)


title: Col-0_nS_root_rep 1

description: normal sulfur supply


title: rpt2_nS_root_rep 1

description: normal sulfur supply


title: Col-0_dS_rosette_rep 3

description: sulfur deficient


title: Col-0_dS_root_rep 2

description: sulfur deficient


title: Brain, 6I


title: CL724


title: Col-0_dS_rosette_rep 1

description: sulfur deficient


title: rpt2_nS_rosette_rep 1

description: normal sulfur supply


title: CL794

organism: Scomber japonicus


title: Brain, 1I

description: C


title: CL722


title: Brain, 4I


title: CL73


title: rpt2_nS_rosette_rep 2

description: normal sulfur supply


title: CL71


title: Col-0_nS_rosette_rep 2

description: normal sulfur supply


title: Col-0_nS_rosette_rep 1

description: normal sulfur supply


title: CL720


title: Brain, 10L


title: Brain, 9L


title: Brain, 8L


title: Brain, 6L


title: Brain, 3L


title: Brain, 2L


title: CL57

data_processing:
Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the ZEBRAFISH genome (GRCZ10) using tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: GRCz10
Supplementary_files_format_and_content:   tab-delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl_gene_id; external_gene_name; description; hsapiens_homolog_ensembl_gene; hgnc_symbol; Human_description; Human_entrez_geneid; ensembl_peptide_ids; ensembl_transcript_ids. The baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, are all derived from DESeq2

organism: Danio rerio

extract_protocol:
Isolation of total liver RNA was performed using TRIzol reagent (Invitrogen), and the extracted RNA were further purified using the RNeasy Mini kit (Qiagen, Valencia, California). All RNA were treated with DNase to ensure no DNA appeared in the results.
To prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA), 100-200 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Male zebrafish (Danio rerio) were housed in aquaria maintained at a temperature 26-29ºC with a 100 W aquarium heater, and had a light-dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial, flaked fish food (Tetra, Germany). The fish were acclimated one week before the beginning of the experiments. For both experiments, 80 L tanks were prepared for each of the experimental groups, housing 40 fish per tank. One tank contained water with 1000 nM of 17β-estradiol (E2), one tank contained 100 nM of nonylphenol (NP), and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH, and stock working solutions were prepared, from which the working experimental concentrations were prepared. All exposures utilized a continuous flow-through system, and all exposures lasted for three weeks. After the end of the experimental period, the zebrafish were anaesthetized using 3-aminobenzoic acid ethyl ester (Sigma-Aldritch, St. Louis, MO; 10 g/L tap water) and sacrificed for removal of their livers, which were immediately frozen in liquid nitrogen and stored at -70ºC for molecular biology analysis.

tag: agent

value: 1000 nM Estradiol (E2)

value: Male


title: CL801


title: Brain, 1L

description: Trt


title: Brain, 9I


title: CL59


title: Brain, 8I


title: Brain, 7I


title: Brain, 5I


title: CL792


title: SW1736_EV_Vehicle_R2

status: Public on May 13 2020

city: Minneapolis

first: Noelle

middle: E

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

institute: University of Minnesota

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Fastq Quality Trimmer
STAR 2.7 was used to align fastq files to hg38
Htseq 0.10 was used to count aligned reads
SARTools/DESeq2 was used for differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files with raw counts values for each sample
Supplementary_files_format_and_content: matrix table with normalized counts; DESeq2 output

source_name: anaplasic thyroid cancer cell line, with control vector

growth_protocol: cells were hormone starved in phenol-red free culture media with charcoal stripped FBS for 24 hours, followed by the addition of  10nM T3 or vehicle (NaOH) treatment for 24 hours

extract_protocol:
cells were lysed in Trizol reagent, RNA was extracted, followed by BioAnalyzer analysis and all RIN values were  >7
Kapa Hyperprep RNA Kit was used for library construction, 1ug of RNA was used per sample per manufacturers instructions.

treatment_protocol: cells were treated with 10nM T3 or vehicle (NaOH) treatment for 24 hours

tag: cell line

tag: vector

value: pCDH-EV

value: vehicle (NaOH)

tag: treatment time

value: 24 hours


title: Brain, 3I

tag: tissue


title: SW1736_EV_Vehicle_R1


title: Brain, 2I


title: CL791


title: SW1736_TRB_T3_R3

source_name: anaplasic thyroid cancer cell line, with stable TRB expression

value: pCDH-TRB

value: 10nM T3


title: CL790


title: CL62

value: 100 nM Nonylphenol (NP)

tag: Sex


title: CL805


title: CL793

value: 12.5 pM Ethinylestradiol (EE2)


title: CL61


title: CL804

value: adult


title: CL58


title: wt batch 2

status: Public on May 12 2020

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

data_processing:
RNA-Seq reads were aligned to Ogataea parapolymorpha DL-1 reference using STAR version 2.5.3a in 2Pass mode
resulted sequence alignment map file (SAM) were filtered on ambigious alignments and sorted with samtools to sorted binary alignement file (BAM)
The sorted BAM file was processed with htseq-count from the HTSeq framework version 0.9.1 with -m union and -stranded reverse to calculate the transcript counts
The raw transcript counts were normalized on fragments per kilobase million (FPKM) by applying rpkm module from edgeR package
Genome_build: Ogataea parapolymorpha DL-1 GCF_000187245.1
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

molecule: polyA RNA

organism: Ogataea parapolymorpha

source_name: wildtype batch_0.37 S2

growth_protocol: O. parapolymorpha CBS11895 was grown in batch bioreactors (initial volume 1.4 L) in synthetic medium (pmid: 1523884) with an initial glucose concentration of 7.5 g/L as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 2M KOH.

extract_protocol:
Processing of samples and isolation of total RNA were performed essentially as described in pmid: 30147677. The resulting frozen biomass was gently thawed on ice and spun down at 4700 x g for 5 min at 0°C. Pellets were then resuspended in 5 ml/g dryweight in ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 5 ml/g dryweight of acid-phenol:chloroform:isoamyalcohol (125:24:1, pH 4.5, Thermo Fisher Scientific) and 0.5 mL/g dryweight 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes. After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNAse-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina)and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).

treatment_protocol: Cultures samples were directly quenched in liquid nitrogen under vigorous stirring.

tag: carbon source

value: Glucose

tag: specific growth rate (h-1)

tag: strain

tag: genotype

value: wildtype


title: CL802

value: Control

tag: gender

value: male

value: liver


title: oNC-HF-D11-3_S6: Infarct organoid 3

status: Public on Apr 14 2020

description: infarct biological replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: hiPSC-CM donor 01434, exp# 43

growth_protocol: organoids were pre-culture for 4 (D-4 to D0) days followed by 10 days (D0 to D10), changing cell ratio media every 2 days

extract_protocol:
30-35 organoids were collected immediately out of culture and put in lysis buffer on D11 (1 day after last media change) Total RNA was extracted with a RNeasy Mini Kit by Qiagen
Total RNA was extracted using standard methods. RNA quality was determined utilizing an Agilent TapeStation, (Santa Clara, CA). Illumina’s Truseq mRNA non-stranded library protocol with 100 ng of RNA was used to prepare sequencing libraries following the manufacture’s protocol with the exception of using half reactions (Illumina, San Diego, CA).
Sequencing was performed on a HiSeq2500 Rapid Run (version 2) single read sequencing (1X50 cycles), (Illumina, San Diego, CA).  Fastq files were generated using Illumina’s bcl2fastq conversion software v2.17.1.14.

treatment_protocol: infarct organoids were grown in 10% oxygen with 1uM norepinephrine added to culture media starting at D0

value: cardiac organoid

tag: developmental stage

value: experimental Day 11 (1 day after media change)

tag: concentration

value: 10% oxygen, 300um diameter, 50% CMs + 50%(4:2:1 ratio) FB:HUVEC:ADSC, cell ratio media+1uM norepinephrine


title: oNC-HF-D11-2_S5: Infarct organoid 2

description: infarct biological replicate 2


title: CL803

tag: exposure


title: CL60

value: Male


title: oNC-HF-D11-1_S4: Infarct organoid 1

description: infarct biological replicate 1


title: oNC-D11-3_S3: Control organoid 3

description: control biological replicate 3

value: normoxia, 300um diameter, 50% CMs + 50%(4:2:1 ratio) FB:HUVEC:ADSC, cell ratio media


title: oNC-D11-1_S1: Control organoid 1

description: control biological replicate 1


title: SW1736_TRB_Vehicle_R2

value: vehicle (NaOH)


title: SW1736_EV_T3_R2

value: pCDH-EV

value: 24 hours


title: SW1736_EV_T3_R1

value: 10nM T3


title: SW1736_TRB_T3_R1

value: pCDH-TRB


title: SW1736_EV_Vehicle_R3


title: SW1736_TRB_Vehicle_R3


title: SW1736_EV_T3_R3


title: SW1736_TRB_Vehicle_R1


title: Infarct organoid 3

description:
infarct biological replicate 3
Organoid_Infarction_vs_Control_deseq_124360_1337.txt

data_processing:
Illumina bcl2fastq conversion software v2.17.1.14 used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

extract_protocol:
30-35 organoids were collected immediately out of culture and put in lysis buffer on D11 (1 day after last media change) Total RNA was extracted with a RNeasy Mini Kit by Qiagen
Illumina’s Truseq mRNA non-stranded library protocol with 100 ng of RNA was used to prepare sequencing libraries following the manufacture’s protocol with the exception of using half reactions


title: wt cs01 1

source_name: wildtype chemostat_0.1 S1

growth_protocol: O. parapolymorpha CBS11895 was grown in chemostat bioreactors (working volume 1.4 L) at a dilution rate of 0.1 h-1 in synthetic medium (pmid: 1523884) with 7.5 g/L glucose as carbon source and 0.15 g/L pluronic 6100 PE antifoam. Cultures were maintained at 30°C, stirred at 800 rpm, aerated at 0.5 vvm with compressed air and pH was kept constant at pH 5.0 by the automatic addition of 2M KOH.


title: SW1736_TRB_T3_R2


title: wt cs01 2

source_name: wildtype chemostat_0.1 S2


title: oNC-D11-2_S2: Control organoid 2

description: control biological replicate 2


title: wt batch 1

source_name: wildtype batch_0.37 S1


title: Infarct organoid 1

description:
infarct biological replicate 1
Organoid_Infarction_vs_Control_deseq_124360_1337.txt


title: Infarct organoid 2

description:
infarct biological replicate 2
Organoid_Infarction_vs_Control_deseq_124360_1337.txt


title: Buffer 2h rep2

status: Public on Apr 07 2020

city: London

first: Jonathan

last: Chubb

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

data_processing:
Paired end reads were mapped to the Dictyostelium genome (version obtained from Gareth Bloomfield, masking the duplication on chromosome 2) using Tophat v2.0.9; library type parameter fr-firststrand, -p 4, -g 0
reads for each gene were counted with HtSeqCount v0.5.4p3. -m union -s reverse -a 0
Genome_build: dicty_2.7
Supplementary_files_format_and_content: tab-delimited text file with read counts for all samples

organism: Dictyostelium discoideum

source_name: dedifferentiating cells

growth_protocol: Before development, cells were grown in HL5 (Formedium, UK).

extract_protocol:
Cells were pelleted and flash frozen. Total RNA was extracted by SDS-based lysis, followed by phenol extraction and ethanol preciptiation to remove protein.
100 ng total RNA was used to prepare mRNA libraries using NEBNext mRNA isolation kit and NEBNext Ultra Directional RNA Library preparation kit. mRNA fragmentation used manufacturer recommended conditions for a 300bp insert size. Library amplification used 13 cycles of PCR. 75bp paired-end reads were generated using an Illumina NextSeq 500.

treatment_protocol: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA and incubated in culture dishes in KK2

tag: replicate

tag: timepoint


title: Buffer 6h rep2


title: Buffer 6h rep1


title: Buffer 4h rep2


title: Buffer 0.5h rep2


title: Buffer 2h rep1


title: Buffer 3h rep1


title: Buffer 3h rep2


title: Buffer 0.5h rep1


title: Buffer 1h rep2


title: Media 4h rep2

treatment_protocol: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA then dedifferentiated in HL5 growth medium as a shaken suspension


title: Buffer 4h rep1


title: Buffer 1h rep1


title: Media 5h rep2


title: Media 4h rep1


title: Media 0.5h rep2


title: Media 3h rep1


title: Media 3h rep2


title: Media 2h rep2


title: Media 1h rep1


title: Media 0.5h rep1


title: Media 5h rep1


title: Media 0h rep1


title: Media 0h rep2


title: Media 1h rep2


title: Media 2h rep1


title: Inactive.12

status: Public on Mar 26 2020

type: genomic

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
08H
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

hyb_protocol: Illumina iScan

scan_protocol: The ChAMP Bioconductor package was used to process the raw methylation array data starting from the idat files generated by the array platform.

data_processing: Normalization was performed on the filtered probe set using the beta-mixture quantile normalization (BMIQ) method (31) and ComBat (32) was used to adjust for the effects of array slide and sex.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Pituitary Adenoma

label_protocol: The amplified and fragmented SBM-DNA was hybridized to the HM450K BeadChip

extract_protocol: Sodium bisulfite modification (SBM) was performed on 1 μg of DNA using Zymo EZ DNA methylation kit

value: Pituitary Adenoma

tag: disease state

value: Endocrine-inactive adenoma

tag: sample type

value: Frozen tissue

tag: age

value: F

tag: plate

tag: well position

tag: sentrix id

tag: terminus

tag: complete barcode


title: Inactive.14

description:
09B
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

tag: tissue

tag: Sex

value: M


title: Inactive.18

description:
09F
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.19

description:
09H
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.11

description:
08G
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.2

description:
07G
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.10

description:
08F
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: GH.3

description:
09G
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Acromegaly


title: ACTH.1

description:
07H
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Cushing's disease


title: GH.5

description:
09E
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: ACTH.2

description:
08A
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.13

description:
09A
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: ACTH.12

description:
08E
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.16

description:
09D
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: ACTH.8

description:
02G
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Frozen Tissue


title: GH.9

description:
07D
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: ACTH.11

description:
08D
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.4

description:
01B
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: ACTH.3

description:
08B
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: GH.11

description:
07F
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.15

description:
09C
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.8

description:
08C
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: GH.13

description:
07A
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Acromegaly Somatulin treated


title: GH.7

description:
01H
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: KO2

status: Public on Mar 13 2020

city: Brooklyn

first: Brahim

last: Chaqour

state: NY

address: 450 Clarkson Avenue

department: Cell Biology

institute: SUNY Downstate Medical Center

description: total RNA

data_processing:
Sequence quality was examined using the FastQC.
The raw sequences were trimmed off 5’, 3’-adaptor bases using cutadapt.
The trimmed sequences were aligned to reference genome using Hisat2 software.
The aligned reads were assembled to transcripts by StringTie and FPKMs were computed.
The differentially expression of the genes and transcripts were analyzed using Ballgown R package.
rMATS was used to analzye alternative splicing events.
Genome_build: GENCODE mouse GRCm38
Supplementary_files_format_and_content: Gene/transcript expression levels in FPKM

organism: Mus musculus

extract_protocol:
Retinas were dissected, flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.
Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT)  magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina HiSeq 4000 system.

tag: strain background

value: post natal day 7

tag: genotype/variation

value: CTGF-/-

value: retina


title: GH.10

description:
07E
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: KO1

description: total RNA


title: Con2

description: total RNA

value: wild-type (WT)


title: Con3

description: total RNA


title: Exposed2

status: Public on Mar 23 2020

description:
Nucleotide exposed
1477_NT3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the ZEBRAFISH genome (GRCZ10) using tophat2
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: GRCZ10
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: whole embryo (33-35 pooled)

growth_protocol: Embryos were held in zebrafish embryo medium

extract_protocol:
Each sample of total RNA was extracted TRIzol® Reagent (Ambion; Carlsbad, CA, USA) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Whole embryos were exposed in embryo medium to dissolved nucleotides

value: whole embryo

tag: developmental stage

value: 7 dpf


title: Control3

description:
Control
1475_EM9

tag: concentration


title: Exposed3

description:
Nucleotide exposed
1478_NT9


title: Control2

description:
Control
1474_EM3


title: Control1

description:
Control
1473_EM2


title: Con1

description: total RNA


title: GH.2

description:
02E
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: RIT1-WT_3

status: Public on Mar 06 2020

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

data_processing:
Illumina NovaSeq reads were aligned by STAR v2.5.3a in 2-pass mode to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts and generate raw counts file
EdgeR v.3.22.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list  down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: counts_all.txt is a tab-separated values file with the quantified read counts from FeatureCounts. Each row is a gene transcript. The first six columns describe the gene, and each of the remaing columns correspond to a sample.
Supplementary_files_format_and_content: transcript_quants_log2TPM.csv is a comma-separated values file of the log2 of TPM values. Each row is a gene transcript and each column is a sample.

source_name: cell line

extract_protocol:
Direct-zol RNA Miniprep plus (Zymo Research)
Illumina TruSeq kit for 50bp paired-end reads, poly-A selection, non-strand-specific

tag: cell line

value: AALE

tag: cell type

value: lung epithelial

tag: genetic perturbation

value: RIT1 WT


title: RIT1-WT_2


title: Inactive.1

description:
07C
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Pituitary Adenoma

tag: disease state

value: Endocrine-inactive adenoma


title: Inactive.3

description:
02B
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

tag: sample type


title: Exposed1

description:
Nucleotide exposed
1476_NT1


title: GH.8

description:
02H
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

tag: age


title: RIT1-M90I_3

value: RIT1 M90I


title: RIT1-M90I_2


title: RIT1-M90I_1


title: Renilla_1

value: KRAS WT


title: Renilla_2


title: KRAS-WT_3


title: KRAS-WT_2


title: KRAS-WT_1


title: KRAS-Q61H_2

value: KRAS Q61H


title: KO3

description: total RNA


title: KRAS-G12V_3

value: KRAS G12V


title: KRAS-G12V_2


title: ACTH.13

description:
02C
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Frozen Tissue

value: M

tag: plate


title: KRAS-Q61H_1


title: KRAS-Q61H_3


title: RIT1-WT_1


title: S42_Participant 6 pDC

status: Public on Mar 05 2020

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline.
STAR and RSEM were used to align to HG38 and to calculate the raw counts for genes, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and TPM in csv

source_name: Healthy donor pDC

growth_protocol: Participants 1-6 without any treatment. For in vitro experiment, the cells were cultured in RPMI with 10% FBS medium.

extract_protocol:
Total RNA was extracted from the 7 cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 500 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database and the ZIKV sequence (ZIKV strain PRVABC59, GenBank: KU501215.1).

treatment_protocol: There is no treatment for participants 1-6; and for in vitro experiment, the cells were infected with ZIKV at MOI=1 for either 24h or 48h

tag: subject id

value: participant 6

tag: infection status

value: healthy donor

value: peripheral blood

tag: environment

value: in vitro

tag: cell subtype

value: pDC


title: Renilla_3


title: S41_Participant 6 NK

source_name: Healthy donor NK

tag: tissue

value: ex vivo

value: NK


title: S39_Participant 6 mDC

source_name: Healthy donor mDC

value: mDC


title: S37_Participant 6 CD4 cell

source_name: Healthy donor CD4


title: S38_Participant 6 CD8 cell

source_name: Healthy donor CD8


title: KRAS-G12V_1

value: AALE

value: lung epithelial


title: S32_Participant 5 mDC

growth_protocol: Participants 1-6 without any treatment.for in vitro experiment.the cells were cultured in RPMI with 10% FBS medium.

value: participant 5


title: S36_Participant 6 B cell

source_name: Healthy donor B cell

value: B cell


title: S35_Participant 5 pDC


title: S30_Participant 5 CD4 cell

growth_protocol: Participants 1-6 without any treatment. For in vitro experiment.the cells were cultured in RPMI with 10% FBS medium.


title: S27_Participant 4 NK

source_name: patient_ZIKV Infected_NK

value: participant 4

value: ZIKV Infected


title: S26_Participant 4 Monocyte

source_name: patient_ZIKV Infected_Monocyte

value: Monocyte


title: Inactive.9

description:
01G
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Pituitary Adenoma

value: Endocrine-inactive adenoma

value: Frozen Tissue

tag: Sex

tag: well position

tag: sentrix id

tag: terminus

tag: complete barcode


title: S40_Participant 6 Monocyte

source_name: Healthy donor Monocyte

value: participant 6

value: healthy donor


title: S22_Participant 4 B cell

source_name: patient_ZIKV Infected_B cell

value: peripheral blood


title: S28_Participant 4 pDC

source_name: patient_ZIKV Infected_pDC

value: pDC


title: S23_Participant 4 CD4 cell

source_name: patient_ZIKV Infected_CD4

value: ex vivo


title: S25_Participant 4 mDC

source_name: patient_ZIKV Infected_mDC


title: S24_Participant 4 CD8 cell

source_name: patient_ZIKV Infected_CD8


title: ACTH.5

description:
01F
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

source_name: Pituitary Adenoma

value: Cushing's disease

value: F


title: S21_Participant 3 pDC

value: participant 3


title: S20_Participant 3 NK

value: NK


title: S16_Participant 3 CD4 cell


title: S18_Participant 3 mDC

value: mDC


title: S17_Participant 3 CD8 cell

growth_protocol: Participant 1-6 without any treatment. For in vitro experiment, the cells were cultured in RPMI with 10% FBS medium.


title: S19_Participant 3 Monocyte


title: S31_Participant 5 CD8 cell

value: participant 5


title: S12_Participant 2 Monocyte

treatment_protocol: there is no treatment for participants 1-6; and for in vitro experiment, the cells were infected with ZIKV at MOI=1 for either 24h or 48h

value: participant 2


title: S15_Participant 3 B cell

value: ZIKV Infected

value: B cell


title: S11_Participant 2 mDC


title: S29_Participant 5 B cell


title: S14_Participant 2 pDC


title: S13_Participant 2 NK

growth_protocol: Participants 1-6 without any treatment For in vitro experiment, the cells were cultured in RPMI with 10% FBS medium.


title: S10_Participant 2 CD8 cell


title: GH.1

description:
01D
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Pituitary Adenoma

value: Acromegaly

value: M


title: ACTH.7

description:
02F
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Frozen Tissue


title: ACTH.4

description:
01A
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.


title: Inactive.20

description:
01C
This retrospective study enrolled adult patients ages 18 to 90 years who had undergone transsphenoidal resection of pituitary adenomas at Providence Health System, Saint John's Health Center and had been consented for tissue and bodily fluid procurement and analysis. Genomic, transcriptomic and DNA methylation data were generated from the three major subtypes of surgically resectable pituitary adenomas, GH-secreting (acromegaly), ACTH-secreting (Cushing's disease) and endocrine-inactive pituitary adenomas.

value: Endocrine-inactive adenoma


title: S07_Participant 1 pDC

value: participant 1

value: peripheral blood


title: S04_Participant 1 mDC

value: ex vivo


title: S02_Participant 1 CD4 cell


title: S03_Participant 1 CD8 cell


title: S05_Participant 1 Monocyte

value: Monocyte


title: S08_Participant 2 B cell

value: healthy donor


title: S09_Participant 2 CD4 cell


title: 48HourTreatment_2

status: Public on Feb 26 2020

description:
09_4848HourTreatment_2
Treatment

data_processing:
Quality check of the Fastq files using FastQC v0.11.5
Sequenced reads (fastq files) were trimmed for adaptor sequence, nucleotides with the phred score below 30 and for overrepresented sequences using cutadapt, version 1.11
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
The analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19).
genome build: Rnor_6.0
processed data files format and content: The processed data files are “.txt” tabular files, contain in as column the identifiers ensembl_gene_id, external_gene_name, description, hsapiens_homolog_ensembl_gene, hsapiens_homolog_perc_id, hgnc_symbol, Human_description, Human_entrez_geneid, ensembl_peptide_ids, ensembl_transcript_ids, with annotation for ENSEMBLE and gene symbols, the original murine gene and its orthologous genes in humans.  In the sequences we have columns with the sample names and the raw counts of the genes mentioned. The last section of the files possess 4 columns: baseMean log2FoldChange, lfcSE ,stat, pvalue, padj. Showing the results from DESeq2 analysis.

organism: Rattus norvegicus albus

source_name: Neonatal rat ventricular myocytes

growth_protocol: All animal procedures were in accordance with the San Diego State University Animal Subjects Committee (UASC) and NIH Animal Welfare Assurance A3728-01. Neonatal rat ventricular myocytes (NRVMs) were harvested from 1-day old Harlan Sprague-Dawley Rats (Rattus norvegicus albinus) and cultured as previously described by Sprenkle et al 1995. Preplating isolated cells to remove fibroblasts yielded >98% NRVMs. Cell count was determined after preplating. Pooled NRVMs were centrifuged and resuspended in 20 ml  DMEM/F-12 (Gibco, Life Technologies, CA, USA) with 10% fetal bovine serum (Irvine Scientific, CA, USA) and quantified via hemacytometer. NRVMs were plated on Fibronectin (Gibco)- coated 35 mm dishes and incubated overnight to allow for recovery. On the following day, NRVMs were washed twice with 1:1 medium DMEM/F-12, kanamycin, ampicillin, and fungizone. NRVMs were incubated overnight in minimal medium consisting of 1:1 medium with 1 mg/ml bovine serum albumin (Sigma, MO, USA). On the third day, cells were washed two times with 1:1 medium. Minimal medium was replaced with Insulin-Transferrin-Selenium medium consisting of minimal medium, 1X Insulin-Transferrin-Selenium (Life Technologies), 0.4X MEM nonessential amino acids mixture (Sigma), and 0.1X MEM vitamins medium (Invitrogen, CA, USA).

extract_protocol:
After the appropriate exposure time, isolation of total RNA for RNA sequencing from
NRVMs was performed using RNeasy Mini Kit (Qiagen) as per the manufacturer’s protocol. RNA purity was determined by spectrophotometry using a NanoDrop 2000 (Thermo Scientific).
Library were prepared using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina (New England Biolabs Inc) and procedures were made are described by the manufacturer.

treatment_protocol: The control group was supplemented with 1% dimethyl sulfoxide (DMSO) and the experimental group was supplemented with 10 μmol/L rosiglitazone (Sigma-Aldrich) and 1% dimethyl sulfoxide (DMSO). NRVMs were exposed to control and experimental conditions for 0.5 hr, 24 hr, and 48 hr.

tag: agent

value: 10 micromol/L rosiglitazone (Sigma-Aldrich) and 1 percent dimethyl sulfoxide (DMSO)

tag: strain

value: Sprague-Dawley

tag: time point


title: S06_Participant 1 NK

value: NK


title: S01_Participant 1 B cell


title: 24HourTreatment_2a

description:
06_24HourTreatment_2a
Treatment


title: 24HourTreatment_2

description:
06_24HourTreatment_2
Treatment


title: 48HourTreatment_1

description:
08_48HourTreatment_1
Treatment


title: 48HourTreatment_2a

description:
09_4848HourTreatment_2a
Treatment


title: 24HourTreatment_1

description:
05_24HourTreatment_1
Treatment


title: 48HourTreatment_1a

description:
08_48HourTreatment_1a
Treatment


title: 24HourTreatment_1a

description:
05_24HourTreatment_1a
Treatment


title: HalfHourTreatment_1

description:
02_HalfHourTreatment_1
Treatment

value: HalfHour


title: HalfHourTreatment_2a

description:
03_HalfHourTreatment_2a
Treatment


title: HalfHourTreatment_2

description:
03_HalfHourTreatment_2
Treatment