title: WholeBlood_CRC305B8014212_Day28 [US22502595_254890810230_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8015214_Day3 [US22502595_254890810362_S01_GE1_1105_Oct12_2_1]

status: Public on Jan 06 2019

type: RNA

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: Whole blood gene expression of participant on day

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: participant

tag: gender

value: male

tag: age

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

tag: protocol

tag: treatment

tag: day

tag: tissue

value: whole blood


title: WholeBlood_CRC305B8015214_Day1 [US22502595_254890810362_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8015214_Day14 [US22502595_254890810363_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8014212_Day21 [US22502595_254890810230_S01_GE1_1105_Oct12_1_2]

value: asian

value: not reported


title: WholeBlood_CRC305B8015214_Day2 [US22502595_254890810362_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8014212_Day14 [US22502595_254890810230_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8014212_Day7 [US22502595_254890810229_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8015214_Day3 [US22502595_254890810230_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8015214_Day1 [US22502595_254890810230_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8014212_Day0 [US22502595_254890810229_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8015214_Day21 [US22502595_254890810363_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8015214_Day5 [US22502595_254890810362_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8015214_Day0 [US22502595_254890810362_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8015214_Day7 [US22502595_254890810362_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8015214_Day4 [US22502595_254890810362_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8014212_Day2 [US22502595_254890810229_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8014212_Day-1 [US22502595_254890810229_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8014212_Day14 [US22502595_254890810361_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8014212_Day4 [US22502595_254890810361_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8014212_Day3 [US22502595_254890810229_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8014212_Day5 [US22502595_254890810361_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8014212_Day3 [US22502595_254890810360_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8014212_Day1 [US22502595_254890810229_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8014212_Day7 [US22502595_254890810361_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8014212_Day-1 [US22502595_254890810360_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8014212_Day1 [US22502595_254890810360_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8014212_Day28 [US22502595_254890810361_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8014212_Day5 [US22502595_254890810229_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8013209_Day28 [US22502595_254890810228_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8014212_Day2 [US22502595_254890810360_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8014212_Day4 [US22502595_254890810229_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8014212_Day21 [US22502595_254890810361_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8013209_Day21 [US22502595_254890810228_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8013209_Day14 [US22502595_254890810228_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8013209_Day3 [US22502595_254890810227_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8013209_Day7 [US22502595_254890810228_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8013209_Day2 [US22502595_254890810227_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8013209_Day5 [US22502595_254890810228_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8013209_Day1 [US22502595_254890810227_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8013209_Day28 [US22502595_254890810360_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8013209_Day5 [US22502595_254890810359_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8013209_Day3 [US22502595_254890810359_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8013209_Day0 [US22502595_254890810227_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8013209_Day14 [US22502595_254890810360_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8013209_Day4 [US22502595_254890810228_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8012207_Day7 [US22502595_254890810226_S01_GE1_1105_Oct12_2_4]

value: black or african american

value: hispanic or latino


title: WholeBlood_CRC305B8012207_Day2 [US22502595_254890810226_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8012207_Day4 [US22502595_254890810226_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8013209_Day21 [US22502595_254890810360_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8013209_Day-1 [US22502595_254890810227_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8013209_Day7 [US22502595_254890810359_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8013209_Day-1 [US22502595_254890810359_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8013209_Day4 [US22502595_254890810359_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8013209_Day1 [US22502595_254890810359_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8012207_Day0 [US22502595_254890810226_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8012207_Day21 [US22502595_254890810227_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8012207_Day28 [US22502595_254890810358_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8012207_Day5 [US22502595_254890810226_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8012207_Day14 [US22502595_254890810358_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8012207_Day14 [US22502595_254890810227_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8012207_Day28 [US22502595_254890810227_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8012207_Day3 [US22502595_254890810226_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8013209_Day2 [US22502595_254890810359_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8013209_Day0 [US22502595_254890810359_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8012207_Day-1 [US22502595_254890810226_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8012207_Day7 [US22502595_254890810358_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8012207_Day21 [US22502595_254890810358_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8012207_Day1 [US22502595_254890810226_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8012207_Day3 [US22502595_254890810357_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8012207_Day-1 [US22502595_254890810357_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8012207_Day5 [US22502595_254890810358_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8012207_Day4 [US22502595_254890810358_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8012207_Day2 [US22502595_254890810357_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8012207_Day1 [US22502595_254890810357_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8011204_Day28 [US22502595_254890810225_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8011204_Day5 [US22502595_254890810225_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8012207_Day0 [US22502595_254890810357_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8011204_Day21 [US22502595_254890810225_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8011204_Day14 [US22502595_254890810225_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8011204_Day1 [US22502595_254890810224_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8011204_Day4 [US22502595_254890810225_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8011204_Day3 [US22502595_254890810224_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8011204_Day7 [US22502595_254890810225_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8011204_Day2 [US22502595_254890810224_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8011204_Day-1 [US22502595_254890810224_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8011204_Day21 [US22502595_254890810357_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8011204_Day0 [US22502595_254890810224_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8011204_Day4 [US22502595_254890810356_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8014212_Day0 [US22502595_254890810360_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8011204_Day28 [US22502595_254890810357_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8011204_Day7 [US22502595_254890810356_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8011204_Day5 [US22502595_254890810356_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8011204_Day14 [US22502595_254890810357_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8011204_Day2 [US22502595_254890810356_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8011204_Day3 [US22502595_254890810356_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8010203_Day28 [US22502595_254890810224_S01_GE1_1105_Oct12_1_3]

value: female


title: WholeBlood_CRC305B8011204_Day1 [US22502595_254890810356_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8011204_Day0 [US22502595_254890810356_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8010203_Day1 [US22502595_254890810223_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8011204_Day-1 [US22502595_254890810356_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8010203_Day3 [US22502595_254890810223_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8010203_Day5 [US22502595_254890810223_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8010203_Day14 [US22502595_254890810224_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8010203_Day4 [US22502595_254890810355_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8010203_Day21 [US22502595_254890810355_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8010203_Day7 [US22502595_254890810223_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8010203_Day21 [US22502595_254890810224_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8010203_Day7 [US22502595_254890810355_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8010203_Day4 [US22502595_254890810223_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8010203_Day-1 [US22502595_254890810223_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8010203_Day2 [US22502595_254890810223_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8010203_Day14 [US22502595_254890810355_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8010203_Day28 [US22502595_254890810355_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8010203_Day0 [US22502595_254890810223_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8010203_Day5 [US22502595_254890810355_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8010203_Day3 [US22502595_254890810354_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8006202_Day14 [US22502595_254890810354_S01_GE1_1105_Oct12_1_1]

value: other


title: WholeBlood_CRC305B8006202_Day28 [US22502595_254890810354_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8010203_Day1 [US22502595_254890810354_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8010203_Day2 [US22502595_254890810354_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8010203_Day0 [US22502595_254890810354_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8010203_Day-1 [US22502595_254890810354_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8006202_Day21 [US22502595_254890810354_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8006202_Day5 [US22502595_254890810353_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8006202_Day3 [US22502595_254890810353_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8006202_Day4 [US22502595_254890810353_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8006202_Day1 [US22502595_254890810353_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8006202_Day7 [US22502595_254890810353_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8006202_Day2 [US22502595_254890810353_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8006202_Day-1 [US22502595_254890810353_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8003201_Day21 [US22502595_254890810222_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8006202_Day0 [US22502595_254890810353_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8003201_Day5 [US22502595_254890810222_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8003201_Day14 [US22502595_254890810222_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8003201_Day28 [US22502595_254890810222_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8003201_Day7 [US22502595_254890810222_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8003201_Day4 [US22502595_254890810222_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8003201_Day2 [US22502595_254890810221_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305B8003201_Day1 [US22502595_254890810221_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8003201_Day-1 [US22502595_254890810221_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8003201_Day7 [US22502595_254890810085_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305B8003201_Day21 [US22502595_254890810085_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8003201_Day3 [US22502595_254890810221_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8003201_Day4 [US22502595_254890810085_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8003201_Day28 [US22502595_254890810085_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8003201_Day5 [US22502595_254890810085_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305B8003201_Day0 [US22502595_254890810221_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305B8003201_Day3 [US22502595_254890810084_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305B8003201_Day14 [US22502595_254890810085_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305B8003201_Day-1 [US22502595_254890810084_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7057145_Day5 [US22502595_254890810172_S01_GE1_1105_Oct12_2_2]

value: STAMARIL


title: WholeBlood_CRC305B8003201_Day1 [US22502595_254890810084_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305B8003201_Day0 [US22502595_254890810084_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7051122_Day4 [US22502595_254890810172_S01_GE1_1105_Oct12_1_4]

value: VARILRIX


title: WholeBlood_CRC305A7071142_Day14 [US22502595_254890810172_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A70871109_Day28 [US22502595_254890810171_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A70871109_Day14 [US22502595_254890810171_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305B8003201_Day2 [US22502595_254890810084_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7039128_Day4 [US22502595_254890810172_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7044119_Day4 [US22502595_254890810172_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A70751139_Day21 [US22502595_254890810172_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A70871109_Day21 [US22502595_254890810171_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A70871109_Day7 [US22502595_254890810165_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A70871109_Day4 [US22502595_254890810165_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A70871109_Day2 [US22502595_254890810165_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7083143_Day28 [US22502595_254890810164_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A70871109_Day0 [US22502595_254890810165_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A70871109_Day3 [US22502595_254890810165_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A70871109_Day5 [US22502595_254890810165_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7083143_Day14 [US22502595_254890810164_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7083143_Day21 [US22502595_254890810164_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A70871109_Day1 [US22502595_254890810165_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A70871109_Day-1 [US22502595_254890810165_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7073144_Day28 [US22502595_254890810163_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7083143_Day7 [US22502595_254890810164_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7083143_Day5 [US22502595_254890810164_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7083143_Day0 [US22502595_254890810163_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7083143_Day4 [US22502595_254890810164_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7083143_Day2 [US22502595_254890810163_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7083143_Day1 [US22502595_254890810163_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7083143_Day3 [US22502595_254890810163_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7073144_Day14 [US22502595_254890810163_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7073144_Day5 [US22502595_254890810162_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7083143_Day-1 [US22502595_254890810163_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7073144_Day4 [US22502595_254890810162_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7073144_Day21 [US22502595_254890810163_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7073144_Day3 [US22502595_254890810162_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7073144_Day-1 [US22502595_254890810162_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7073144_Day7 [US22502595_254890810162_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7073144_Day2 [US22502595_254890810162_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7073144_Day0 [US22502595_254890810162_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7073144_Day1 [US22502595_254890810162_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7071142_Day5 [US22502595_254890810161_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7071142_Day28 [US22502595_254890810161_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7071142_Day21 [US22502595_254890810161_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7071142_Day7 [US22502595_254890810161_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7071142_Day4 [US22502595_254890810161_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7071142_Day2 [US22502595_254890810155_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7066129_Day14 [US22502595_254890810155_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7071142_Day3 [US22502595_254890810155_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7071142_Day1 [US22502595_254890810155_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7071142_Day0 [US22502595_254890810155_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7071142_Day-1 [US22502595_254890810155_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7066129_Day5 [US22502595_254890810154_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7066129_Day28 [US22502595_254890810155_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7066129_Day21 [US22502595_254890810155_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7066129_Day4 [US22502595_254890810154_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7066129_Day3 [US22502595_254890810154_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7066129_Day0 [US22502595_254890810154_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7066129_Day2 [US22502595_254890810154_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7066129_Day7 [US22502595_254890810154_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7072127_Day5 [US22502595_254890810153_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7072127_Day28 [US22502595_254890810153_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7066129_Day1 [US22502595_254890810154_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7066129_Day-1 [US22502595_254890810154_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7072127_Day3 [US22502595_254890810152_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7072127_Day14 [US22502595_254890810153_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7072127_Day21 [US22502595_254890810153_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7072127_Day1 [US22502595_254890810152_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7072127_Day4 [US22502595_254890810153_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7072127_Day-1 [US22502595_254890810152_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7072127_Day7 [US22502595_254890810153_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7067130_Day28 [US22502595_254890810152_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7067130_Day4 [US22502595_254890810151_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7067130_Day2 [US22502595_254890810151_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7067130_Day5 [US22502595_254890810151_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7067130_Day0 [US22502595_254890810151_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7072127_Day2 [US22502595_254890810152_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7067130_Day14 [US22502595_254890810152_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7072127_Day0 [US22502595_254890810152_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7067130_Day21 [US22502595_254890810152_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7015113_Day28 [US22502595_254890810145_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7067130_Day3 [US22502595_254890810151_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7067130_Day1 [US22502595_254890810151_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7067130_Day-1 [US22502595_254890810151_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7067130_Day7 [US22502595_254890810151_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7015113_Day21 [US22502595_254890810145_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7015113_Day1 [US22502595_254890810144_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7015113_Day5 [US22502595_254890810145_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7015113_Day-1 [US22502595_254890810144_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7015113_Day14 [US22502595_254890810145_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7015113_Day4 [US22502595_254890810145_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7015113_Day3 [US22502595_254890810144_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7014112_Day21 [US22502595_254890810144_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7015113_Day7 [US22502595_254890810145_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7014112_Day4 [US22502595_254890810143_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7014112_Day7 [US22502595_254890810143_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7015113_Day2 [US22502595_254890810144_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7014112_Day2 [US22502595_254890810143_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7014112_Day28 [US22502595_254890810144_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7015113_Day0 [US22502595_254890810144_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7014112_Day14 [US22502595_254890810144_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7014112_Day5 [US22502595_254890810143_S01_GE1_1105_Oct12_2_3]


title: P28-1

type: SRA

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND28_1

library_source: transcriptomic

data_processing:
Embryos and mice for this study were collected from timed pregnant mice. Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) 1, 3, 7, 14, and 28
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA).
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample.
The raw sequenced reads were aligned from FASTQ files to the human genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using Tophat 2.0.9.
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet including Reads and TPM expression

organism: Mus musculus

source_name: Whole lung

extract_protocol:
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA)
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

tag: strain

tag: genotype

value: WT

value: lung


title: WholeBlood_CRC305A7014112_Day0 [US22502595_254890810143_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7014112_Day3 [US22502595_254890810143_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7014112_Day1 [US22502595_254890810143_S01_GE1_1105_Oct12_1_3]


title: P14-2

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND14_2

growth_protocol: Embryos and mice for this study were collected from timed pregnant mice.

treatment_protocol: Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) 1, 3, 7, 14, and 28


title: P7-2

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND7_2


title: P7-1

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND7_1


title: P28-2

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND28_2


title: P14-1

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND14_1


title: E18-2

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_E18.5_2


title: E18-3

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_E18.5_3


title: HepG2_homo2

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Rm 405A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
tophat v2.0.13 for alignment
isoform assembly and quantification using Cufflinks
differential expression was perfermed in edgeR
Genome_build: hg19

source_name: HepG2_C/EBPβ enh-/-

growth_protocol: HepG2 cells were maintained in Dulbecco's modified Eagle's medium (Gibco) with 10% FBS (HyClone). All cells were cultured at 37°C in a humidified chamber containing 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina RNAseq library

treatment_protocol: CRISPR/Cas9 blank vector was purchased from Addgene. Construction of CRISPR-C/EBPβ eRNA-sgRNA vectors was performed following the protocol by Addgene.

tag: cell line

tag: genotype/variation

value: C/EBPbeta enh-/-


title: P1-1

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND1_1


title: HepG2_homo1


title: WholeBlood_CRC305A7014112_Day-1 [US22502595_254890810143_S01_GE1_1105_Oct12_1_1]


title: E18-1

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_E18.5_1


title: P3-1

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND3_1


title: WholeBlood_CRC305A70651120_Day14 [US22502595_254890810142_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A70651120_Day28 [US22502595_254890810142_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A70651120_Day5 [US22502595_254890810142_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A70651120_Day3 [US22502595_254890810141_S01_GE1_1105_Oct12_2_4]


title: P3-2

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND3_2


title: E16-3

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_E16.5_3


title: WholeBlood_CRC305A70651120_Day7 [US22502595_254890810142_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A70651120_Day21 [US22502595_254890810142_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A70651120_Day2 [US22502595_254890810141_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A70651120_Day4 [US22502595_254890810142_S01_GE1_1105_Oct12_1_1]


title: E16-2

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_E16.5_2


title: WholeBlood_CRC305A70651120_Day0 [US22502595_254890810141_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A70651120_Day1 [US22502595_254890810141_S01_GE1_1105_Oct12_2_2]


title: HepG2_WT2


title: P1-2

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND1_2


title: HepG2_WT1


title: HepG2_WT_C/EBPβ enh-/-_Input_all

library_source: genomic

data_processing:
Bowtie2 version 2.3.4.1 for alignment
MACS v2.1.0 for peak calling
Homer v4.8 for enrichment
UCSC tools bedClip, bed-Graph-ToBigWig for generating the bw files
Genome_build: hg19

molecule: genomic DNA

source_name: pooled input sample

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
After recovery of ChIP and input DNA, whole-genome amplification was performed using the WGA4 kit (Sigma-Aldrich) and BpmI-WGA primers. Amplified DNA was digested with BpmI (New England Biolab). After that, 30 ng of the amplified DNA was used with the NEBNext ChIP-seq library prep reagent set (New England Biolab).

tag: chip antibody

value: none (input)


title: mouse whole lung at PND1_Pool4

description: mouse scRNAseq PND1 expression(TPM).xlsx

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
paired reads were aligned against mm10 using tophat-Tophat 2.0.9.
Transcripts Per Kilobase Million(TPM ) values were computed using Partek (http://www.partek.com/) E/M quantification model.
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet including TPM expression for 130 cells

source_name: mouse whole lung at PND1

growth_protocol: Left and right lobes of PND1 mouse lungs were rapidly dissected in ice-cold PBS and then finely minced in a Petri dish on ice using a razor blade.Lung pieces were transferred to a 1.5 ml conical tubes using P1 pipetman, cut tip, using 700 ul of TrypLE(10X)/tube and then with 500 ul of collagenase (10mg/ml in PBS) per tube.

extract_protocol:
Cell concentration was examined with a hemocytometer and adjusted to around 300 cells per microliter for Fluidigm C1.Fluidigm C1 experiments were carried out as per Fluidigm recommended protocols.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: The suspension was incubated in a 37°C water bath for 1 minute and then triturated for 30 seconds with cut tip 1 ml blue tip. The 1 minute 37°C incubation and 30 seconds trituration were repeated for a total of 7.5-10 minutes until most clumps were gone. Cell suspension was passed through a 40 micron strainer into 50 ml Falcon tube and the filter was rinsed with 5 ml of ice cold PBS with 0.1% BSA. Then 15 ml more were added to filtrate. Cells were transferred to 2X 14 ml conical blue tip tubes and spinned 300g for 5 minutes at 4°C. Supernatant was gently pipetted off. 5 ml of room temp Sigma RBC lysis buffer were added and lysis was monitored by removing a small aliquot and watching under a microscope. The suspension was incubated for 2-5 minutes at room temperature until red blood cells were lysed. 1/10 vol of 10X PBS was added, gently mixed, and spinned down 300g for 5 minutes at 4°C. Supernatant was discarded. Pellet was re-suspended in 0.8 ml of PBS with 0.1% BSA. Cells were settled on ice for about 2 minutes and then top 3/4 of cells were taken very gently. The settling onice and top 3/4 taking procedure was repeated once.

value: wt


title: HepG2_C/EBPβ enh-/-_C/EBPB_ChIPseq

value: C/EBPB (sc-150, Lot#G1814, Santa Cruz Biotechnology)


title: mouse whole lung at PND1_Pool3


title: mouse whole lung at PND1_Pool2


title: HepG2_WT_BRD4_ChIPseq


title: mouse whole lung at PND1_Batch1

data_processing:
Read alignment and  digital expression matrix were processed using Drop-seq tools (http://mccarrolllab.com/download/922/, version 1.12). The two runs of batch2 were merged and deconvoluted together.
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited gene counts per cell

extract_protocol:
Cell concentration was examined with a hemocytometer and adjusted to around 100 cells per microliter for Drop-seq. Drop-seq experiments were carried out largely followed the protocol described in Macosko et al.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.


title: HepG2_C/EBPβ enh-/-_H3K27ac_ChIPseq


title: mouse whole lung at PND1_Pool1


title: mouse whole lung at PND1_Batch2


title: HepG2_C/EBPβ enh-/-_BRD4_ChIPseq


title: E16-1

description:
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_E16.5_1


title: HepG2_WT_C/EBPB_ChIPseq


title: HepG2_WT_H3K27ac_ChIPseq


title: MuRF1 Tg+ I/R above LAD_02

status: Public on Jan 05 2019

city: Chapel Hill

first: Monte

middle: Shaw

last: Willis

state: NC

address: 103 Mason Farm Road, MBRB 2340B

department: Pathology & Laboratory Medicine

institute: University of North Carolina

description: Biological replicate 2 of 3

hyb_protocol: Cy-5 labeled cRNA was co-hybridized to Agilent 014868 Whole Mouse Genome Microarrays with equimolar amounts of Cy-3 labeled whole mouse reference RNA-derived cRNA. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner and processed using Agilent FeatureExtractor 9.5.3.1.

data_processing: Data were uploaded into Genespring 12.4 using LOWESS normalized, background subtracted data obtained from processed Red signal/processed Green signal.

source_name: murine heart labeled with Cyanine-5 (red).

label_protocol: 50 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

extract_protocol: Total RNA extracted using Qiagen All-Prep kit following manufacturer's instructions

tag: tissue type

value: Cardiac tissue

value: MuRF1 Tg+

tag: surgery

value: Cardiac ischemia reperfusion injury

tag: location

value: above left anterior descending artery ligation site

value: 12-16 weeks

source_name: Total RNA from pooled whole mouse neonates (day 1)

value: postnatal Day 1

value: whole pup


title: MuRF1 Tg+ I/R below LAD_02

description: Biological replicate 2 of 3

value: below left anterior descending artery ligation site


title: MuRF1 Tg+ I/R below LAD_03

description: Biological replicate 3 of 3


title: Wildtype I/R below LAD_02

description: Biological replicate 2 of 3

value: Wild-type


title: Wildtype I/R above LAD_03

description: Biological replicate 3 of 3


title: Wildtype I/R above LAD_01

description: Biological replicate 1 of 3


title: MuRF1 Tg+ sham below_02

description: Biological replicate 2 of 3

value: Sham operation


title: Wildtype sham below_03

description: Biological replicate 3 of 3


title: MuRF1 Tg+ I/R below LAD_01

description: Biological replicate 1 of 3


title: MuRF1 Tg+ sham below_03

description: Biological replicate 3 of 3


title: MuRF1 Tg+ sham above_01

description: Biological replicate 1 of 3


title: Wildtype sham above_03

description: Biological replicate 3 of 3


title: MuRF1 Tg+ sham below_01

description: Biological replicate 1 of 3


title: MuRF1 Tg+ sham above_03

description: Biological replicate 3 of 3


title: Wildtype sham below_01

description: Biological replicate 1 of 3


title: WholeBlood_CRC305A70751139_Day5 [US22502595_254890810140_S01_GE1_1105_Oct12_2_3]

description: Whole blood gene expression of participant on day

tag: participant

value: male

value: white

value: not hispanic or latino

value: STAMARIL

value: whole blood


title: MuRF1 Tg+ I/R above LAD_03

description: Biological replicate 3 of 3


title: Wildtype I/R below LAD_03

description: Biological replicate 3 of 3


title: Wildtype I/R below LAD_01

description: Biological replicate 1 of 3


title: MuRF1 Tg+ sham above_02

description: Biological replicate 2 of 3


title: WholeBlood_CRC305A70751139_Day4 [US22502595_254890810140_S01_GE1_1105_Oct12_2_2]

tag: gender


title: WholeBlood_CRC305A70751139_Day28 [US22502595_254890810141_S01_GE1_1105_Oct12_1_3]

tag: age


title: Wildtype sham above_01

description: Biological replicate 1 of 3


title: Wildtype sham below_02

description: Biological replicate 2 of 3


title: MuRF1 Tg+ I/R above LAD_01

description: Biological replicate 1 of 3


title: WholeBlood_CRC305A70751139_Day14 [US22502595_254890810141_S01_GE1_1105_Oct12_1_1]

tag: race


title: Wildtype I/R above LAD_02

description: Biological replicate 2 of 3


title: Wildtype sham above_02

description: Biological replicate 2 of 3


title: WholeBlood_CRC305A70751139_Day7 [US22502595_254890810140_S01_GE1_1105_Oct12_2_4]

tag: ethnicity


title: WholeBlood_CRC305A70651120_Day-1 [US22502595_254890810141_S01_GE1_1105_Oct12_1_4]

tag: protocol


title: WholeBlood_CRC305A70751139_Day3 [US22502595_254890810140_S01_GE1_1105_Oct12_2_1]

tag: treatment


title: WholeBlood_CRC305A70741114_Day21 [US22502595_254890810139_S01_GE1_1105_Oct12_2_1]

value: female

tag: day


title: WholeBlood_CRC305A70741114_Day7 [US22502595_254890810139_S01_GE1_1105_Oct12_1_3]

tag: tissue


title: WholeBlood_CRC305A70751139_Day1 [US22502595_254890810140_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A70751139_Day-1 [US22502595_254890810140_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A70751139_Day0 [US22502595_254890810140_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A70741114_Day5 [US22502595_254890810139_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7069148_Day7 [US22502595_254890810137_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7069148_Day21 [US22502595_254890810138_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7069148_Day28 [US22502595_254890810138_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A70741114_Day-1 [US22502595_254890810138_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A70751139_Day2 [US22502595_254890810140_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7069148_Day5 [US22502595_254890810137_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A70741114_Day14 [US22502595_254890810139_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A70741114_Day0 [US22502595_254890810138_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7069148_Day0 [US22502595_254890810137_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A70741114_Day1 [US22502595_254890810138_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A70741114_Day28 [US22502595_254890810139_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7069148_Day3 [US22502595_254890810137_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7069148_Day14 [US22502595_254890810138_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A70741114_Day4 [US22502595_254890810139_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7069148_Day1 [US22502595_254890810137_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7068147_Day21 [US22502595_254890810136_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7069148_Day2 [US22502595_254890810137_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7068147_Day14 [US22502595_254890810136_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7068147_Day28 [US22502595_254890810136_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7069148_Day4 [US22502595_254890810137_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7068147_Day5 [US22502595_254890810136_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7068147_Day3 [US22502595_254890810135_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7069148_Day-1 [US22502595_254890810137_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7068147_Day1 [US22502595_254890810135_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7068147_Day7 [US22502595_254890810136_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7068147_Day2 [US22502595_254890810135_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7061136_Day4 [US22502595_254890810133_S01_GE1_1105_Oct12_1_1]

value: asian


title: WholeBlood_CRC305A7068147_Day4 [US22502595_254890810136_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A70741114_Day2 [US22502595_254890810138_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7063140_Day-1 [US22502595_254890810134_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7061136_Day2 [US22502595_254890810132_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7063140_Day0 [US22502595_254890810134_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7063140_Day7 [US22502595_254890810134_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7063140_Day2 [US22502595_254890810134_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7063140_Day21 [US22502595_254890810135_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7061136_Day14 [US22502595_254890810133_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7063140_Day1 [US22502595_254890810134_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7061136_Day0 [US22502595_254890810132_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7063140_Day28 [US22502595_254890810135_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7061136_Day28 [US22502595_254890810133_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7063140_Day5 [US22502595_254890810134_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7063140_Day3 [US22502595_254890810134_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7061136_Day21 [US22502595_254890810133_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7061136_Day5 [US22502595_254890810133_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7061136_Day-1 [US22502595_254890810132_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7060135_Day28 [US22502595_254890810132_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7061136_Day1 [US22502595_254890810132_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7061136_Day7 [US22502595_254890810133_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7063140_Day4 [US22502595_254890810134_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7063140_Day14 [US22502595_254890810135_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7068147_Day-1 [US22502595_254890810135_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7061136_Day3 [US22502595_254890810132_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7060135_Day21 [US22502595_254890810132_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A70741114_Day3 [US22502595_254890810138_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7060135_Day14 [US22502595_254890810132_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7057145_Day21 [US22502595_254890810130_S01_GE1_1105_Oct12_2_1]

value: other


title: WholeBlood_CRC305A7060135_Day7 [US22502595_254890810131_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7057145_Day28 [US22502595_254890810130_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7057145_Day14 [US22502595_254890810130_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7060135_Day4 [US22502595_254890810131_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7058146_Day28 [US22502595_254890810129_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7057145_Day3 [US22502595_254890810129_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7057145_Day4 [US22502595_254890810130_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7060135_Day3 [US22502595_254890810131_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7057145_Day2 [US22502595_254890810129_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7060135_Day1 [US22502595_254890810131_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7060135_Day5 [US22502595_254890810131_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7058146_Day5 [US22502595_254890810128_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7058146_Day1 [US22502595_254890810128_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7057145_Day0 [US22502595_254890810129_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7058146_Day14 [US22502595_254890810129_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7058146_Day7 [US22502595_254890810128_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7057145_Day-1 [US22502595_254890810129_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7058146_Day21 [US22502595_254890810129_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7057145_Day7 [US22502595_254890810130_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7060135_Day2 [US22502595_254890810131_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7060135_Day0 [US22502595_254890810131_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7060135_Day-1 [US22502595_254890810131_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7058146_Day3 [US22502595_254890810128_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7058146_Day2 [US22502595_254890810128_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7058146_Day4 [US22502595_254890810128_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7055141_Day14 [US22502595_254890810127_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7055141_Day5 [US22502595_254890810127_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7068147_Day0 [US22502595_254890810135_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7055141_Day7 [US22502595_254890810127_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7044119_Day21 [US22502595_254890810124_S01_GE1_1105_Oct12_2_1]

value: not reported


title: WholeBlood_CRC305A7055141_Day4 [US22502595_254890810127_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7044119_Day28 [US22502595_254890810124_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7058146_Day0 [US22502595_254890810128_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7058146_Day-1 [US22502595_254890810128_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7055141_Day21 [US22502595_254890810127_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7048125_Day-1 [US22502595_254890810125_S01_GE1_1105_Oct12_1_1]

value: VARILRIX


title: WholeBlood_CRC305A7055141_Day2 [US22502595_254890810126_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7055141_Day1 [US22502595_254890810126_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7048125_Day28 [US22502595_254890810126_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7055141_Day-1 [US22502595_254890810126_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7055141_Day3 [US22502595_254890810126_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7055141_Day0 [US22502595_254890810126_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7048125_Day21 [US22502595_254890810126_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7044119_Day14 [US22502595_254890810124_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7048125_Day7 [US22502595_254890810125_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7048125_Day3 [US22502595_254890810125_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7048125_Day1 [US22502595_254890810125_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7048125_Day14 [US22502595_254890810126_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7048125_Day2 [US22502595_254890810125_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7048125_Day5 [US22502595_254890810125_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7048125_Day0 [US22502595_254890810125_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7057145_Day1 [US22502595_254890810129_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7044119_Day7 [US22502595_254890810124_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7044119_Day3 [US22502595_254890810123_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7044119_Day2 [US22502595_254890810123_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7050121_Day21 [US22502595_254890810121_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7051122_Day1 [US22502595_254890810122_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7051122_Day21 [US22502595_254890810123_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7051122_Day3 [US22502595_254890810122_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7044119_Day5 [US22502595_254890810124_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7044119_Day-1 [US22502595_254890810123_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7051122_Day28 [US22502595_254890810123_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7044119_Day0 [US22502595_254890810123_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7050121_Day3 [US22502595_254890810120_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7044119_Day1 [US22502595_254890810123_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7051122_Day7 [US22502595_254890810122_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7050121_Day1 [US22502595_254890810120_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7051122_Day0 [US22502595_254890810122_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7051122_Day-1 [US22502595_254890810122_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7051122_Day14 [US22502595_254890810123_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7050121_Day5 [US22502595_254890810121_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7050121_Day28 [US22502595_254890810121_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7050121_Day2 [US22502595_254890810120_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7051122_Day5 [US22502595_254890810122_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7050121_Day7 [US22502595_254890810121_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7051122_Day2 [US22502595_254890810122_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7050121_Day0 [US22502595_254890810120_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7048125_Day4 [US22502595_254890810125_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7050121_Day-1 [US22502595_254890810120_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7050121_Day4 [US22502595_254890810121_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7050121_Day14 [US22502595_254890810121_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7049138_Day21 [US22502595_254890810120_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7049138_Day28 [US22502595_254890810120_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7049138_Day7 [US22502595_254890810119_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7049138_Day4 [US22502595_254890810119_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7055141_Day28 [US22502595_254890810127_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7049138_Day5 [US22502595_254890810119_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7049138_Day0 [US22502595_254890810119_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7049138_Day14 [US22502595_254890810120_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7049138_Day3 [US22502595_254890810119_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7045137_Day5 [US22502595_254890810118_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7049138_Day2 [US22502595_254890810119_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7045137_Day14 [US22502595_254890810118_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7045137_Day21 [US22502595_254890810118_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7049138_Day1 [US22502595_254890810119_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7045137_Day3 [US22502595_254890810117_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7045137_Day28 [US22502595_254890810118_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7049138_Day-1 [US22502595_254890810119_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7045137_Day1 [US22502595_254890810117_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7045137_Day-1 [US22502595_254890810117_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7042134_Day21 [US22502595_254890810117_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7042134_Day28 [US22502595_254890810117_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7045137_Day0 [US22502595_254890810117_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7042134_Day3 [US22502595_254890810116_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7042134_Day14 [US22502595_254890810117_S01_GE1_1105_Oct12_1_1]


title: sham-day 3 [9-3-READs]

city: Augusta

first: Sang-Ho

last: Kwon

state: GA

address: 1460 Laney Walker Blvd  CB2820

department: Cellular biology and Anatomy

institute: Augusta University

data_processing:
small RNAs were sequenced and miRNAs were recognized using CAP-miRseq pipeline. Briefly, adaptor and primer sequences from the library were trimmed using Cutadapt, sequence reads were then aligned to the rat genome (version 5) using Bowtie and miRDeep2 mapper, gene-level count data were generated using HTSeq, and finally differential expression analysis were performed using EdgeR
Genome_build: rat genome version version 5
Supplementary_files_format_and_content: excel-output of EdgeR

organism: Rattus norvegicus

source_name: sham-day 3

extract_protocol:
Urine exosomes RNA purification kit (Norgen Biotek)
miRNA library kit

treatment_protocol: renal ischemia-reperfusion injury

tag: strain

value: Sprague Dawley

tag: animal id

tag: sample collection

value: day 3 post ischemia-reperfusion injury

tag: experimental group

value: sham (control)

value: urine (exosomes)

tag: molecule subtype

value: miRNA


title: sham-day 14 [9-14-READs]

source_name: sham-day 14

value: day 14 post ischemia-reperfusion injury


title: sham-day 7 [9-7-READs]

source_name: sham-day 7

value: day 7 post ischemia-reperfusion injury


title: sham-day 14 [6-14-READs]


title: sham-day 2 [9-2-READs]

source_name: sham-day 2

value: day 2 post ischemia-reperfusion injury


title: sham-day 7 [6-7-READs]


title: sham-day 3 [6-3-READs]


title: WholeBlood_CRC305A7042134_Day2 [US22502595_254890810116_S01_GE1_1105_Oct12_1_4]

value: male

value: white


title: sham-day 2 [6-2-READs]


title: WholeBlood_CRC305A7042134_Day4 [US22502595_254890810116_S01_GE1_1105_Oct12_2_2]

value: not hispanic or latino

value: STAMARIL


title: WholeBlood_CRC305A7042134_Day7 [US22502595_254890810116_S01_GE1_1105_Oct12_2_4]

value: whole blood


title: WholeBlood_CRC305A7045137_Day2 [US22502595_254890810117_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7042134_Day5 [US22502595_254890810116_S01_GE1_1105_Oct12_2_3]


title: sham-day 1 [6-1-READs]

source_name: sham-day 1

value: day 1 post ischemia-reperfusion injury


title: sham-day 14 [3-14-READs]


title: sham-day 7 [3-7-READs]


title: sham-day 1 [9-1-READs]


title: WholeBlood_CRC305A7042134_Day1 [US22502595_254890810116_S01_GE1_1105_Oct12_1_3]


title: sham-day 3 [3-3-READs]


title: WholeBlood_CRC305A7042134_Day-1 [US22502595_254890810116_S01_GE1_1105_Oct12_1_1]


title: sham-day 1 [3-1-READs]


title: sham-day 2 [3-2-READs]


title: WholeBlood_CRC305A7037116_Day28 [US22502595_254890810115_S01_GE1_1105_Oct12_2_2]

value: female


title: WholeBlood_CRC305A7037116_Day7 [US22502595_254890810115_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7037116_Day21 [US22502595_254890810115_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7037116_Day5 [US22502595_254890810115_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7045137_Day4 [US22502595_254890810118_S01_GE1_1105_Oct12_1_1]


title: renal IRI-day14 [2-14-READs]

source_name: renal IRI-day14

value: renal ischemia-reperfusion injury


title: renal IRI-day7 [2-7-READs]

source_name: renal IRI-day7


title: renal IRI-day1 [2-1-READs]

source_name: renal IRI-day1


title: renal IRI-day2 [2-2-READs]

source_name: renal IRI-day2


title: renal IRI-day14 [13-14-READs]


title: renal IRI-day7 [13-7-READs]


title: WholeBlood_CRC305A7037116_Day3 [US22502595_254890810114_S01_GE1_1105_Oct12_2_4]


title: renal IRI-day3 [2-3-READs]

source_name: renal IRI-day3


title: renal IRI-day3 [13-3-READs]


title: WholeBlood_CRC305A7037116_Day1 [US22502595_254890810114_S01_GE1_1105_Oct12_2_2]

source_name: Peripheral Blood, PaxGene


title: renal IRI-day1 [13-1-READs]


title: WholeBlood_CRC305A7037116_Day2 [US22502595_254890810114_S01_GE1_1105_Oct12_2_3]


title: renal IRI-day7 [1-7-READs]


title: renal IRI-day2 [13-2-READs]


title: renal IRI-day14 [1-14-READs]


title: renal IRI-day3 [1-3-READs]


title: WholeBlood_CRC305A7037116_Day0 [US22502595_254890810114_S01_GE1_1105_Oct12_2_1]


title: renal IRI-day2 [1-2-READs]


title: WholeBlood_CRC305A7041133_Day5 [US22502595_254890810113_S01_GE1_1105_Oct12_2_3]

value: asian


title: WholeBlood_CRC305A7041133_Day14 [US22502595_254890810114_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7037116_Day-1 [US22502595_254890810114_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7041133_Day3 [US22502595_254890810113_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7041133_Day21 [US22502595_254890810114_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7042134_Day0 [US22502595_254890810116_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7041133_Day1 [US22502595_254890810113_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7041133_Day28 [US22502595_254890810114_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7041133_Day4 [US22502595_254890810113_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7041133_Day0 [US22502595_254890810113_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7041133_Day2 [US22502595_254890810113_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7041133_Day-1 [US22502595_254890810113_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7041133_Day7 [US22502595_254890810113_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7040131_Day28 [US22502595_254890810112_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7040131_Day21 [US22502595_254890810112_S01_GE1_1105_Oct12_2_1]


title: 18187_50_DE_Liver_Rep_5

city: Morrisville

first: June

last: Dunnick

address: 530 Davis Dr.

department: NIEHS

institute: NIH

hyb_protocol: Labeled aRNA was fragmented and subsequently hybridized to the Affymetrix Rat Genome 230 2.0 Array (Cat #: 900505; 31,099 probe sets) using an Affymetrix GeneChip® Hybridization Oven 645.

scan_protocol: After washing and staining, arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G, and the raw microarray data (.CEL files) were acquired using Affymetrix GeneChip® Command Console® Software.

data_processing: Probe set intensities from raw microarray data (CEL files from Affymetrix Rat Genome 230 2.0 Arrays) were normalized by applying the Robust Multi-array Average (RMA) algorithm from the genomics analysis tool, GeneSpring GX 12.6 (Agilent Technology, Foster City, CA).

label: Biotin

label_protocol: Total RNA (100 ng), isolated from each liver sample, was used to synthesize single-stranded DNA, which was subsequently converted into a double-stranded complementary DNA (cDNA) template for transcription. An in vitro transcription (IVT) reaction, which incorporates biotinylated ribonucleotide analogs, then was used to create labeled amplified RNA (aRNA).

growth_protocol: Wistar Han rat (Crl: WI (Han)) ragts were exposed in utero and with postnatal exposure until PND22 by daily oral gavage

extract_protocol: Three pieces (3-mm cubes) of left liver lobe were dissected and flash frozen. The frozen liver tissues were submerged in 10 volumes of prechilled RNAlater®-ICE (Life Technologies, Carlsbad, CA) and stored at −20°C ± 10°C for a minimum of 16 hours. The tissues were removed from the RNAlater®-ICE and weighed. Each liver tissue sample, weighing between 21 and 30 mg, was added to lysis buffer and homogenized using plastic disposable pestles (Fisher Scientific, Pittsburgh, PA). Following homogenization, samples were stored at −70°C ± 10°C until RNA was isolated. Samples were thawed and centrifuged. RNA was extracted from the supernatant, subjected to DNase digestion, and isolated using the Qiagen RNeasy Mini Kit (Cat #: 74104; Qiagen, Valencia, CA).

treatment_protocol: Wistar Han rats were assigned to one of four dose groups, each containing five rats. The rats in each dose group then were administered DE-71 or BDE-47  by gavage at a dose level of 0, 0.1, 15, or 50 mg/kg body weight.

value: Wistar Han rat (Crl:WI (Han))

tag: agent

tag: dose

value: 50 mg/kg

tag: route

value: Oral Gavage

value: Liver


title: renal IRI-day1 [1-1-READs]

value: Sprague Dawley

value: urine (exosomes)

value: miRNA


title: WholeBlood_CRC305A7045137_Day7 [US22502595_254890810118_S01_GE1_1105_Oct12_1_3]

tag: participant

value: VARILRIX


title: 18184_50_DE_Liver_Rep_2


title: WholeBlood_CRC305A7040131_Day3 [US22502595_254890810111_S01_GE1_1105_Oct12_2_4]

tag: gender

value: male


title: WholeBlood_CRC305A7040131_Day14 [US22502595_254890810112_S01_GE1_1105_Oct12_1_4]

tag: age

value: white


title: 18186_50_DE_Liver_Rep_4


title: WholeBlood_CRC305A7040131_Day5 [US22502595_254890810112_S01_GE1_1105_Oct12_1_2]

tag: race

value: not hispanic or latino


title: 18185_50_DE_Liver_Rep_3


title: 18180_15_DE_Liver_Rep_3

value: 15 mg/kg


title: 18181_15_DE_Liver_Rep_4


title: 18182_15_DE_Liver_Rep_5


title: WholeBlood_CRC305A7040131_Day1 [US22502595_254890810111_S01_GE1_1105_Oct12_2_2]

tag: ethnicity

value: STAMARIL

value: whole blood


title: WholeBlood_CRC305A7040131_Day7 [US22502595_254890810112_S01_GE1_1105_Oct12_1_3]

tag: protocol


title: WholeBlood_CRC305A7040131_Day4 [US22502595_254890810112_S01_GE1_1105_Oct12_1_1]

tag: treatment


title: 18177_0.1_DE_Liver_Rep_5

value: 0.1 mg/kg


title: 18176_0.1_DE_Liver_Rep_4


title: WholeBlood_CRC305A7040131_Day2 [US22502595_254890810111_S01_GE1_1105_Oct12_2_3]

tag: day


title: WholeBlood_CRC305A7039128_Day14 [US22502595_254890810111_S01_GE1_1105_Oct12_1_1]

tag: tissue


title: WholeBlood_CRC305A7040131_Day-1 [US22502595_254890810111_S01_GE1_1105_Oct12_1_4]


title: 18179_15_DE_Liver_Rep_2

tag: strain


title: WholeBlood_CRC305A7039128_Day7 [US22502595_254890810110_S01_GE1_1105_Oct12_2_4]


title: 18175_0.1_DE_Liver_Rep_3


title: 18178_15_DE_Liver_Rep_1


title: 18173_0.1_DE_Liver_Rep_1


title: 18174_0.1_DE_Liver_Rep_2


title: WholeBlood_CRC305A7040131_Day0 [US22502595_254890810111_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7039128_Day5 [US22502595_254890810110_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7039128_Day21 [US22502595_254890810111_S01_GE1_1105_Oct12_1_2]


title: 18172_0_DE_Liver_Rep_5

value: 0 mg/kg


title: WholeBlood_CRC305A7039128_Day3 [US22502595_254890810110_S01_GE1_1105_Oct12_2_1]


title: 18170_0_DE_Liver_Rep_3


title: 18167_50_BDE_Liver_Rep_5


title: 18169_0_DE_Liver_Rep_2


title: WholeBlood_CRC305A7039128_Day2 [US22502595_254890810110_S01_GE1_1105_Oct12_1_4]


title: 18171_0_DE_Liver_Rep_4


title: 18166_50_BDE_Liver_Rep_4


title: 18168_0_DE_Liver_Rep_1


title: WholeBlood_CRC305A7039128_Day1 [US22502595_254890810110_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7039128_Day-1 [US22502595_254890810110_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7038126_Day21 [US22502595_254890810109_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7039128_Day0 [US22502595_254890810110_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7038126_Day28 [US22502595_254890810109_S01_GE1_1105_Oct12_2_2]


title: 18165_50_BDE_Liver_Rep_3


title: 18163_50_BDE_Liver_Rep_1


title: 18162_15_BDE_Liver_Rep_5


title: WholeBlood_CRC305A7037116_Day4 [US22502595_254890810115_S01_GE1_1105_Oct12_1_1]

value: female


title: 18164_50_BDE_Liver_Rep_2

value: Wistar Han rat (Crl:WI (Han))


title: WholeBlood_CRC305A7038126_Day7 [US22502595_254890810109_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7038126_Day4 [US22502595_254890810109_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7038126_Day2 [US22502595_254890810108_S01_GE1_1105_Oct12_2_3]


title: 18161_15_BDE_Liver_Rep_4


title: WholeBlood_CRC305A7038126_Day14 [US22502595_254890810109_S01_GE1_1105_Oct12_1_4]


title: 18158_15_BDE_Liver_Rep_1


title: WholeBlood_CRC305A7038126_Day0 [US22502595_254890810108_S01_GE1_1105_Oct12_2_1]


title: 18155_0.1_BDE_Liver_Rep_3


title: WholeBlood_CRC305A7038126_Day3 [US22502595_254890810108_S01_GE1_1105_Oct12_2_4]


title: 18154_0.1_BDE_Liver_Rep_2


title: WholeBlood_CRC305A7033124_Day28 [US22502595_254890810108_S01_GE1_1105_Oct12_1_3]

value: asian


title: WholeBlood_CRC305A7038126_Day1 [US22502595_254890810108_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7033124_Day14 [US22502595_254890810108_S01_GE1_1105_Oct12_1_1]


title: 18152_0_BDE_Liver_Rep_5

value: Oral Gavage


title: 18157_0.1_BDE_Liver_Rep_5

value: Liver


title: 18156_0.1_BDE_Liver_Rep_4


title: WholeBlood_CRC305A7038126_Day5 [US22502595_254890810109_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7038126_Day-1 [US22502595_254890810108_S01_GE1_1105_Oct12_1_4]


title: 18153_0.1_BDE_Liver_Rep_1


title: WholeBlood_CRC305A7033124_Day5 [US22502595_254890810107_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7033124_Day21 [US22502595_254890810108_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7033124_Day7 [US22502595_254890810107_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7037116_Day14 [US22502595_254890810115_S01_GE1_1105_Oct12_1_4]


title: 18148_0_BDE_Liver_Rep_1


title: 18149_0_BDE_Liver_Rep_2


title: WholeBlood_CRC305A7033124_Day1 [US22502595_254890810107_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7033124_Day4 [US22502595_254890810107_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7033124_Day3 [US22502595_254890810107_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7033124_Day2 [US22502595_254890810107_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7033124_Day-1 [US22502595_254890810107_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7033124_Day0 [US22502595_254890810107_S01_GE1_1105_Oct12_1_2]


title: 18147_250_PCB_Liver_Rep_5

value: 250 mg/kg


title: WholeBlood_CRC305A7032123_Day28 [US22502595_254890810106_S01_GE1_1105_Oct12_2_2]


title: 18143_250_PCB_Liver_Rep_1


title: 18145_250_PCB_Liver_Rep_3


title: 18141_50_PCB_Liver_Rep_4

value: 50 mg/kg


title: WholeBlood_CRC305A7032123_Day14 [US22502595_254890810106_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7032123_Day21 [US22502595_254890810106_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7032123_Day7 [US22502595_254890810106_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7032123_Day5 [US22502595_254890810106_S01_GE1_1105_Oct12_1_2]


title: 18140_50_PCB_Liver_Rep_3


title: 18151_0_BDE_Liver_Rep_4


title: 18146_250_PCB_Liver_Rep_4


title: WholeBlood_CRC305A7032123_Day3 [US22502595_254890810105_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7039128_Day28 [US22502595_254890810111_S01_GE1_1105_Oct12_1_3]


title: 18142_50_PCB_Liver_Rep_5


title: 18139_50_PCB_Liver_Rep_2


title: WholeBlood_CRC305A7032123_Day2 [US22502595_254890810105_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7032123_Day1 [US22502595_254890810105_S01_GE1_1105_Oct12_2_2]


title: 18137_10_PCB_Liver_Rep_5

value: 10 mg/kg


title: 18138_50_PCB_Liver_Rep_1


title: 18134_10_PCB_Liver_Rep_2


title: 18150_0_BDE_Liver_Rep_3


title: WholeBlood_CRC305A7032123_Day4 [US22502595_254890810106_S01_GE1_1105_Oct12_1_1]

value: VARILRIX


title: 18136_10_PCB_Liver_Rep_4


title: WholeBlood_CRC305A7032123_Day0 [US22502595_254890810105_S01_GE1_1105_Oct12_2_1]

value: male


title: WholeBlood_CRC305A7030111_Day28 [US22502595_254890810105_S01_GE1_1105_Oct12_1_3]

value: white


title: 18133_10_PCB_Liver_Rep_1


title: 18144_250_PCB_Liver_Rep_2


title: WholeBlood_CRC305A7032123_Day-1 [US22502595_254890810105_S01_GE1_1105_Oct12_1_4]

value: not hispanic or latino


title: 18132_0_PCB_Liver_Rep_5


title: 18135_10_PCB_Liver_Rep_3


title: WholeBlood_CRC305A7030111_Day14 [US22502595_254890810105_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7030111_Day21 [US22502595_254890810105_S01_GE1_1105_Oct12_1_2]


title: 18160_15_BDE_Liver_Rep_3

value: 15 mg/kg


title: WholeBlood_CRC305A7030111_Day7 [US22502595_254890810104_S01_GE1_1105_Oct12_2_4]


title: 18128_0_PCB_Liver_Rep_1


title: 18122_5_PB_Liver_Rep_5

value: Phenobarbital

value: 5 mg/kg


title: 18129_0_PCB_Liver_Rep_2


title: 18130_0_PCB_Liver_Rep_3


title: 18159_15_BDE_Liver_Rep_2


title: 18126_45_PB_Liver_Rep_4

value: 45 mg/kg


title: WholeBlood_CRC305A7030111_Day4 [US22502595_254890810104_S01_GE1_1105_Oct12_2_2]

value: whole blood


title: 18127_45_PB_Liver_Rep_5


title: WholeBlood_CRC305A7030111_Day5 [US22502595_254890810104_S01_GE1_1105_Oct12_2_3]

value: female


title: 18125_45_PB_Liver_Rep_3

value: Wistar Han rat (Crl:WI (Han))


title: 18123_45_PB_Liver_Rep_1


title: WholeBlood_CRC305A7030111_Day1 [US22502595_254890810104_S01_GE1_1105_Oct12_1_3]


title: 18124_45_PB_Liver_Rep_2


title: WholeBlood_CRC305A7030111_Day-1 [US22502595_254890810104_S01_GE1_1105_Oct12_1_1]


title: 18121_5_PB_Liver_Rep_4


title: 18120_5_PB_Liver_Rep_3


title: WholeBlood_CRC305A7030111_Day2 [US22502595_254890810104_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7029118_Day7 [US22502595_254890810103_S01_GE1_1105_Oct12_1_3]


title: 18119_5_PB_Liver_Rep_2


title: 18131_0_PCB_Liver_Rep_4

value: 0 mg/kg


title: 18118_5_PB_Liver_Rep_1

value: Oral Gavage


title: WholeBlood_CRC305A7029118_Day4 [US22502595_254890810103_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7030111_Day0 [US22502595_254890810104_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7029118_Day28 [US22502595_254890810103_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7029118_Day14 [US22502595_254890810103_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7029118_Day5 [US22502595_254890810103_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7029118_Day21 [US22502595_254890810103_S01_GE1_1105_Oct12_2_1]


title: 18116_0_PB_Liver_Rep_4

value: Liver


title: 18113_0_PB_Liver_Rep_1


title: 18115_0_PB_Liver_Rep_3


title: NCH441 PF

city: Heidelberg

first: Emma

last: Phillips

address: In Neuenheimer Feld 580

department: Brain Tumor Translational Targets

country: Germany

institute: DKFZ

hyb_protocol: The Quick Amp labelling Kit (Agilent Technologies) was used. Briefly, RNA was fragmented by incubation at 60°C for 30 minutes and 2× Hi-RPM Hybridization Buffer was added. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.1).
Agilent Feature Extraction Software (v9.1) was used for background subtraction and LOWESS normalization.

label: biotin

source_name: Transduction of NCH441 GSCs with shPFKFB4 for 4 days

label_protocol: The Quick Amp labelling Kit (Agilent Technologies) was used. Briefly, 200 ng of total RNA were primed with 0.8 µl of 100 µM T7 DNA primer at 65°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of T7 RNA plymerase blend, and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3/Cy5-label

growth_protocol: The GSC lines NCH421k, NCH644 and NCH441 were derived from primary GBM patients who underwent surgical resection according to the research proposals approved by the Institutional Review Board at the Medical Faculty of Heidelberg. Tissues were enzymatically dissociated and cells were cultivated as floating neurospheres in serum-free DMEM/F-12 medium, supplemented with 20 % BIT-admixture (Pelo Biotech, Planegg, Germany) and basal fibroblast growth factor (Biomol, Hamburg, Germany) and epidermal growth factor (Life Technologies, Hamburg, Germany) at 20 ng/ml each. Genotypic and phenotypic studies have been carried out in previous investigations. Passaging and seeding was carried out by dissociation with accutase (Sigma-Aldrich, Munich, Germany).

extract_protocol: RNA was extracted from cells using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol and examined for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: GSCs were seeded at a density of 100000 cells per ml and transduced with a multiplicity of infection (MOI) of 5. plko.1 TurboGFP containing lentivirus was used to estimate transduction efficiency via FACS. Experiments were discarded if <70 % of cells were green.

tag: cell line

tag: cell type

value: GSCs

tag: time

value: 4 days after transduction


title: 18117_0_PB_Liver_Rep_5


title: SH-SY5Y_SETD1A_siRNA_s18790_replicate_3

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

institute: Cardiff University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina protocol

data_processing: Sample probe profile were exported from GenomeStudio. Data were then imported into lumi (bioconductor) and Variance Stabilizing transformation applied, Robust Spline Normalized and log2 transformed. NB: samples Control_1.4 and siRNA_2.2 were romeved as outliers in downstream analysis

source_name: SH-SY5Y neuroblastoma cell line

label_protocol: Biotinylated cDNA were prepared using the Custom Illumina® TotalPrep™-96 Kit (Ambion)

growth_protocol: Cells were maintained in DMEM/F12 (Gibco) containing glutamine and 10% fetal bovine serum.

extract_protocol: Standard Trizol, RNA dissolved in water

treatment_protocol: Transfection of siRNA, either control or two separate siRNAs targeting SETD1A (s18789 or s18790) using the Lipofectamine RNAi Max. Cells were harvested using acutase 96 hours after transfection

tag: genotype/variation

value: SETD1A siRNA


title: WholeBlood_CRC305A7029118_Day2 [US22502595_254890810102_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7029118_Day3 [US22502595_254890810102_S01_GE1_1105_Oct12_2_4]


title: SH-SY5Y_SETD1A_siRNA_s18790_replicate_1


title: NCH644 NT

source_name: Transduction of NCH644 GSCs with shNT for 4 days

value: shNT


title: 18114_0_PB_Liver_Rep_2

tag: agent


title: SH-SY5Y_SETD1A_siRNA_s18790_replicate_4


title: SH-SY5Y_SETD1A_siRNA_s18790_replicate_2


title: NCH441 NT

source_name: Transduction of NCH441 GSCs with shNT for 4 days


title: NCH421k PF

source_name: Transduction of NCH421k GSCs with shPFKFB4 for 4 days


title: WholeBlood_CRC305A7028110_Day5 [US22502595_254890810101_S01_GE1_1105_Oct12_2_3]

value: asian

value: STAMARIL


title: NCH421k NT

source_name: Transduction of NCH421k GSCs with shNT for 4 days


title: NCH644 PF

source_name: Transduction of NCH644 GSCs with shPFKFB4 for 4 days


title: WholeBlood_CRC305A7028110_Day14 [US22502595_254890810102_S01_GE1_1105_Oct12_1_1]

value: not hispanic or latino


title: WholeBlood_CRC305A7028110_Day7 [US22502595_254890810101_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7028110_Day28 [US22502595_254890810102_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7029118_Day-1 [US22502595_254890810102_S01_GE1_1105_Oct12_1_4]

value: male

value: white


title: WholeBlood_CRC305A7028110_Day3 [US22502595_254890810101_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7028110_Day1 [US22502595_254890810101_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7029118_Day1 [US22502595_254890810102_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7028110_Day4 [US22502595_254890810101_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7028110_Day2 [US22502595_254890810101_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7028110_Day21 [US22502595_254890810102_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7029118_Day0 [US22502595_254890810102_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7030111_Day3 [US22502595_254890810104_S01_GE1_1105_Oct12_2_1]


title: SH-SY5Y_SETD1A_siRNA_s18789_replicate_3


title: SH-SY5Y_control_siRNA_replicate_4

value: control siRNA


title: SH-SY5Y_SETD1A_siRNA_s18789_replicate_2


title: SH-SY5Y_SETD1A_siRNA_s18789_replicate_4


title: SH-SY5Y_control_siRNA_replicate_2


title: SH-SY5Y_SETD1A_siRNA_s18789_replicate_1


title: SH-SY5Y_control_siRNA_replicate_1


title: WholeBlood_CRC305A7028110_Day-1 [US22502595_254890810101_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7026117_Day28 [US22502595_254890810100_S01_GE1_1105_Oct12_2_2]

value: VARILRIX


title: WholeBlood_CRC305A7026117_Day3 [US22502595_254890810099_S01_GE1_1105_Oct12_2_4]

value: whole blood


title: Breasttumour_PatientX416_Timepoint1

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

hyb_protocol: Labeled cDNA was hybridized to bead arrays according to the standard protocol for NuGEN amplified samples.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2 tranformed, normalised using quantile normalisation, and detectiona and probe quality filtered using lumi and illuminaHumanv4.db in R

source_name: breast tumour

label_protocol: RNA was then biotinylated using the Encore Biotin IL Module (NuGEN) and purified using minElute Reaction Cleanup Kit (Qiagen).

extract_protocol: RNA was extracted with Trizol reagent, followed by column-based purification (miRNeasy mini kit, Qiagen) in accordance with the protocol provided. Quality control was performed with Agilent Bioanalyser. RNA was then reverse transcribed and amplified using the Ovation FFPE WTA System (NuGEN), followed by purification using the Qiaquick PCR Purification Kit (Qiagen).

value: breast tumour


title: Breasttumour_PatientX416_Timepoint2


title: WholeBlood_CRC305A7028110_Day0 [US22502595_254890810101_S01_GE1_1105_Oct12_1_2]

value: female


title: WholeBlood_CRC305A7026117_Day14 [US22502595_254890810100_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7026117_Day-1 [US22502595_254890810099_S01_GE1_1105_Oct12_1_4]


title: Breasttumour_PatientX50_Timepoint2


title: WholeBlood_CRC305A7026117_Day7 [US22502595_254890810100_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7026117_Day1 [US22502595_254890810099_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7026117_Day4 [US22502595_254890810100_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7026117_Day5 [US22502595_254890810100_S01_GE1_1105_Oct12_1_2]


title: WholeBlood_CRC305A7026117_Day2 [US22502595_254890810099_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7023108_Day21 [US22502595_254890810099_S01_GE1_1105_Oct12_1_2]


title: Breasttumour_PatientX50_Timepoint1


title: clonal iPSC line with 71 CAG repeats_719-5

city: Poznan

first: Maciej

last: Figiel

address: Noskowskiego 12/14

department: Department of Molecular Neurobiology

country: Poland

institute: Institute of Bioorganic Chemistry Polish Academy of Sciences

data_processing:
NGSQCToolkit (v 2.2.3) was used to generate quality metrics for assessment of FASTQ  input files
FASTQ files were aligned to the GRCh38.p10 reference genome using STAR (v 2.5.3a) with default parameters suggested by QoRTs (v 1.3.0) used for genes and exons hits count
Differential gene expression was calculated using the Bioconductor package DESeq2 (v 1.14.1). Prior to DESeq2 genes localized to X and Y chromosomes were removed from analysis.
After calculation of DE by DESeq2, the shrinkage of effect size was performed (function lfcShrink of DESeq2 package)
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: xls (statistical values for three comparison groups, HD vs. WT, HD71Q vs. WT, and HD109Q vs. WT)

source_name: induced pluripotent stem cells (iPSCs)

growth_protocol: Human iPSCs were cultured in chemically defined conditions in Essential 8 medium (Life Technologies) and grown on recombinant human vitronectin-coated surfaces (VTN-N, Life Technologies). Cells were passaged using gentle dissociation with 0.5 mM EDTA in PBS.

extract_protocol:
After medium removal, iPS cells were washed once with PBS and subsequently covered with 1 mL of RNAzol RT RNA Isolation Reagent (GeneCopoeia, Inc.), scraped and frozen in -80°C. Upon thaw, total RNA isolation was performed according to the manufacturer’s protocol with 75% ethanol, isopropanol, and RNase-free water. Isolated total RNA was then treated with TURBO DNase (ambion) and purified with QIAquick® Nucleotide Removal Kit (QIAGEN). Each reaction was performed in PCR probes and contained 10 μg of RNA sample, 10 x TURBO Buffer, RNaseOUT (Invitrogen), DNase TURBO and RNase-
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Huntington disease

tag: genotype

value: mutant (HD)

tag: number of cag repeats

tag: line number according to ninds human genetics resource center dna and cell line repository

tag: parental cell type

value: fibroblast

value: clonal iPSC line with 71 CAG repeats


title: clonal iPSC line with 109 CAG repeats_706-2

value: clonal iPSC line with 109 CAG repeats


title: clonal iPSC line with 109 CAG repeats_719-7


title: clonal iPSC line with 71 CAG repeats_719-6


title: clonal iPSC line with 109 CAG repeats_719-8


title: Breasttumour_PatientX413_Timepoint4


title: WholeBlood_CRC305A7023108_Day28 [US22502595_254890810099_S01_GE1_1105_Oct12_1_3]

tag: participant

tag: gender

tag: age

tag: race


title: WholeBlood_CRC305A7026117_Day21 [US22502595_254890810100_S01_GE1_1105_Oct12_2_1]

tag: ethnicity

tag: protocol

tag: treatment

tag: day


title: Breasttumour_PatientX413_Timepoint2

tag: tissue


title: Breasttumour_PatientX50_Timepoint4


title: Breasttumour_PatientX416_Timepoint4


title: control iPSC line_719-3

value: control

value: wild type (WT)

tag: cell line

value: control iPSC line


title: control iPSC line_706-1


title: control iPSC line_719-1


title: WholeBlood_CRC305A7023108_Day14 [US22502595_254890810099_S01_GE1_1105_Oct12_1_1]

value: STAMARIL


title: clonal iPSC line with 71 CAG repeats_719-4


title: WholeBlood_CRC305A7023108_Day7 [US22502595_254890810098_S01_GE1_1105_Oct12_2_4]

value: not hispanic or latino


title: Breasttumour_PatientX409_Timepoint2


title: Breasttumour_PatientX409_Timepoint4


title: Breasttumour_PatientX413_Timepoint1


title: SH-SY5Y_control_siRNA_replicate_3

tag: genotype/variation


title: Breasttumour_PatientX409_Timepoint1


title: WholeBlood_CRC305A7023108_Day4 [US22502595_254890810098_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7023108_Day3 [US22502595_254890810098_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7023108_Day1 [US22502595_254890810098_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7023108_Day2 [US22502595_254890810098_S01_GE1_1105_Oct12_1_4]


title: mPAC-Ad-Neurog3+shAtoh8-rep2

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description: mouse pancreatic duct (mPAC) cells overexpressing Neurogenin 3 infected with an adenovirus encoding for an Atonal Homolog 8-specific shRNA, biological replicate 2

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor on R language.

source_name: mouse pancreatic duct (mPAC) cells overexpressing Neurogenin3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mouse pancreatic duct mPAC L20 cells were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics as previously described (Proc Natl Acad Sci U S A, 2004. 101(36): p. 13245-50)

extract_protocol: Rneasy kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: For viral treatment, 250000 mPAC cells were seeded onto 6-well plates the day before infection. Adenovirus were added at a multiplicity of infection (moi) of 40 and incubated for 2 h at 37ºC in culture medium. Then, cells were cultured for an additional 44-46 h period.  Double infections were conducted using moi=40 for each individual adenovirus. Adenoviruses expressing shRNAs were added first for 4h, then removed and cells incubated for additional  1.5h with Ad.CMV.Neurog3. Adenovirus expressing a short hairpin specific for Math6 was generated by homologous recombination in HEK293 cells.  Control adenoviruses Ad-shControl were kindly provided by Dr. CB.Newgard (Duke University, NC, USA).

value: Atonal Homolog 8 shRNA

value: mPAC L20


title: Clock∆19/∆19 hippocampus baseline, biological rep 4

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

state: Ontario

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hydridized on Affymetrix GeneChip Mouse Gene 2.0 ST arrays, according to manufacturer's instructions. GeneChips were washed and stained on the Gene Atlas platform.

scan_protocol: GeneChips were scanned on the GeneAtlas platform.

data_processing: The data were analyzed with GeneSpring GX software v. 14.9 using default Affymetrix settings.

source_name: Clock∆19/∆19 baseline hippocampus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

growth_protocol: The mice were collected at 8 weeks of age (baseline and 64h post-MI surgery) and at 16 weeks of age (8 weeks post-MI surgery) at 7 hours after lights off.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: The brain regions (mPFC and hippocampus) were collected and snap frozen in liquid nitrogen and stored at -80C.

value: hippocampus

tag: Sex

value: male

value: baseline


title: WholeBlood_CRC305A7023108_Day0 [US22502595_254890810098_S01_GE1_1105_Oct12_1_2]

value: white

value: whole blood


title: WT hippocampus baseline, biological rep 1

source_name: WT baseline hippocampus

value: WT

tag: disease state


title: WT hippocampus baseline, biological rep 4

tag: genotype


title: mPAC-Ad-Neurog3+shAtoh8-rep3

description: mouse pancreatic duct (mPAC) cells overexpressing Neurogenin 3 infected with an adenovirus encoding for an Atonal Homolog 8-specific shRNA, biological replicate 3


title: mPAC-Ad-Neurog3+shControl-rep3

description: mouse pancreatic duct (mPAC) cells overexpressing Neurogenin 3 infected with an adenovirus encoding for an scrambled shRNA, biological replicate 3

value: Scramble (control)


title: Breasttumour_PatientX400_Timepoint2

value: breast tumour


title: WholeBlood_CRC305A7023108_Day5 [US22502595_254890810098_S01_GE1_1105_Oct12_2_3]

value: female


title: mPAC-Ad-Neurog3+shControl-rep1

description: mouse pancreatic duct (mPAC) cells overexpressing Neurogenin 3 infected with an adenovirus encoding for an scrambled shRNA, biological replicate 1


title: mPAC-Ad-Neurog3+shAtoh8-rep1

description: mouse pancreatic duct (mPAC) cells overexpressing Neurogenin 3 infected with an adenovirus encoding for an Atonal Homolog 8-specific shRNA, biological replicate 1


title: Breasttumour_PatientX400_Timepoint4


title: WholeBlood_CRC305A7017115_Day28 [US22502595_254890810097_S01_GE1_1105_Oct12_2_2]

value: asian

value: hispanic or latino


title: WholeBlood_CRC305A7023108_Day-1 [US22502595_254890810098_S01_GE1_1105_Oct12_1_1]


title: Clock∆19/∆19 hippocampus baseline, biological rep 2


title: WT hippocampus baseline, biological rep 3


title: WholeBlood_CRC305A7026117_Day0 [US22502595_254890810099_S01_GE1_1105_Oct12_2_1]

value: VARILRIX


title: mPAC-Ad-Neurog3+shControl-rep2

description: mouse pancreatic duct (mPAC) cells overexpressing Neurogenin 3 infected with an adenovirus encoding for an scrambled shRNA, biological replicate 2


title: Breasttumour_PatientX405_Timepoint4


title: Breasttumour_PatientX400_Timepoint1


title: Clock∆19/∆19 hippocampus baseline, biological rep 3


title: Breasttumour_PatientX405_Timepoint1


title: WholeBlood_CRC305A7017115_Day14 [US22502595_254890810097_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7017115_Day7 [US22502595_254890810097_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7017115_Day4 [US22502595_254890810097_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7017115_Day5 [US22502595_254890810097_S01_GE1_1105_Oct12_1_2]


title: Clock∆19/∆19 hippocampus MI, biological rep 4

source_name: Clock∆19/∆19 MI hippocampus

value: short-term post-MI


title: Breasttumour_PatientX395_Timepoint1


title: WT hippocampus MI, biological rep 2

source_name: WT MI hippocampus


title: WT hippocampus MI, biological rep 3


title: Breasttumour_PatientX395_Timepoint2


title: Clock∆19/∆19 hippocampus MI, biological rep 2


title: Breasttumour_PatientX399_Timepoint4


title: Clock∆19/∆19 hippocampus baseline, biological rep 1


title: Breasttumour_PatientX395_Timepoint4


title: WT hippocampus MI, biological rep 1


title: WholeBlood_CRC305A7017115_Day21 [US22502595_254890810097_S01_GE1_1105_Oct12_2_1]

value: STAMARIL


title: Clock∆19/∆19 hippocampus MI, biological rep 3


title: WT hippocampus HF, biological rep 4

source_name: WT HF hippocampus

value: long-term post-MI (heart failure)


title: WT hippocampus HF, biological rep 3


title: Clock∆19/∆19 hippocampus MI, biological rep 1


title: WT hippocampus baseline, biological rep 2


title: Breasttumour_PatientX394_Timepoint4


title: WholeBlood_CRC305A7017115_Day3 [US22502595_254890810096_S01_GE1_1105_Oct12_2_4]


title: Breasttumour_PatientX394_Timepoint1


title: WT hippocampus HF, biological rep 1


title: WT hippocampus HF, biological rep 2


title: Clock∆19/∆19 hippocampus HF, biological rep 4

source_name: Clock∆19/∆19 HF hippocampus


title: Clock∆19/∆19 hippocampus HF, biological rep 2


title: Breasttumour_PatientX394_Timepoint2


title: Clock∆19/∆19 hippocampus HF, biological rep 1


title: Clock∆19/∆19 hippocampus HF, biological rep 3


title: WholeBlood_CRC305A7017115_Day1 [US22502595_254890810096_S01_GE1_1105_Oct12_2_2]

source_name: Peripheral Blood, PaxGene


title: WholeBlood_CRC305A7017115_Day2 [US22502595_254890810096_S01_GE1_1105_Oct12_2_3]


title: WT mPFC baseline, biological rep 4

source_name: WT baseline mPFC

value: medial prefrontal cortex


title: WT mPFC baseline, biological rep 2


title: WT mPFC baseline, biological rep 3


title: Breasttumour_PatientX393_Timepoint2


title: Breasttumour_PatientX393_Timepoint1


title: WholeBlood_CRC305A7017115_Day-1 [US22502595_254890810096_S01_GE1_1105_Oct12_1_4]


title: Clock∆19/∆19 mPFC baseline, biological rep 4

source_name: Clock∆19/∆19 baseline mPFC


title: WholeBlood_CRC305A7016107_Day28 [US22502595_254890810096_S01_GE1_1105_Oct12_1_3]

value: not hispanic or latino


title: Clock∆19/∆19 mPFC baseline, biological rep 3


title: WT mPFC baseline, biological rep 1


title: Breasttumour_PatientX382_Timepoint4


title: Breasttumour_PatientX382_Timepoint2


title: WholeBlood_CRC305A7017115_Day0 [US22502595_254890810096_S01_GE1_1105_Oct12_2_1]


title: Clock∆19/∆19 mPFC baseline, biological rep 1


title: Breasttumour_PatientX393_Timepoint4


title: WholeBlood_CRC305A7016107_Day21 [US22502595_254890810096_S01_GE1_1105_Oct12_1_2]


title: Clock∆19/∆19 mPFC baseline, biological rep 2


title: Breasttumour_PatientX381_Timepoint4


title: Clock∆19/∆19 mPFC MI, biological rep 4

source_name: Clock∆19/∆19 MI mPFC


title: WT mPFC MI, biological rep 4

source_name: WT MI mPFC


title: WholeBlood_CRC305A7016107_Day5 [US22502595_254890810095_S01_GE1_1105_Oct12_2_3]


title: WT mPFC MI, biological rep 1


title: WT mPFC MI, biological rep 2


title: Clock∆19/∆19 mPFC MI, biological rep 1


title: WT mPFC MI, biological rep 3


title: Clock∆19/∆19 mPFC MI, biological rep 2


title: WholeBlood_CRC305A7016107_Day4 [US22502595_254890810095_S01_GE1_1105_Oct12_2_2]


title: Breasttumour_PatientX381_Timepoint1


title: WholeBlood_CRC305A7016107_Day7 [US22502595_254890810095_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7016107_Day14 [US22502595_254890810096_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX382_Timepoint1


title: WholeBlood_CRC305A7016107_Day3 [US22502595_254890810095_S01_GE1_1105_Oct12_2_1]


title: Breasttumour_PatientX378_Timepoint4


title: WT mPFC HF, biological rep 4

source_name: WT HF mPFC


title: Breasttumour_PatientX381_Timepoint2


title: Clock∆19/∆19 mPFC MI, biological rep 3


title: WT mPFC HF, biological rep 2


title: Breasttumour_PatientX378_Timepoint2


title: Clock∆19/∆19 mPFC HF, biological rep 4

source_name: Clock∆19/∆19 HF mPFC


title: WT mPFC HF, biological rep 3


title: WholeBlood_CRC305A7016107_Day1 [US22502595_254890810095_S01_GE1_1105_Oct12_1_3]


title: Clock∆19/∆19 mPFC HF, biological rep 3


title: WholeBlood_CRC305A7016107_Day-1 [US22502595_254890810095_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX378_Timepoint1


title: WT mPFC HF, biological rep 1


title: Breasttumour_PatientX373R_Timepoint4


title: Clock∆19/∆19 mPFC HF, biological rep 1


title: 2 month ENT1-null AF, 2

middle: A

last: Veras

state: ON

address: 1151 Richmond St.

institute: Western University

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Command Console v3.2.4 using Affymetrix default analysis settings and RMA as normalization method.

source_name: Pool of 5-6 thoracic AF tissues from 2 month ENT1-null mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in standard cages and maintained on a 12 hr light/dark cycle, with rodent chow and water available ad libitum

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: ENT1-null mice were generated by deletion of exons 2-4 of the gene encoding ENT1 (Slc29a1)

tag: strain

value: Black 6

value: thoracic annulus fibrosus

value: 2 months


title: 2 month ENT1-null AF, 1


title: Breasttumour_PatientX373R_Timepoint1

source_name: breast tumour


title: 6 month WT AF, 2

source_name: Pool of 5-6 thoracic AF tissues from 6 month WT mouse

value: 6 months


title: WholeBlood_CRC305A7016107_Day2 [US22502595_254890810095_S01_GE1_1105_Oct12_1_4]

value: white

value: whole blood


title: 2 month WT AF, 2

source_name: Pool of 5-6 thoracic AF tissues from 2 month WT mouse

value: WT


title: Clock∆19/∆19 mPFC HF, biological rep 2

value: male


title: WholeBlood_CRC305A7016107_Day0 [US22502595_254890810095_S01_GE1_1105_Oct12_1_2]

value: female


title: 2 month WT AF, 1


title: Breasttumour_PatientX350_Timepoint4

value: breast tumour


title: ot8-3

city: Seoul

first: Chul-Yong

last: Park

address: Yonsei-ro 50-1

department: Physiology

country: South Korea

institute: Yonsei University

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then merged by flash2 (version 1.2.11)
Merged sequences were mapped to hg19 by bowtie2 software(version 2.3.2).
CrispRVariants performed from the merged reads were to investigate CRISPR-Cas9 mutagenesis
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file includes counts of variants from CrispRVariants results

source_name: HEK293T_Cas9 Treated

extract_protocol:
Genomic DNA was isolated from the cells using the DNeasy Blood &     Tissue kit (Qiagen) according to the manufacturer's instructions.
The quantity and quality of the amplocon were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The amplicon was processed for preparing amplicon sequencing library using TruSeq DNA Nano Sample Preparation Kit(Illumina) according to the manufacturer's protocol

tag: cell type

value: transient transfection

value: Cas9 Treated

tag: molecule subtype

value: PCR amplicon


title: ot8-2


title: 6 month ENT1-null AF, 2

source_name: Pool of 5-6 thoracic AF tissues from 6 month ENT1-null mouse


title: ot7-3