title: PBMC_NightOrientedSchedule_RelTime_36.3_Subject_T23

status: Public on May 08 2018

city: Montreal

first: Laura

last: Kervezee

state: Quebec

address: 6875 LaSalle Boulevard

department: Douglas Mental Health University Institute

institute: McGill University

description: PBMC sample taken at 36.3 h after habitual wake time during night-oriented schedule in Subject T23

hyb_protocol: After fragmentation and labeling, 2.8 µg DNA target was hybridized on Clariom™S HT, Human (ThermoFisher Scientific-Affymetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology using the Oligo package (v1.38.0) in R (v3.4.1). Probe sets were included in downstream analysis if they were expressed above background probe signal (mean + 2*SD) in at least 25% of the samples.

label: Biotin

label_protocol: Sense-strand cDNA was synthesized from 10 ng of total RNA, and fragmentation and labeling were performed to produce ds-cDNA with the GeneChip® Pico Reagent Kit according to manufacturer’s instructions (ThermoFisher Scientific-Affymetrix).

growth_protocol: An indwelling catheter was inserted in a forearm vein at least 4 hours prior to the start of each 24-hour measurement period.

extract_protocol: Extraction of RNA was performed by addition of chloroform in order to separate organic and aqueous components. Isopropanol and subsequent ethanol washes were used to precipitate and purify the RNA. RNA was dissolved in RNase-free H2O (Qiagen, Toronto, ON, Canada). Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by centrifugation for 30 minutes at 1600rpm on a density gradient (Histopaque-1077, Sigma Aldrich, Oakville, ON, Canada). PBMCs were washed 3 times in phosphate-buffered saline (PBS), lysed in TRIzol (Life Technologies, Burlington, ON, Canada) and stored at -80°C until further processing.

tag: subject

tag: condition

value: NightOrientedSchedule

tag: relclocktime


title: PBMC_DayOrientedSchedule_RelTime_24.2_Subject_T23

type: RNA

country: Canada

description: PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T23

molecule: total RNA

organism: Homo sapiens

value: DayOrientedSchedule


title: STING+cGAS-1

status: Public on Aug 02 2018

city: Hangzhou

first: Hanchu

last: Xiong

address: Jiefang Road NO.88

country: China

institute: Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University

description: Gene expression data from HEK293T cells transfected with STING and cGAS expression vector

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Affymetrix OElncRNA for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: not provided

data_processing: Samples were analyzed with Affymetrix software.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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.

growth_protocol: Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin solution.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Empty plasmid or various expression plasmids were transfected using Lipofectamine™ 2000 (Invitrogen) according to the manufacturer’s protocol.

tag: cell line

tag: cell type

value: fibroblast


title: null-1

description: Gene expression data from HEK293T cells transfected with control vector


title: null-2

source_name: HEK293T cells transfected with control vector


title: null-3


title: PBMC_DayOrientedSchedule_RelTime_17.2_Subject_T23

description: PBMC sample taken at 17.2 h after habitual wake time during day-oriented schedule in Subject T23


title: PBMC_DayOrientedSchedule_RelTime_14.4_Subject_T22

description: PBMC sample taken at 14.4 h after habitual wake time during day-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_24.2_Subject_T19

description: PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T19


title: PBMC_NightOrientedSchedule_RelTime_42.2_Subject_T19

description: PBMC sample taken at 42.2 h after habitual wake time during night-oriented schedule in Subject T19


title: PBMC_DayOrientedSchedule_RelTime_20.2_Subject_T23

description: PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T23


title: PBMC_DayOrientedSchedule_RelTime_24.3_Subject_T21

description: PBMC sample taken at 24.3 h after habitual wake time during day-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_42.1_Subject_T18

description: PBMC sample taken at 42.1 h after habitual wake time during night-oriented schedule in Subject T18


title: PBMC_NightOrientedSchedule_RelTime_34.3_Subject_T23

description: PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T23


title: PBMC_NightOrientedSchedule_RelTime_22.3_Subject_T23

description: PBMC sample taken at 22.3 h after habitual wake time during night-oriented schedule in Subject T23


title: PBMC_DayOrientedSchedule_RelTime_24.2_Subject_T15

description: PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T15


title: PBMC_NightOrientedSchedule_RelTime_30.3_Subject_T23

description: PBMC sample taken at 30.3 h after habitual wake time during night-oriented schedule in Subject T23


title: PBMC_NightOrientedSchedule_RelTime_42.2_Subject_T21

description: PBMC sample taken at 42.2 h after habitual wake time during night-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_18.3_Subject_T23

description: PBMC sample taken at 18.3 h after habitual wake time during night-oriented schedule in Subject T23


title: PBMC_DayOrientedSchedule_RelTime_4.3_Subject_T23

description: PBMC sample taken at 4.3 h after habitual wake time during day-oriented schedule in Subject T23


title: PBMC_DayOrientedSchedule_RelTime_6.2_Subject_T14

description: PBMC sample taken at 6.2 h after habitual wake time during day-oriented schedule in Subject T14


title: PBMC_NightOrientedSchedule_RelTime_38.8_Subject_T22

description: PBMC sample taken at 38.8 h after habitual wake time during night-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_0.3_Subject_T23

description: PBMC sample taken at 0.3 h after habitual wake time during day-oriented schedule in Subject T23


title: PBMC_NightOrientedSchedule_RelTime_26.2_Subject_T22

description: PBMC sample taken at 26.2 h after habitual wake time during night-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_8.3_Subject_T23

description: PBMC sample taken at 8.3 h after habitual wake time during day-oriented schedule in Subject T23


title: PBMC_NightOrientedSchedule_RelTime_26.2_Subject_T23

description: PBMC sample taken at 26.2 h after habitual wake time during night-oriented schedule in Subject T23


title: PBMC_DayOrientedSchedule_RelTime_12.3_Subject_T23

description: PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T23


title: PBMC_NightOrientedSchedule_RelTime_34.3_Subject_T22

description: PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T22


title: PBMC_NightOrientedSchedule_RelTime_30.2_Subject_T22

description: PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_18.2_Subject_T17

description: PBMC sample taken at 18.2 h after habitual wake time during day-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_22.3_Subject_T22

description: PBMC sample taken at 22.3 h after habitual wake time during night-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_24.2_Subject_T14

description: PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T14


title: PBMC_DayOrientedSchedule_RelTime_20.2_Subject_T22

description: PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T22


title: PBMC_NightOrientedSchedule_RelTime_18.2_Subject_T22

description: PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_12.2_Subject_T22

description: PBMC sample taken at 12.2 h after habitual wake time during day-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_0.2_Subject_T22

description: PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T22


title: PBMC_DayOrientedSchedule_RelTime_4.2_Subject_T22

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T22


title: PBMC_NightOrientedSchedule_RelTime_22.2_Subject_T21

description: PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T21


title: PBMC_DayOrientedSchedule_RelTime_8.3_Subject_T22

description: PBMC sample taken at 8.3 h after habitual wake time during day-oriented schedule in Subject T22


title: PBMC_NightOrientedSchedule_RelTime_30.2_Subject_T21

description: PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_38.3_Subject_T21

description: PBMC sample taken at 38.3 h after habitual wake time during night-oriented schedule in Subject T21


title: PBMC_DayOrientedSchedule_RelTime_20.3_Subject_T21

description: PBMC sample taken at 20.3 h after habitual wake time during day-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_34.3_Subject_T21

description: PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T21


title: PBMC_DayOrientedSchedule_RelTime_8.5_Subject_T21

description: PBMC sample taken at 8.5 h after habitual wake time during day-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_26.3_Subject_T21

description: PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T21


title: PBMC_DayOrientedSchedule_RelTime_0.2_Subject_T21

description: PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T21


title: PBMC_DayOrientedSchedule_RelTime_16.3_Subject_T21

description: PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_30.2_Subject_T19

description: PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T19


title: PBMC_NightOrientedSchedule_RelTime_18.3_Subject_T19

description: PBMC sample taken at 18.3 h after habitual wake time during night-oriented schedule in Subject T19


title: PBMC_NightOrientedSchedule_RelTime_34.2_Subject_T19

description: PBMC sample taken at 34.2 h after habitual wake time during night-oriented schedule in Subject T19


title: PBMC_NightOrientedSchedule_RelTime_26.3_Subject_T19

description: PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T19


title: PBMC_DayOrientedSchedule_RelTime_20.2_Subject_T19

description: PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T19


title: PBMC_DayOrientedSchedule_RelTime_12.3_Subject_T21

description: PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_22.2_Subject_T19

description: PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T19


title: PBMC_DayOrientedSchedule_RelTime_12.3_Subject_T19

description: PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T19


title: PBMC_NightOrientedSchedule_RelTime_38.2_Subject_T19

description: PBMC sample taken at 38.2 h after habitual wake time during night-oriented schedule in Subject T19


title: PBMC_DayOrientedSchedule_RelTime_4.2_Subject_T21

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T21


title: PBMC_DayOrientedSchedule_RelTime_8.3_Subject_T19

description: PBMC sample taken at 8.3 h after habitual wake time during day-oriented schedule in Subject T19


title: PBMC_DayOrientedSchedule_RelTime_0.3_Subject_T19

description: PBMC sample taken at 0.3 h after habitual wake time during day-oriented schedule in Subject T19


title: PBMC_DayOrientedSchedule_RelTime_4.2_Subject_T19

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T19


title: PBMC_NightOrientedSchedule_RelTime_39.2_Subject_T18

description: PBMC sample taken at 39.2 h after habitual wake time during night-oriented schedule in Subject T18


title: PBMC_DayOrientedSchedule_RelTime_16.2_Subject_T19

description: PBMC sample taken at 16.2 h after habitual wake time during day-oriented schedule in Subject T19


title: PBMC_NightOrientedSchedule_RelTime_30.2_Subject_T18

description: PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T18


title: PBMC_NightOrientedSchedule_RelTime_22.2_Subject_T18

description: PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T18


title: PBMC_NightOrientedSchedule_RelTime_26.2_Subject_T18

description: PBMC sample taken at 26.2 h after habitual wake time during night-oriented schedule in Subject T18


title: PBMC_NightOrientedSchedule_RelTime_34.3_Subject_T18

description: PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T18


title: PBMC_DayOrientedSchedule_RelTime_20.3_Subject_T18

description: PBMC sample taken at 20.3 h after habitual wake time during day-oriented schedule in Subject T18


title: PBMC_DayOrientedSchedule_RelTime_16.3_Subject_T18

description: PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T18


title: PBMC_NightOrientedSchedule_RelTime_18.2_Subject_T18

description: PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T18


title: PBMC_DayOrientedSchedule_RelTime_8.4_Subject_T18

description: PBMC sample taken at 8.4 h after habitual wake time during day-oriented schedule in Subject T18


title: PBMC_DayOrientedSchedule_RelTime_0.2_Subject_T18

description: PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T18


title: PBMC_NightOrientedSchedule_RelTime_26.3_Subject_T17

description: PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_34.4_Subject_T17

description: PBMC sample taken at 34.4 h after habitual wake time during night-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_30.3_Subject_T17

description: PBMC sample taken at 30.3 h after habitual wake time during night-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_38.2_Subject_T17

description: PBMC sample taken at 38.2 h after habitual wake time during night-oriented schedule in Subject T17


title: PBMC_DayOrientedSchedule_RelTime_4.2_Subject_T18

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T18


title: PBMC_DayOrientedSchedule_RelTime_12.3_Subject_T18

description: PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T18


title: PBMC_NightOrientedSchedule_RelTime_22.3_Subject_T17

description: PBMC sample taken at 22.3 h after habitual wake time during night-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_18.9_Subject_T17

description: PBMC sample taken at 18.9 h after habitual wake time during night-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_18.2_Subject_T21

description: PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T21


title: PBMC_NightOrientedSchedule_RelTime_38.3_Subject_T15

description: PBMC sample taken at 38.3 h after habitual wake time during night-oriented schedule in Subject T15


title: PBMC_DayOrientedSchedule_RelTime_20.2_Subject_T17

description: PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T17


title: PBMC_DayOrientedSchedule_RelTime_12.3_Subject_T17

description: PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T17


title: PBMC_DayOrientedSchedule_RelTime_4.2_Subject_T17

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_22.2_Subject_T15

description: PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T15


title: PBMC_NightOrientedSchedule_RelTime_30.2_Subject_T15

description: PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T15


title: PBMC_NightOrientedSchedule_RelTime_19_Subject_T15

description: PBMC sample taken at 19 h after habitual wake time during night-oriented schedule in Subject T15


title: PBMC_DayOrientedSchedule_RelTime_0.2_Subject_T17

description: PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T17


title: PBMC_NightOrientedSchedule_RelTime_26.5_Subject_T15

description: PBMC sample taken at 26.5 h after habitual wake time during night-oriented schedule in Subject T15


title: PBMC_DayOrientedSchedule_RelTime_16.3_Subject_T15

description: PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T15


title: PBMC_NightOrientedSchedule_RelTime_26.3_Subject_T14

description: PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T14


title: PBMC_NightOrientedSchedule_RelTime_18.2_Subject_T14

description: PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T14


title: PBMC_DayOrientedSchedule_RelTime_0.3_Subject_T15

description: PBMC sample taken at 0.3 h after habitual wake time during day-oriented schedule in Subject T15


title: PBMC_DayOrientedSchedule_RelTime_12.3_Subject_T15

description: PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T15


title: PBMC_NightOrientedSchedule_RelTime_22.2_Subject_T14

description: PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T14


title: PBMC_NightOrientedSchedule_RelTime_38.3_Subject_T14

description: PBMC sample taken at 38.3 h after habitual wake time during night-oriented schedule in Subject T14


title: PBMC_DayOrientedSchedule_RelTime_22.2_Subject_T15

description: PBMC sample taken at 22.2 h after habitual wake time during day-oriented schedule in Subject T15


title: PBMC_NightOrientedSchedule_RelTime_34.4_Subject_T15

description: PBMC sample taken at 34.4 h after habitual wake time during night-oriented schedule in Subject T15


title: PBMC_DayOrientedSchedule_RelTime_8.8_Subject_T17

description: PBMC sample taken at 8.8 h after habitual wake time during day-oriented schedule in Subject T17


title: OSCC patient T21

status: Public on May 03 2018

city: Shanghai

first: Shi

last: Jianbo

state: Shanghai

address: 639, ZhiZaoJu Road, Shanghai

department: Department of Oral & Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital

institute: Shanghai Jiao Tong University School of Medicine

description: serum miRNA expression of OSCC patients from age, gender, smoking and drinking matched normal control people. The clinical characteristics of OCSS patients contain pathological grade, lymph node metastasis, TNM stage and survival status.

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner. The scanned images were imported into the GenePix Pro 6.0 software (Axon Instruments) for grid alignment and data extraction. Replicated miRNAs were averaged, and the miRNAs with intensities in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.

data_processing:
The scanned images were imported into the GenePix Pro 6.0 software (Axon Instruments) for grid alignment and data extraction.Replicated miRNAs were averaged, and the miRNAs with intensities in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.
[Filtering criteria] We only analyzed the detected human related microRNAs. We excluded the probes of which signal intensity was less than 30.0 in all samples.

source_name: OSCC patient serum

label_protocol: After RNA isolation from the samples, the miRCURYTM Hy3TM/Hy5TM Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: TRIzolTM LS reagent (Invitrogen Life Technologies) was used according to the manufacturer instructions for isolating total RNA.

tag: age

tag: Sex

value: male

tag: somking

value: no

tag: drinking

tag: lymph node metastasis

value: yes

tag: pathological grade

tag: tnm stage

tag: status after 5 years

value: Alive

tag: tissue

value: serum


title: OSCC patient T25

value: female

value: Dead


title: PBMC_DayOrientedSchedule_RelTime_4.2_Subject_T15

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T15


title: OSCC patient T23


title: OSCC patient T20


title: PBMC_NightOrientedSchedule_RelTime_34.4_Subject_T14

description: PBMC sample taken at 34.4 h after habitual wake time during night-oriented schedule in Subject T14


title: OSCC patient T24


title: OSCC patient T22


title: OSCC patient T19


title: PBMC_DayOrientedSchedule_RelTime_8.8_Subject_T14

description: PBMC sample taken at 8.8 h after habitual wake time during day-oriented schedule in Subject T14


title: PBMC_DayOrientedSchedule_RelTime_20.2_Subject_T14

description: PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T14


title: PBMC_DayOrientedSchedule_RelTime_0.5_Subject_T14

description: PBMC sample taken at 0.5 h after habitual wake time during day-oriented schedule in Subject T14


title: PBMC_DayOrientedSchedule_RelTime_16.3_Subject_T14

description: PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T14


title: PBMC_NightOrientedSchedule_RelTime_30.3_Subject_T14

description: PBMC sample taken at 30.3 h after habitual wake time during night-oriented schedule in Subject T14


title: OSCC patient T16


title: OSCC patient T17


title: PBMC_DayOrientedSchedule_RelTime_13.2_Subject_T14

description: PBMC sample taken at 13.2 h after habitual wake time during day-oriented schedule in Subject T14


title: OSCC patient T15


title: OSCC patient T13


title: OSCC patient T12


title: OSCC patient T14


title: OSCC patient T18


title: OSCC patient T9


title: OSCC patient T10


title: OSCC patient T7


title: OSCC patient T5


title: OSCC patient T8


title: INS_A_Hela_1

status: Public on Apr 06 2018

type: SRA

city: Bethesda

first: Gary

last: Felsenfeld

state: MD

address: 5 Memorial Drive, Room 212

department: NIDDK

country: USA

institute: National Institutes of Health

description: Cervical cancer cells

library_source: genomic

data_processing:
Library strategy: 4C-seq
Barcode sequences were removed from the reads.
The reads were mapped with Bowtie2 version2.2.
The reads mapped to the bait (self-ligation reads) were filtered out.
The remain reads were mapped with Bowtie2 again.
Genome_build: hg19
Supplementary_files_format_and_content: BED

molecule: genomic DNA

source_name: HeLa

growth_protocol: EndoC βH1 cells were grown in were cultured in low-glucose Dulbecco's modified Eagle's medium (Life Technology, cat. # 11885) with 2% BSA (fatty acid free and heat shocked, Equitech, cat. #BAH66), 50 μM 2-mercaptoethanol, 10 mM nicotinamide, 5.5 mg/ml human transferrin (Sigma–Aldrich, cat. #T8158), 6.7 ng/ml sodium selenite, 100 U/ml penicillin, and 0.1 mg/ml streptomycin. Cells were seeded at a density of 6 × 105/cm2 on ECM-gel (1%) (Sigma-Aldrich, cat. # E1270) /fibronectin (2 g/ml; Sigma–Aldrich, cat #. F1141) coated plates and cultured at 37 °C and 5% CO2. Hela cells were grown in low-glucose Dulbecco's modified Eagle's medium with 10% Fetal Bovine Serum and cultured at 37 °C and 5% CO2.

extract_protocol:
Phenol-Chloroform and ethanol precipitate.
Direct PCR from 4C library

treatment_protocol: Cells were fixed by formaldehyde. The cross-linked chromatin was digested by BglII (New England Biolabs) and re-ligated by T4 DNA ligase (New England Biolabs). After reversal of crosslinks, DNA was digested by NlaIII (New England Biolabs) and re-ligated by T4 DNA ligase (New England Biolabs). The DNA product served as template for 4C-PCR.

value: Cervical cancer cells

value: HeLa


title: INS_A_beta_3

description: Pancreatic β cells

source_name: EndoC βH1

value: Pancreatic beta cells

value: EndoC betaH1


title: INS_A_beta_2

description: Pancreatic β cells


title: OSCC patient T6


title: INS_A_Hela_3

description: Cervical cancer cells


title: OSCC patient T1


title: OSCC patient T2


title: OSCC patient T3


title: INS_A_beta_1

description: Pancreatic β cells


title: GSK126-10days-rep3

status: Public on Apr 01 2018

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrüch Center

library_source: transcriptomic

data_processing:
Sequence reads were mapped to mm9 using tophat version 2.0.6 with parameters --library-type fr-unstranded, --no-coverage-search -M --transcriptome-index, Ensembl GTF version 66
Readcounts were obtained by counting the number of reads per gene using HTSeq-count.
Supplementary_files_format_and_content: The file expression_normalized.txt contains expression values that are normalized to 10 million reads per sample. Reads that have no expression across all samples, were removed.

organism: Mus musculus

source_name: lung tumors

growth_protocol: NSCLC were grown in F12 medium supplemented with 10% FBS, and 5% penicillin and streptomycin, hydrocortisone, recombinant hEGF, insulin-transferrin selenium and tail vein inected in Nude mice

extract_protocol:
Trypsin/Collegenase/Hyarulonydase/DNaseI digestion followed by GFP cell sorting using FACSAria (BD Biosciences) and Trizol
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Sample Prep protocols.

treatment_protocol: NSCLC-bearing Nude mice were daily treated with GSK126 50mg/kg in Captisol daily via IP, and control animals only received Captisol. Doxycycline-treated animals received the drug via drinking water supplemented with 1% sucrose.

value: primary mouse NSCLC

tag: cell population


title: OSCC patient T4


title: GSK126-10days-rep2


title: doxycycline-30days-rep1


title: GSK126-30days-rep4


title: GSK126-30days-rep3


title: GSK126-30days-rep1


title: INS_A_Hela_2

description: Cervical cancer cells


title: Vehicle-30days-rep2


title: GSK126-10days-rep1


title: Vehicle-30days-rep1


title: mOSN_Ldb1_ChIPseq_rep2

status: Public on Mar 29 2018

city: Piscataway

first: Kevin

last: Monahan

state: NJ

address: 604 Allison Rd

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

extract_protocol:
Crosslinked-ChIP: Chromatin from formaldehyde cross-linked cells was sheared on a Covaris S220 Focused-ultrasonicator to a size range of 200-500bp. Approximately 1-2ug of sheared chromatin was used for immunoprecipitation with antibodies, and precipitated DNA was column purified. RNA: Cells were lysed in Trizol-LS (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
Crosslinked-ChIP: ChIP-seq Libraries were prepared using a Nugen Ultralow V2 kit. RNA: RNA-seq libraries were prepared using a TruSeq Stranded Total RNA with Ribo-Zero Gold Set B kit (Illumina RS-1222302).

treatment_protocol: = Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting. For Krt5Cre knockout cells, at 6-weeks of age, deletion of the conditional allele in horizontal basal cells was induced by two intraperitoneal injections of tamoxifen twenty-four hours apart. One week later, differentiation of horizontal basal cells into olfactory cell types was induced by intraperitoneal injection with methimazole, which triggers ablation of olfactory epithelium and regeneration of the tissue from horizontal basal cells. The olfactory epithelium was allowed to regenerate for 8-weeks, and then  TdTomato+ cell were purified by FACS. TdTomato bright and dim populations were collected separately, followed by RNA-seq.

tag: genotype/variation

value: OMP-IRES-GFP

tag: tissue/cell type

value: mature olfactory sensory neurons

tag: chip antibody

value: anti-Ldb1 (Santa Cruz Biotechnology, sc-11198)

tag: molecule subtype

value: Crosslinked-ChIP


title: mOSN_CTCF_ChIPseq_rep2

value: anti-CTCF (Millipore, 07-729)


title: mOSN_Rad21_ChIPseq_rep2

value: anti-Rad21 (Abcam, ab992)


title: mOSN_Rad21_ChIPseq_rep1


title: mOSN_Ldb1KO_RNAseq_rep1


title: mOSN_Ldb1_ChIPseq_rep1


title: Cry1_TSS-Liver_WT-Batch3-ZT0-WT-S322

status: Public on Mar 26 2018

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description:
4CSeq of Liver_WT of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz

data_processing:
Library strategy: 4C-Seq
mm9
Mapping was done using HTS station (http://htsstation.epfl.ch). See Supplemental methods of paper for detailed processing methods. In brief, read counts were normalized by total counts on the cis chromosome. For each fragment, we fit a weighted linear model with a Gaussian window of 2.5kb in order to incorporate signal from neighboring fragments.
Log10 4CSeq signal (value A with variance Avar). Processed formats show fragments within +/- 2MB of the bait. Zscore and p-value represent differential contacts between liver and kidney

source_name: Crosslinked genomic DNA

extract_protocol: Liver and kidney nuclei were prepared as previously described (Ripperger and Schibler 2006) with some minor changes.         In brief, liver and kidneys from individual animals were homogenized and fixed in 4ml of PBS including 1.5percent formaldehyde for 10 minutes at room temperature.         Cross-linking reaction was stopped by adding 25 ml of ice-cold stop reaction buffer (2.2 M sucrose; 150 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         to the homogenates and kept 5 minutes on ice. Homogenates were then loaded on top of 10 ml cushion buffer (2.05 M sucrose; 10 % glycerol; 125 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         and centrifuged for 45 minutes at 105g at  4degC. Nuclei were washed twice in PBS and immediately frozen.

tag: strain

tag: feeding

value: Ad libitum

value: post-natal 8-12 weeks

tag: genotype

value: WT


title: mOSN_CTCF_ChIPseq_rep1


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S323

description:
4CSeq of Liver_Cry1intronKO of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz

tag: age


title: mOSN_Ldb1KO_RNAseq_rep2


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S311


title: GSK126-30days-rep2

tag: cell line


title: OSCC patient T11

tag: Sex

tag: somking

value: no

value: Alive

value: serum


title: Cry1_TSS-Liver_WT-Batch3-ZT0-WT-S310


title: H46 24h IL3+ [28_C4EANACXX_TGACCA_L008]

status: Public on Feb 02 2018

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

country: Australia

institute: CSL Limited / bio21 Institute

description:
28_C4EANACXX_TGACCA_L008
H46 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.58 and Real Time Analysis (RTA) v1.18.64, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Reads were mapped to Homo sapiens GRCh37.p10 genome, using TopHat (TopHat v2.0.8, bowtie v2.1.0; Trapnell et al.,2009).
Mapped reads were summarized on a gene level using Ensembl ID gene annotation (Ensembl Release 70 based on GRCh37.p10 genome build) and HTSeq (v0.5.3p9; Anders et al., 2014) software.
Summarised read counts in this submission were NOT normalised nor filtered. We recommend using Bioconductor edgeR package functions: i) calcNormFactors (TMM method) to normalise between samples based on library sizes, and ii) rpkm function to normalise between genes within a sample based on gene lengths.
Genome_build: GRCh37.p10
Supplementary_files_format_and_content: *txt: All processed data files are in a tab-delimited file format. They contain raw read counts summarised on a gene level according to Ensembl Release 70 annotation.

source_name: RNA from lysed whole blood cells

growth_protocol: Cell pellets were suspended in RNAprotect Cell Reagent (Qiagen, Catalog number 76526) and frozen at -80 degrees Celsius until RNA extraction.

extract_protocol:
RNA was extracted from pDCs using an RNeasy pus micro kit (Qiagen, catalog number 74034).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNA was extracted with an RNA Protect Cell Mini Kit (Qiagen, Catalog number 74624).

value: blood

tag: donor

tag: gender

value: Female

tag: ancestry

value: Indian

tag: disease status

value: Healthy

tag: treatment

tag: time point


title: Cry1_TSS-Liver_Cry1intronKO-Batch3-ZT0-Cry1intronKO-S302

tag: tissue


title: mOSN_Lhx2KO_Ldb1_ChIPseq_rep1

tag: genotype/variation

tag: tissue/cell type


title: mOSN_Ldb1_ChIPseq_rep3

tag: chip antibody

tag: molecule subtype


title: Cry1_TSS-Liver_WT-Batch3-ZT0-WT-S301

tag: strain

tag: feeding


title: H46 24h IL3+ [28_C4EANACXX_TGACCA_L007]

description:
28_C4EANACXX_TGACCA_L007
H46 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt

tag: age


title: H46 6h IL3+ [26_C4EANACXX_CGATGT_L008]

description:
26_C4EANACXX_CGATGT_L008
H46 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 6h [27_C4EANACXX_TTAGGC_L008]

description:
27_C4EANACXX_TTAGGC_L008
H44 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt

value: Male

value: Aboriginal


title: H49 24h IL3+ [24_C4EANACXX_ATTCCT_L008]

description:
24_C4EANACXX_ATTCCT_L008
H49 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 24h [25_C4EANACXX_ATCACG_L008]

description:
25_C4EANACXX_ATCACG_L008
H48 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt

value: German


title: H50 6h [23_C4EANACXX_ACTGAT_L007]

description:
23_C4EANACXX_ACTGAT_L007
H50 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt

value: Caucasian


title: H49 24h IL3+ [24_C4EANACXX_ATTCCT_L007]

description:
24_C4EANACXX_ATTCCT_L007
H49 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 24h [25_C4EANACXX_ATCACG_L007]

description:
25_C4EANACXX_ATCACG_L007
H48 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H50 6h [23_C4EANACXX_ACTGAT_L008]

description:
23_C4EANACXX_ACTGAT_L008
H50 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 24h IL3+ [22_C4EANACXX_GAGTGG_L008]

description:
22_C4EANACXX_GAGTGG_L008
H44 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 24h IL3+ [22_C4EANACXX_GAGTGG_L007]

description:
22_C4EANACXX_GAGTGG_L007
H44 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 6h [21_C4EANACXX_CGTACG_L007]

description:
21_C4EANACXX_CGTACG_L007
H48 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 6h [21_C4EANACXX_CGTACG_L008]

description:
21_C4EANACXX_CGTACG_L008
H48 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H50 24h IL3+ [19_C4EANACXX_GTGGCC_L008]

description:
19_C4EANACXX_GTGGCC_L008
H50 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 6h IL3+ [20_C4EANACXX_GTTTCG_L008]

description:
20_C4EANACXX_GTTTCG_L008
H48 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H49 24h [17_C4EANACXX_GTCCGC_L008]

description:
17_C4EANACXX_GTCCGC_L008
H49 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H49 24h [17_C4EANACXX_GTCCGC_L007]

description:
17_C4EANACXX_GTCCGC_L007
H49 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 24h [16_C4EANACXX_CCGTCC_L008]

description:
16_C4EANACXX_CCGTCC_L008
H47 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 24h [16_C4EANACXX_CCGTCC_L007]

description:
16_C4EANACXX_CCGTCC_L007
H47 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 24h [18_C4EANACXX_GTGAAA_L008]

description:
18_C4EANACXX_GTGAAA_L008
H45 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 6h [27_C4EANACXX_TTAGGC_L007]

description:
27_C4EANACXX_TTAGGC_L007
H44 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H46 6h IL3+ [26_C4EANACXX_CGATGT_L007]

description:
26_C4EANACXX_CGATGT_L007
H46 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 6h [15_C4EANACXX_ATGTCA_L007]

description:
15_C4EANACXX_ATGTCA_L007
H45 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 6h [15_C4EANACXX_ATGTCA_L008]

description:
15_C4EANACXX_ATGTCA_L008
H45 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H46 24h [14_C4EANACXX_AGTTCC_L005]

description:
14_C4EANACXX_AGTTCC_L005
H46 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H46 24h [14_C4EANACXX_AGTTCC_L006]

description:
14_C4EANACXX_AGTTCC_L006
H46 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 6h IL3+ [13_C4EANACXX_AGTCAA_L006]

description:
13_C4EANACXX_AGTCAA_L006
H45 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 6h IL3+ [20_C4EANACXX_GTTTCG_L007]

description:
20_C4EANACXX_GTTTCG_L007
H48 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H50 24h IL3+ [19_C4EANACXX_GTGGCC_L007]

description:
19_C4EANACXX_GTGGCC_L007
H50 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 6h IL3+ [11_C4EANACXX_GGCTAC_L005]

description:
11_C4EANACXX_GGCTAC_L005
H44 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 6h [12_C4EANACXX_CTTGTA_L006]

description:
12_C4EANACXX_CTTGTA_L006
H47 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 6h IL3+ [13_C4EANACXX_AGTCAA_L005]

description:
13_C4EANACXX_AGTCAA_L005
H45 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 6h IL3+ [11_C4EANACXX_GGCTAC_L006]

description:
11_C4EANACXX_GGCTAC_L006
H44 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 6h [12_C4EANACXX_CTTGTA_L005]

description:
12_C4EANACXX_CTTGTA_L005
H47 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 24h [18_C4EANACXX_GTGAAA_L007]

description:
18_C4EANACXX_GTGAAA_L007
H45 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H50 6h IL3+ [1_C4EANACXX_ATCACG_L005]

description:
1_C4EANACXX_ATCACG_L005
H50 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 24h IL3+ [2_C4EANACXX_CGATGT_L005]

description:
2_C4EANACXX_CGATGT_L005
H47 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H50 6h IL3+ [1_C4EANACXX_ATCACG_L006]

description:
1_C4EANACXX_ATCACG_L006
H50 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H50 24h [8_C4EANACXX_ACTTGA_L005]

description:
8_C4EANACXX_ACTTGA_L005
H50 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H50 24h [8_C4EANACXX_ACTTGA_L006]

description:
8_C4EANACXX_ACTTGA_L006
H50 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 24h IL3+ [7_C4EANACXX_CAGATC_L006]

description:
7_C4EANACXX_CAGATC_L006
H45 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 24h IL3+ [6_C4EANACXX_GCCAAT_L006]

description:
6_C4EANACXX_GCCAAT_L006
H48 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H45 24h IL3+ [7_C4EANACXX_CAGATC_L005]

description:
7_C4EANACXX_CAGATC_L005
H45 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H46 6h [5_C4EANACXX_ACAGTG_L005]

description:
5_C4EANACXX_ACAGTG_L005
H46 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H49 6h IL3+ [10_C4EANACXX_TAGCTT_L005]

description:
10_C4EANACXX_TAGCTT_L005
H49 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H46 6h [5_C4EANACXX_ACAGTG_L006]

description:
5_C4EANACXX_ACAGTG_L006
H46 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H49 6h [4_C4EANACXX_TGACCA_L006]

description:
4_C4EANACXX_TGACCA_L006
H49 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H49 6h [4_C4EANACXX_TGACCA_L005]

description:
4_C4EANACXX_TGACCA_L005
H49 6h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 24h IL3+ [2_C4EANACXX_CGATGT_L006]

description:
2_C4EANACXX_CGATGT_L006
H47 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 24h [3_C4EANACXX_TTAGGC_L005]

description:
3_C4EANACXX_TTAGGC_L005
H44 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H48 24h IL3+ [6_C4EANACXX_GCCAAT_L005]

description:
6_C4EANACXX_GCCAAT_L005
H48 24h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 6h IL3+ [9_C4EANACXX_GATCAG_L005]

description:
9_C4EANACXX_GATCAG_L005
H47 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H47 6h IL3+ [9_C4EANACXX_GATCAG_L006]

description:
9_C4EANACXX_GATCAG_L006
H47 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H49 6h IL3+ [10_C4EANACXX_TAGCTT_L006]

description:
10_C4EANACXX_TAGCTT_L006
H49 6h IL3+
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: H44 24h [3_C4EANACXX_TTAGGC_L006]

description:
3_C4EANACXX_TTAGGC_L006
H44 24h
PolyA RNA
processed data file: counts-matrix-EnsembIDs-GRCh37.p10.txt


title: 227294_C

status: Public on Dec 01 2017

type: genomic

city: Winston-Salem

first: Gaddamanugu

middle: L

last: Prasad

state: NC

institute: RAI Services Company

hyb_protocol: DNA is purified by alcohol precipitation and resuspended prior to hybridization on Illumina Methyl450k BeadChips at 48 °C for 16-24h.  Single base extension and fluorescent labeling allows allele-specificity to be determined

scan_protocol: BeadChips are scanned and intensities determined using an Illumina iScan

data_processing:
Genotypes will be extracted from intensity data and called using a standard cluster file within the Illumina Genome Studio software.
Unmethylated and methylated signal intensities

label: biotin and dinitrophenyl

source_name: buccal cells

label_protocol: Bisulfite conversion was performed using Zymo EZ-96 DNA Methylation Kits (D5004 or D5001).  Briefly, bisulfite conversion occurred at 50 °C for 12-16 h.  Samples were subsequently washed and desulphonated over a provided silicon binding plate.  Samples were eluted in 12 µl molecular grade water before processing through Illumina’s Infinium protocol. Infinium processing occurred according to standard Illumina workflow using Infinium HumanMethylation450 BeadChip Kits (WG-314-1003).  The Illumina Infinium workflow consists of three steps: whole genome amplification of input DNA, fragmentation, and a two-step allele detection involving hybridization and single base extension.  Briefly, whole genome amplification occurs for 20-24h at 37 °C followed by enzymatic fragmentation for 1h at 37 °C.

extract_protocol: Adult male subjects, aged 35 – 60 years, were enrolled into three cohorts of 40 or 41 subjects each: exclusive smokers (SMK), moist snuff consumers (MSC) and Non-Tobacco Consumers (NTC). Buccal cells were collected following a 2h fasting from food and tobacco by a swishing method. Subjects rinsed their mouth with Scope® mouth wash followed by a water rinse. Buccal cells were collected in water by vigorously swishing. The cell pellet was washed in phosphate buffered saline and used for DNA extraction.

tag: class

value: Moist Snuff User

tag: race


title: 227292_A

value: Cigarette Smoker


title: 227293_E


title: 227288_C


title: 227284_C


title: 227285_C


title: 227281_C

value: Non-Tobacco User


title: 227286_C


title: 227290_C

value: Other


title: 227276_C


title: 227283_C


title: 227277_B


title: 227289_C


title: 227279_C


title: 227282_C


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title: 227270_B


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title: 227263_B


title: 227262_B


title: 227264_B


title: 227257_A


title: 227258_B


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title: 227256_B


title: 227251_A


title: 227252_A


title: 227239_A


title: 227254_B


title: 227245_A


title: 227244_A


title: 227260_A


title: 227253_B


title: 227261_B


title: 227238_A


title: 227247_A


title: 227237_Y


title: 227242_Y


title: 227250_B


title: 227234_Y


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title: 227243_A


title: 227255_A


title: 227248_Y


title: 227240_A


title: 227236_A


title: 227259_A


title: 227231_Y


title: 227232_Y


title: 227229_Y


title: 227233_Y


title: 227228_Y


title: 227235_A


title: 227227_Y


title: 227224_Y


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title: 227226_Y


title: 227230_Y


title: 227223_Y


title: 227216_X


title: 227214_X


title: 227210_X


title: 227215_X


title: 227212_X


title: 227219_Y


title: 227225_Y


title: 227208_X


title: 227220_X


title: 227213_X


title: 227222_Y


title: 227217_X


title: 227207_Y


title: 227241_A


title: 227206_Y


title: 227209_X


title: 227202_X


title: 227211_X


title: 227221_Y


title: 227201_X


title: 227203_Y


title: 227204_X


title: 227199_X


title: 227205_X


title: 227198_X


title: 227200_L


title: 209

status: Public on Jun 29 2017

city: Albuquerque

first: Ksenia

last: Matlawska

state: NM

address: 915 Camino de Salud

department: Pediatrics

institute: University of New Mexico

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 209
COG study 0434

hyb_protocol: 15 ug aliquots of fragmented, labelled cRNA were hybridized to the U133 Plus 2 chip (Affymetrix)

scan_protocol: Affymerix microarray scanner (Hewlett Packard), gene fluorescence was captured using GeneChip software.

data_processing: The Robust Multi-array Average (RMA) algorithm was used to generate and normalize signal intensities (Bioconductor/R).  Scale factor < 40; GAPDH M33197 3′ intensity > 15 000; and GAPDH M33197 3′/5′ ratio < 3 were applied as array experimental quality parameters. From 54,675 genes and expressed sequence tags, we selectively filtered out probes for gender, globins, and internal controls, and corrected for batch effects using z-score transformations.

source_name: Newly diagnosed T-ALL patient (bone marrow)

label_protocol: Biotin-labed cRNA from 1 micrograms of tissue using a one-step method usng Affymetrix technical approach

growth_protocol: Derived from bone marrow in newly diagnosed T-ALL patients

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

treatment_protocol: COG study 9404/0434 (diagnostic samples)

tag: diagnosis

value: T-ALL

value: bone marrow


title: 211

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 211
COG study 0434


title: 213

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 213
COG study 0434


title: 208

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 208
COG study 0434


title: 210

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 210
COG study 0434


title: 227195_L


title: 212

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 212
COG study 0434


title: 207

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 207
COG study 0434


title: 227184_I


title: 227196_I


title: 227190_L


title: 227193_L


title: 206

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 206
COG study 0434


title: 227197_X


title: 227189_L


title: 227183_L


title: 227187_I


title: 227182_I


title: 227186_I


title: 204

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 204
COG study 0434


title: 201

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 201
COG study 0434


title: 227194_I


title: 227181_Q


title: 200

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 200
COG study 0434


title: 227188_L


title: 227185_I


title: 227178_Q


title: 202

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 202
COG study 0434


title: 198

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 198
COG study 0434


title: 197

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 197
COG study 0434


title: 196

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 196
COG study 0434


title: 227191_L


title: 195

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 195
COG study 0434


title: 227179_Q


title: 227192_L


title: 193

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 193
COG study 0434


title: 194

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 194
COG study 0434


title: 191

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 191
COG study 0434


title: 205

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 205
COG study 0434


title: 227180_I


title: 227176_Q


title: 227177_Q


title: 190

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 190
COG study 0434


title: 187

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 187
COG study 0434


title: 185

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 185
COG study 0434


title: 181

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 181
COG study 0434


title: 184

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 184
COG study 0434


title: 189

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 189
COG study 0434


title: 180

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 180
COG study 0434


title: 182

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 182
COG study 0434


title: 177

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 177
COG study 0434


title: 172

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 172
COG study 0434


title: 169

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 169
COG study 0434


title: 174

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 174
COG study 0434


title: 166

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 166
COG study 0434


title: 179

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 179
COG study 0434


title: 188

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 188
COG study 0434


title: 176

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 176
COG study 0434


title: 167

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 167
COG study 0434


title: 170

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 170
COG study 0434


title: 171

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 171
COG study 0434


title: 175

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 175
COG study 0434


title: 178

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 178
COG study 0434


title: 183

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 183
COG study 0434


title: 165

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 165
COG study 0434


title: 199

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 199
COG study 0434


title: 173

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 173
COG study 0434


title: 203

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 203
COG study 0434


title: 164

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 164
COG study 0434


title: 154

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 154
COG study 0434


title: 153

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 153
COG study 0434


title: 148

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 148
COG study 0434


title: 156

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 156
COG study 0434


title: 150

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 150
COG study 0434


title: 147

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 147
COG study 0434


title: 146

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 146
COG study 0434


title: 151

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 151
COG study 0434


title: 160

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 160
COG study 0434


title: 162

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 162
COG study 0434


title: 163

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 163
COG study 0434


title: 155

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 155
COG study 0434


title: 149

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 149
COG study 0434


title: 168

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 168
COG study 0434


title: 145

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 145
COG study 0434


title: 161

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 161
COG study 0434


title: 157

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 157
COG study 0434


title: 192

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 192
COG study 0434


title: 144

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 144
COG study 0434


title: 152

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 152
COG study 0434


title: 158

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 158
COG study 0434


title: 159

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 159
COG study 0434


title: 143

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 143
COG study 0434


title: 141

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 141
COG study 0434


title: 134

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 134
COG study 0434


title: 136

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 136
COG study 0434


title: 139

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 139
COG study 0434


title: 138

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 138
COG study 0434


title: 126

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 126
COG study 0434


title: 131

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 131
COG study 0434


title: 135

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 135
COG study 0434


title: 129

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 129
COG study 0434


title: 122

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 122
COG study 0434


title: 140

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 140
COG study 0434


title: 127

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 127
COG study 0434


title: 121

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 121
COG study 0434


title: 137

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 137
COG study 0434


title: 130

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 130
COG study 0434


title: 132

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 132
COG study 0434


title: 124

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 124
COG study 0434


title: 119

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 119
COG study 0434


title: 117

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 117
COG study 0434


title: 142

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 142
COG study 0434


title: 123

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 123
COG study 0434


title: 133

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 133
COG study 0434


title: 128

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 128
COG study 0434


title: 125

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 125
COG study 0434


title: 186

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 186
COG study 0434


title: 118

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 118
COG study 0434


title: 114

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 114
COG study 0434


title: 120

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 120
COG study 0434


title: 116

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 116
COG study 0434


title: 115

description:
Gene expression data from primary T-ALL samples at diagnosis
sample name: 115
COG study 0434


title: non-ERG-related_sample 102

status: Public on Mar 21 2017

city: Padova

first: Elena

last: Vendramini

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description:
batch 3
NON_ERG_REL-102
Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 12.5ug were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000

data_processing: The data were normalized using RMA algorithm in R software [www.r-ptoject.org] and ComBat function was applied to adjust for batches (SVA package), BioConductor package [www.bioconductor.org]

label: biotin

source_name: non-ERG-related without ERG intragenic deletion

label_protocol: Biotinylated cRNA were prepared using GeneChip® 3’IVT express kit and protocol from 100 ng total RNA (Affymetrix).

extract_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation.  Total RNA was extracted using TRIZOL reagent following manufacturer's instructions.

tag: cell type

value: white blood cells

tag: disease state

value: pediatric acute leukemia


title: non-ERG-related_sample 104

description:
batch 3
NON_ERG_REL-104
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 89

description:
batch 3
NON_ERG_REL-89
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 90

description:
batch 3
NON_ERG_REL-90
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 98

description:
batch 3
NON_ERG_REL-98
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 84

description:
batch 1
NON_ERG_REL-84
Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation.  Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns.


title: non-ERG-related_sample 96

description:
batch 2
NON_ERG_REL-96
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 108

description:
batch 3
NON_ERG_REL-108
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 106

description:
batch 3
NON_ERG_REL-106
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 100

description:
batch 3
NON_ERG_REL-100
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 95

description:
batch 1
NON_ERG_REL-95
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 88

description:
batch 2
NON_ERG_REL-88
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 93

description:
batch 3
NON_ERG_REL-93
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 86

description:
batch 2
NON_ERG_REL-86
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 97

description:
batch 3
NON_ERG_REL-97
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 99

description:
batch 3
NON_ERG_REL-99
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 92

description:
batch 3
NON_ERG_REL-92
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 94

description:
batch 3
NON_ERG_REL-94
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 105

description:
batch 3
NON_ERG_REL-105
Gene expression data from pediatric acute leukemia samples at diagnosis

source_name: non-ERG-related no data about ERG intragenic deletion

value: peripheral blood


title: non-ERG-related_sample 91

description:
batch 3
NON_ERG_REL-91
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 79

description:
batch 2
NON_ERG_REL-79
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 82

description:
batch 1
NON_ERG_REL-82
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 81

description:
batch 3
NON_ERG_REL-81
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 83

description:
batch 1
NON_ERG_REL-83
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 85

description:
batch 2
NON_ERG_REL-85
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 103

description:
batch 3
NON_ERG_REL-103
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 87

description:
batch 2
NON_ERG_REL-87
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 101

description:
batch 3
NON_ERG_REL-101
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 80

description:
batch 2
NON_ERG_REL-80
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 78

description:
batch 2
NON_ERG_REL-78
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 77

description:
batch 2
NON_ERG_REL-77
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 75

description:
batch 2
NON_ERG_REL-75
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 69

description:
batch 2
NON_ERG_REL-69
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 74

description:
batch 2
NON_ERG_REL-74
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 70

description:
batch 2
NON_ERG_REL-70
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 62

description:
batch 1
NON_ERG_REL-62
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 76

description:
batch 2
NON_ERG_REL-76
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 61

description:
batch 1
NON_ERG_REL-61
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 65

description:
batch 1
NON_ERG_REL-65
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 60

description:
batch 1
NON_ERG_REL-60
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 66

description:
batch 1
NON_ERG_REL-66
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 58

description:
batch 1
NON_ERG_REL-58
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 73

description:
batch 2
NON_ERG_REL-73
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 56

description:
batch 1
NON_ERG_REL-56
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 54

description:
batch 3
NON_ERG_REL-54
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 67

description:
batch 2
NON_ERG_REL-67
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 53

description:
batch 3
NON_ERG_REL-53
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 72

description:
batch 2
NON_ERG_REL-72
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 55

description:
batch 3
NON_ERG_REL-55
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 59

description:
batch 1
NON_ERG_REL-59
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 52

description:
batch 3
NON_ERG_REL-52
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 57

description:
batch 1
NON_ERG_REL-57
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 64

description:
batch 1
NON_ERG_REL-64
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 51

description:
batch 3
NON_ERG_REL-51
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 68

description:
batch 2
NON_ERG_REL-68
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 71

description:
batch 2
NON_ERG_REL-71
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 107

description:
batch 3
NON_ERG_REL-107
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 63

description:
batch 1
NON_ERG_REL-63
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 49

description:
batch 2
NON_ERG_REL-49
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 45

description:
batch 1
NON_ERG_REL-45
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 40

description:
batch 1
NON_ERG_REL-40
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 44

description:
batch 3
NON_ERG_REL-44
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 39

description:
batch 3
NON_ERG_REL-39
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 33

description:
batch 1
NON_ERG_REL-33
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 29

description:
batch 3
NON_ERG_REL-29
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 42

description:
batch 2
NON_ERG_REL-42
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 31

description:
batch 1
NON_ERG_REL-31
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 41

description:
batch 1
NON_ERG_REL-41
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 48

description:
batch 2
NON_ERG_REL-48
Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 46

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 35

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Gene expression data from pediatric acute leukemia samples at diagnosis


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Gene expression data from pediatric acute leukemia samples at diagnosis


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Gene expression data from pediatric acute leukemia samples at diagnosis


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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 34

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 37

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 32

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 30

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 38

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 23

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 28

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 26

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 21

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 27

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 24

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 25

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 22

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 20

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 17

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 18

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 19

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 15

description:
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title: non-ERG-related_sample 13

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title: non-ERG-related_sample 14

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 11

description:
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title: non-ERG-related_sample 50

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 8

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_sample 35

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis

source_name: ERG-related no data about ERG intragenic deletion


title: non-ERG-related_sample 7

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 16

description:
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title: non-ERG-related_sample 1

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title: non-ERG-related_sample 9

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title: non-ERG-related_sample 12

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title: non-ERG-related_sample 5

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title: non-ERG-related_sample 3

description:
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title: non-ERG-related_sample 4

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title: non-ERG-related_sample 2

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis


title: non-ERG-related_sample 6

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_ERG-not deleted_sample 34

description:
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source_name: ERG-related without ERG intragenic deletion


title: ERG-related_ERG-not deleted_sample 31

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_ERG-not deleted_sample 33

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_ERG-not deleted_sample 32

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: ERG-related_ERG-not deleted_sample 28

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title: ERG-related_ERG-not deleted_sample 27

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title: ERG-related_ERG-not deleted_sample 26

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title: ERG-related_ERG-not deleted_sample 24

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title: ERG-related_ERG-not deleted_sample 22

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title: ERG-related_ERG-not deleted_sample 21

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title: ERG-related_ERG-not deleted_sample 20

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title: ERG-related_ERG-deleted_sample 10

description:
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Gene expression data from pediatric acute leukemia samples at diagnosis

source_name: ERG-related with ERG intragenic deletion


title: ERG-related_ERG-deleted_sample 7

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title: ERG-related_ERG-deleted_sample 13

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title: ERG-related_ERG-not deleted_sample 15

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title: ERG-related_ERG-not deleted_sample 17

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title: ERG-related_ERG-not deleted_sample 19

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title: ERG-related_ERG-deleted_sample 12

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title: ERG-related_ERG-deleted_sample 8

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title: ERG-related_ERG-deleted_sample 14

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title: ERG-related_ERG-deleted_sample 11

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title: ERG-related_ERG-deleted_sample 6

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title: ERG-related_ERG-deleted_sample 2

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Gene expression data from pediatric acute leukemia samples at diagnosis


title: ALL_patient_205 [HG-U133_Plus_2]

status: Public on Feb 28 2017

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

description: Sample name: LfL2004_551

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols.

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner.

data_processing: Data normalization was performed using the Robust Multichip Average (RMA) method as described by Irizarry et al. 2003. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization. Only the 44754 probe sets present both on the A, B chips and the 2.0 Plus chips were included in the analysis. Some probe sets on the A, B chips tend to have lower mean signal levels and higher standard deviations than the corresponding probe sets on the Plus 2.0 chips. To eliminate this batch effect resulting from the different chip designs, we performed a second normalization using an empirical Bayesian method.

source_name: bone marrow mononuclear cells, MLL-positive ALL

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols.

extract_protocol: Mononuclear cells from bone marrow (BM) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute lymphoblastic leukemia (ALL).

value: adult

value: bone marrow mononuclear cells

value: acute lymphoblastic leukemia (ALL)

tag: all type

value: MLL-positive


title: ALL_patient_206 [HG-U133_Plus_2]

description: Sample name: LfL2004_569


title: ALL_patient_185 [HG-U133_Plus_2]

description: Sample name: BER_00203

source_name: bone marrow mononuclear cells, B-other ALL

value: B-other


title: ALL_patient_198 [HG-U133_Plus_2]

description: Sample name: LfL2004_266

source_name: bone marrow mononuclear cells, Ph-positive ALL

value: Ph-positive


title: ALL_patient_207 [HG-U133_Plus_2]

description: Sample name: LfL2005_107


title: ALL_patient_194 [HG-U133_Plus_2]

description: Sample name: LfL2004_079


title: ALL_patient_193 [HG-U133_Plus_2]

description: Sample name: LfL2004_047


title: ALL_patient_202 [HG-U133_Plus_2]

description: Sample name: LfL2004_414


title: ALL_patient_186 [HG-U133_Plus_2]

description: Sample name: BER_00204


title: ALL_patient_195 [HG-U133_Plus_2]

description: Sample name: LfL2004_090


title: ALL_patient_184 [HG-U133_Plus_2]

description: Sample name: BER_00202


title: ALL_patient_200 [HG-U133_Plus_2]

description: Sample name: LfL2004_371

source_name: bone marrow mononuclear cells, Ph-like ALL

value: Ph-like


title: ALL_patient_203 [HG-U133_Plus_2]

description: Sample name: LfL2004_416


title: ALL_patient_197 [HG-U133_Plus_2]

description: Sample name: LfL2004_154


title: ALL_patient_182 [HG-U133_Plus_2]

description: Sample name: BER_00200


title: ALL_patient_187 [HG-U133_Plus_2]

description: Sample name: BER_00205


title: ALL_patient_192 [HG-U133_Plus_2]

description: Sample name: LfL2004_011


title: ALL_patient_188 [HG-U133_Plus_2]

description: Sample name: BER_00206


title: ALL_patient_190 [HG-U133_Plus_2]

description: Sample name: BER_00210


title: ALL_patient_191 [HG-U133_Plus_2]

description: Sample name: LfL2004_002


title: ALL_patient_199 [HG-U133_Plus_2]

description: Sample name: LfL2004_355


title: ALL_patient_183 [HG-U133_Plus_2]

description: Sample name: BER_00201


title: ALL_patient_196 [HG-U133_Plus_2]

description: Sample name: LfL2004_150


title: ALL_patient_179 [HG-U133_Plus_2]

description: Sample name: BER_00196


title: ALL_patient_189 [HG-U133_Plus_2]

description: Sample name: BER_00209


title: ALL_patient_201 [HG-U133_Plus_2]

description: Sample name: LfL2004_400


title: ALL_patient_181 [HG-U133_Plus_2]

description: Sample name: BER_00199


title: ALL_patient_180 [HG-U133_Plus_2]

description: Sample name: BER_00197


title: ALL_patient_174 [HG-U133_Plus_2]

description: Sample name: BER_00189


title: ALL_patient_176 [HG-U133_Plus_2]

description: Sample name: BER_00191


title: ALL_patient_172 [HG-U133_Plus_2]

description: Sample name: BER_00187


title: ALL_patient_175 [HG-U133_Plus_2]

description: Sample name: BER_00190


title: ALL_patient_171 [HG-U133_Plus_2]

description: Sample name: BER_00186


title: non-ERG-related_sample 10

description:
batch 2
NON_ERG_REL-10
Gene expression data from pediatric acute leukemia samples at diagnosis


title: ALL_patient_166 [HG-U133_Plus_2]

description: Sample name: BER_00179


title: ALL_patient_178 [HG-U133_Plus_2]

description: Sample name: BER_00195


title: ALL_patient_161 [HG-U133_Plus_2]

description: Sample name: BER_00148


title: ALL_patient_170 [HG-U133_Plus_2]

description: Sample name: BER_00184


title: ALL_patient_163 [HG-U133_Plus_2]

description: Sample name: BER_00173


title: ALL_patient_165 [HG-U133_Plus_2]

description: Sample name: BER_00176


title: ALL_patient_173 [HG-U133_Plus_2]

description: Sample name: BER_00188


title: ALL_patient_158 [HG-U133_Plus_2]

description: Sample name: BER_00142


title: ALL_patient_160 [HG-U133_Plus_2]

description: Sample name: BER_00145


title: ALL_patient_168 [HG-U133_Plus_2]

description: Sample name: BER_00182


title: ALL_patient_177 [HG-U133_Plus_2]

description: Sample name: BER_00192


title: ALL_patient_159 [HG-U133_Plus_2]

description: Sample name: BER_00144


title: ALL_patient_167 [HG-U133_Plus_2]

description: Sample name: BER_00180


title: ALL_patient_164 [HG-U133_Plus_2]

description: Sample name: BER_00174


title: ALL_patient_157 [HG-U133_Plus_2]

description: Sample name: BER_00141


title: ALL_patient_156 [HG-U133_Plus_2]

description: Sample name: BER_00140


title: ALL_patient_169 [HG-U133_Plus_2]

description: Sample name: BER_00183


title: ALL_patient_153 [HG-U133_Plus_2]

description: Sample name: BER_00136


title: ALL_patient_155 [HG-U133_Plus_2]

description: Sample name: BER_00139


title: ALL_patient_152 [HG-U133_Plus_2]

description: Sample name: BER_00133


title: ALL_patient_162 [HG-U133_Plus_2]

description: Sample name: BER_00150


title: ALL_patient_151 [HG-U133_Plus_2]

description: Sample name: BER_00131


title: ALL_patient_154 [HG-U133_Plus_2]

description: Sample name: BER_00137


title: ALL_patient_150 [HG-U133_Plus_2]

description: Sample name: BER_00130


title: ALL_patient_148 [HG-U133_Plus_2]

description: Sample name: BER_00127


title: ALL_patient_146 [HG-U133_Plus_2]

description: Sample name: BER_00125


title: ALL_patient_147 [HG-U133_Plus_2]

description: Sample name: BER_00126


title: ALL_patient_134 [HG-U133_Plus_2]

description: Sample name: BER_00105


title: ALL_patient_142 [HG-U133_Plus_2]

description: Sample name: BER_00115


title: ALL_patient_136 [HG-U133_Plus_2]

description: Sample name: BER_00107


title: ALL_patient_149 [HG-U133_Plus_2]

description: Sample name: BER_00129


title: ALL_patient_143 [HG-U133_Plus_2]

description: Sample name: BER_00116


title: ALL_patient_145 [HG-U133_Plus_2]

description: Sample name: BER_00118


title: ALL_patient_140 [HG-U133_Plus_2]

description: Sample name: BER_00111


title: ALL_patient_141 [HG-U133_Plus_2]

description: Sample name: BER_00113


title: ALL_patient_130 [HG-U133_Plus_2]

description: Sample name: BER_00101


title: ALL_patient_135 [HG-U133_Plus_2]

description: Sample name: BER_00106


title: ALL_patient_133 [HG-U133_Plus_2]

description: Sample name: BER_00104


title: ALL_patient_137 [HG-U133_Plus_2]

description: Sample name: BER_00108


title: ALL_patient_144 [HG-U133_Plus_2]

description: Sample name: BER_00117


title: ALL_patient_131 [HG-U133_Plus_2]

description: Sample name: BER_00102


title: ALL_patient_127 [HG-U133_Plus_2]

description: Sample name: BER_00096


title: ALL_patient_126 [HG-U133_Plus_2]

description: Sample name: BER_00095


title: ALL_patient_132 [HG-U133_Plus_2]

description: Sample name: BER_00103


title: ALL_patient_123 [HG-U133_Plus_2]

description: Sample name: BER_00092


title: ALL_patient_139 [HG-U133_Plus_2]

description: Sample name: BER_00110


title: ALL_patient_128 [HG-U133_Plus_2]

description: Sample name: BER_00098


title: ALL_patient_129 [HG-U133_Plus_2]

description: Sample name: BER_00100


title: ALL_patient_204 [HG-U133_Plus_2]

description: Sample name: LfL2004_502


title: ALL_patient_124 [HG-U133_Plus_2]

description: Sample name: BER_00093


title: ALL_patient_138 [HG-U133_Plus_2]

description: Sample name: BER_00109


title: ALL_patient_125 [HG-U133_Plus_2]

description: Sample name: BER_00094


title: ALL_patient_121 [HG-U133_Plus_2]

description: Sample name: BER_00084_2


title: ALL_patient_122 [HG-U133_Plus_2]

description: Sample name: BER_00090


title: ALL_patient_119 [HG-U133_Plus_2]

description: Sample name: BER_00080


title: ALL_patient_120 [HG-U133_Plus_2]

description: Sample name: BER_00083


title: ALL_patient_118 [HG-U133_Plus_2]

description: Sample name: BER_00076


title: ALL_patient_115 [HG-U133_Plus_2]

description: Sample name: BER_00066


title: ALL_patient_116 [HG-U133_Plus_2]

description: Sample name: BER_00070


title: ALL_patient_117 [HG-U133_Plus_2]

description: Sample name: BER_00075


title: ALL_patient_112 [HG-U133_Plus_2]

description: Sample name: BER_00048


title: ALL_patient_113 [HG-U133_Plus_2]

description: Sample name: BER_00050


title: ALL_patient_110 [HG-U133_Plus_2]

description: Sample name: BER_00010


title: ALL_patient_114 [HG-U133_Plus_2]

description: Sample name: BER_00053


title: ALL_patient_111 [HG-U133_Plus_2]

description: Sample name: BER_00040