title: M18_56

description:
M18_56
7196763028_J.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes


title: M13_150

status: Public on Oct 27 2016

type: RNA

city: Dallas

first: Jason

middle: A

last: Skinner

state: TX

address: 3434 Live Oak

country: USA

institute: Baylor Institute for Immunology Research

description:
M13_150
7196763028_H.AVG_Signal

hyb_protocol: Standard Illumina HT-12 V4 hybridization protocol

scan_protocol: Standard Illumina iScan protocol

data_processing: Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the datase to yield the Matrix normalized data available here.  Data was further filtered on probes for which pval detection  was below 0.01 in at least one sample were kept for analysis. The ComBat method (Johnson et al, Biostatistics, 2007) was used on those normalized data to correct for batch effects (namely a small Hybridization chamber effect and the Training/test set effect), that was identified through Principal Variance Component Analysis (PVCA)

label: Biotin

molecule: total RNA

organism: Macaca fascicularis

source_name: total RNA (globin reduced)

label_protocol: Biotinylated cRNA were prepared using Illumina Totalprep-96 Amplification Kits with 250ng input

extract_protocol: RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using the Ambion MagMax-96 total RNA Isolation kits, Globin message reduction was conducted using Ambion GlobinClear Human 96 Kits

tag: tissue

value: Whole Blood

tag: ChIP

tag: hyb chamber

tag: dataset

value: Training

tag: synchroset

value: No

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

value: Latent

tag: FDG avidity

tag: FDG group

value: High

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M4_150

description:
M4_150
7196763028_F.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

value: Low

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes


title: M9_10

description:
M9_10
7196763044_A.AVG_Signal

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M15_120

description:
M15_120
7196763028_I.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: hemoglobin

tag: hematocrit

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M18_90

description:
M18_90
7196763028_C.AVG_Signal

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

value: Active

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes


title: M6_Pre1

description:
M6_Pre1
7196763028_G.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

value: Yes

tag: FDG avidity

tag: FDG group


title: M17_150

description:
M17_150
7196763028_E.AVG_Signal

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: hemoglobin

tag: hematocrit

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M19_120

description:
M19_120
6303281024_J.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: FDG avidity

tag: FDG group

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes


title: M16_30

description:
M16_30
6303281024_H.AVG_Signal

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status


title: M7_42

description:
M7_42
6303281024_G.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: hemoglobin

tag: hematocrit

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M2_3

description:
M2_3
6303281024_I.AVG_Signal

tag: FDG avidity

tag: FDG group


title: M3_120

description:
M3_120
7196763028_B.AVG_Signal

tag: pittid

tag: monkeyid

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes


title: M5_7

description:
M5_7
6303281024_K.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: time point

tag: infection time

tag: clinical status


title: M4_10

description:
M4_10
6303281024_L.AVG_Signal

tag: pittid

tag: monkeyid

tag: FDG avidity

tag: FDG group


title: M13_90

description:
M13_90
7196763028_A.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M5_42

description:
M5_42
6303256042_I.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: time point

tag: infection time


title: M3_Pre1

description:
M3_Pre1
6303256042_J.AVG_Signal

tag: pittid

tag: monkeyid

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M5_10

description:
M5_10
6303281024_C.AVG_Signal


title: M3_150

description:
M3_150
6303281024_E.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M12_7

description:
M12_7
7196763028_D.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M14_10

description:
M14_10
6303281024_A.AVG_Signal


title: M13_7

description:
M13_7
6303256042_K.AVG_Signal


title: M12_120

description:
M12_120
6303281024_F.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained


title: M2_150

description:
M2_150
6303281024_D.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M10_Pre1

description:
M10_Pre1
6303281024_B.AVG_Signal


title: M4_3

description:
M4_3
6303256042_L.AVG_Signal


title: M1_180

description:
M1_180
6303256042_H.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained


title: M15_7

description:
M15_7
6303256042_G.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M12_150

description:
M12_150
6303256042_D.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M15_3

description:
M15_3
6303256042_F.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M7_56

description:
M7_56
6303256042_E.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M5_150

description:
M5_150
6303256038_L.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M13_42

description:
M13_42
6303256042_B.AVG_Signal

tag: FDG group


title: M3_Pre2

description:
M3_Pre2
6303256038_D.AVG_Signal

tag: tissue


title: M19_30

description:
M19_30
6303256042_C.AVG_Signal

tag: ChIP


title: M9_90

description:
M9_90
6303256034_L.AVG_Signal

tag: hyb chamber

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M1_56

description:
M1_56
6303256038_A.AVG_Signal

tag: tissue

tag: ChIP

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M16_180

description:
M16_180
6303256038_F.AVG_Signal

tag: hyb chamber

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M14_Pre2

description:
M14_Pre2
6303256038_K.AVG_Signal

tag: tissue

tag: ChIP

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M2_20

description:
M2_20
6303256038_I.AVG_Signal

tag: hyb chamber


title: M8_Pre1

description:
M8_Pre1
6303256042_A.AVG_Signal


title: M14_3

description:
M14_3
6303256034_E.AVG_Signal


title: M18_30

description:
M18_30
6303256038_G.AVG_Signal


title: M18_Pre1

description:
M18_Pre1
6303256038_B.AVG_Signal


title: M6_42

description:
M6_42
6303256038_H.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M13_Pre2

description:
M13_Pre2
6303256038_C.AVG_Signal

tag: tissue

tag: ChIP

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M4_20

description:
M4_20
6303256038_E.AVG_Signal

tag: hyb chamber


title: M18_120

description:
M18_120
6303256034_D.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M4_Pre2

description:
M4_Pre2
6303256034_I.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M17_Pre1

description:
M17_Pre1
6303256034_K.AVG_Signal


title: M8_150

description:
M8_150
6303256034_G.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained


title: M11_7

description:
M11_7
6303256034_C.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M19_150

description:
M19_150
6303256032_L.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M4_56

description:
M4_56
6303256034_J.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M1_20

description:
M1_20
6303256034_B.AVG_Signal


title: M19_3

description:
M19_3
6303256034_A.AVG_Signal


title: M17_7

description:
M17_7
6303256032_G.AVG_Signal


title: M16_120

description:
M16_120
6303256032_I.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained


title: M14_30

description:
M14_30
6303256038_J.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M3_30

description:
M3_30
6303256032_K.AVG_Signal


title: M3_180

description:
M3_180
6303256032_J.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M6_150

description:
M6_150
7196763044_B.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained


title: M9_30

description:
M9_30
6303256032_H.AVG_Signal


title: M17_10

description:
M17_10
6303256020_K.AVG_Signal


title: M19_56

description:
M19_56
6303256020_D.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes


title: M2_42

description:
M2_42
6303256032_E.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M6_120

description:
M6_120
6303256032_A.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M17_120

description:
M17_120
6303256032_D.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M1_42

description:
M1_42
6303256020_I.AVG_Signal


title: M18_20

description:
M18_20
6303256020_G.AVG_Signal


title: M15_20

description:
M15_20
6303256032_C.AVG_Signal


title: MDA-MB-468_siALPK1_rep2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using Illumina's BeadStudio Data Analysis Software.

organism: Homo sapiens

source_name: MDA-MB-468_si KD of ALPK1

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: MDA-MB-468 cells were purchased from ATCC and cultivated in standard medium (DMEM/10%, FBS/1%Pen-Strep).

extract_protocol: Total RNA was isolated from sub-confluent cultures grown in 6-well plates using the RNeasy Plus Kit from Qiagen, applying the Qiagen Supplementary Protocol: Purification of miRNA from animal cells using the RNeasy® Plus Mini kit and RNeasy MinElute® Cleanup Kit (Protocol 1). RNA concentration was quantified using the NanoDrop 2000 (Thermo Scientific). Reverse transcription was performed using the RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific) according to the manufacturer’s manual. A maximum of 2 µg total RNA was reverse transcribed.

treatment_protocol: shRNA mediated Knockdown:  shRNA knockdown  was performed using a subset of SIGMA’s Lentiviral Human Kinome Mission shRNA library. For viral production, 50 ng of each construct were combined with PCMV dR8.74 (35 ng) and PMD.G-VSVG, (17.5 ng) packaging plasmids and transfected into 293FT cells using X-tremegene HP (Roche) in 96-well format in collagen coated plates. Twenty-four hrs after transfection, culture media was replaced and viral supernatants were collected 48 hrs later. siRNA mediated Knockdown: Cells were transfected in suspension with control nonspecific or GFP-targeting siRNAs or siRNAs targeted against ERN1 or ALPK1 (10 nM) using Lipofectamine® RNAiMAX Transfection Reagent (Life Technologies). In the siRNA combination approach 2x5 nM siRNA was used, single siRNAs were used together with 5 nM non-specific control. The following siRNAs were used: siGFP (M. Truss, Berlin), Silencer® Negative Control #1 (Ambion, Life Technologies, #AM4611), ERN1 pre-designed Silencer® siRNA (Ambion, Life Technologies, #289308), ALPK1 validated Silencer® siRNA (Ambion, Life Technologies, #1074). After 24 hrs transfection medium was replaced by normal growth medium and the cells were cultured for further 48 hrs. Subsequently, cells were either lysed for RNA extraction, seeded for colony formation assays or fixed in ice-cold methanol for immunocytochemistry.

tag: cell line

tag: tissue origin

value: Breast

tag: gender

value: female

tag: cell type

value: breast cancer cell line

tag: genotype/variation

value: siRNA knockdown of ALPK1

tag: array id


title: M18_10

description:
M18_10
6303256020_L.AVG_Signal

tag: tissue

tag: ChIP


title: M19_90

description:
M19_90
6303256020_E.AVG_Signal

tag: hyb chamber

tag: dataset

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M16_150

description:
M16_150
6303256020_A.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: M17_3

description:
M17_3
6303256020_B.AVG_Signal

tag: dataset


title: M14_90

description:
M14_90
6303256032_B.AVG_Signal

tag: tissue

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: M1_7

description:
M1_7
6303256020_F.AVG_Signal

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: M13_180

description:
M13_180
6303256020_J.AVG_Signal

tag: tissue

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: per lymphosstained

tag: per cd3stained

tag: per cd8

tag: per cd16pos cd3neg

tag: per cd20


title: MDA-MB-468_siCTL_rep2

source_name: MDA-MB-468_si Ctl

tag: cell line

tag: tissue origin

tag: gender

tag: cell type

tag: genotype/variation

value: siRNA knockdown of control vector

tag: array id


title: M8_Pre2

description:
M8_Pre2
6303256020_C.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group


title: MDA-MB-468_siCTL_rep1

tag: cell line

tag: tissue origin


title: MDA-MB-468_siALPK1_rep1

tag: gender

tag: cell type


title: M9_120

description:
M9_120
6303256032_F.AVG_Signal

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet

tag: per neutrophils

tag: per lymphocytes

tag: per monocytes

tag: per eosinophils

tag: per basophils

tag: abs neutrophils

tag: abs lymphocytes

tag: abs monocytes

tag: abs eosinophils

tag: per monos by lymphos

tag: abs monos by lymphos


title: MDA-MB-468_shCTL_rep2

source_name: MDA-MB-468_sh Ctl

tag: cell line

tag: tissue origin

tag: gender

tag: genotype/variation

value: shRNA knockdown control vector

tag: array id


title: M15_90

description:
M15_90
6303256020_H.AVG_Signal

tag: tissue

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid

tag: monkeyid

tag: time point

tag: infection time

tag: clinical status

tag: FDG avidity

tag: FDG group

tag: hemoglobin

tag: hematocrit

tag: wbc

tag: platelet


title: MDA-MB-468_shALPK1_rep2

source_name: MDA-MB-468_sh KD of ALPK1

tag: cell line

tag: tissue origin

tag: gender

tag: cell type

tag: genotype/variation

value: shRNA knockdown of ALPK1

tag: array id


title: MDA-MB-468_siERN1_rep2

source_name: MDA-MB-468_si KD of ERN1

value: siRNA knockdown of ERN1


title: MDA-MB-468_siERN1_rep1


title: MDA-MB-468_shERN1_rep2

source_name: MDA-MB-468_sh KD of ERN1

value: shRNA knockdown of ERN1


title: MDA-MB-468_shERN1_rep1


title: MDA-MB-468_shCTL_rep1


title: MDA-MB-468_shALPK1_rep1


title: M7_3

description:
M7_3
6303256034_F.AVG_Signal

tag: tissue

value: Whole Blood

tag: ChIP

tag: hyb chamber

tag: dataset

tag: synchroset

tag: pittid


title: T20 miR210 vec rep2

city: Belvaux

first: Elisabeth

last: Letellier

address: 6, Avenue du Swing

department: Life Sciences Research Unit

country: Luxembourg

institute: University of Luxembourg

hyb_protocol: 3.5 ug of labeled DNA + hybridization controls are injected into Affymetrix cartridge. Incubate with rotation at 60 rpm for 16 hr at 45°C then arrays are washed and scanned

scan_protocol: Arrays were scanned with the Affymetrix® GeneChip® Scanner 3000 following the protocol: GeneChip® Expression Wash, Stain and Scan For Cartridge Arrays P/N 702731 Rev. 4

data_processing: The data were imported, normalized and summarized to transcript cluster level using Partek GS software. We used GC RMA method with quantile normalization.

label: biotin

source_name: T20 miR210 vec

label_protocol: In this procedure, the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA is required for fragmentation and labeling

growth_protocol: Sphere cultures were maintained in serum-free medium containing growth factors

extract_protocol: Total RNA was extracted with Qiazol, using the miRNeasy extraction kit (Qiagen), following the user manual

value: Colorectal cancer patient-derived sphere cultures

tag: transduced with

value: miR-210 lentiviral particles


title: Liver tissue  from MET flox mice at D2 Phx

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

source_name: met flox_liver_D2 PHx

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Following systemic inhibition of MET-EGFR liver a partial hepatectomy was carried out and liver tissues harveted at D0,D2,D7,D14 PHx  time points. There were 4 groups, METKO+canertinib, METFLOX+canertinib, MET KO and MET FLOX

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

treatment_protocol: METK0 were generated by delting Exon 16 of met  by using a tamoxiphen inducible syste, EGFR was inhibited by adding Canertinib in the diet with tha aim of administrating 80 mg/kg.  The four experimental groups were METKO + canertinib,  the second group was METFlox+canertinib, the third group was METKO and the fourth group was METFlox.

tag: strain background

value: Metff/ff:ERCre+/+ mice

tag: time point

value: at d2 PHx MET flox

value: liver


title: Liver tissue  from MET flox mice at D0 Phx

source_name: met flox_liver_D0 PHx

value: at d0 PHx MET flox


title: Liver tissue  from MET flox + canertinib  mice at D14 Phx

source_name: METFLOX+canertinib_liver_D14 PHx

value: at d14 PHx MET flox +canertinib


title: T20 miR210 vec rep3


title: gastrocnemius from transgenic mice, biological rep3

city: wuhan

first: fei

last: ying

address: shizishan street

country: China

institute: hzau

description: Gene expression data from gastrocnemius of transgenic mice  konckout DGAT1 gene

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouth Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed withGC-RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: gastrocnemius from transgenic mice of konckout DGAT1 gene

growth_protocol: gastrocnemius collections of three month mice at room temperature (RT) according to the different mouth.

treatment_protocol: mice were knocked out DGAT1gene.Selected gastrocnemius were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: DGAT1 knockout transgenic

value: male

tag: age

value: 3 months

value: gastrocnemius


title: Liver tissue  from MET flox mice at D7 Phx

source_name: met flox_liver_D7 PHx

value: at d7 PHx MET flox


title: gastrocnemius from WT mice, biological rep2

description: Gene expression data from gastrocnemius of WT mice

source_name: gastrocnemius from WT mice

value: wild type


title: gastrocnemius from WT mice, biological rep3


title: gastrocnemius from WT mice, biological rep1


title: Liver tissue  from METKO  mice at D14 Phx

source_name: METKO_liver_D14 PHx

value: at d14 PHx METKO


title: gastrocnemius from transgenic mice, biological rep1


title: Liver tissue  from METKO mice at D7 Phx

source_name: METKO_liver_D7 PHx

value: at d7 PHx METKO


title: T20 miR210 vec rep1


title: T20 control vec rep1

source_name: T20 control vec

value: control vector


title: Liver tissue  from MET flox + canertinib  mice at D7 Phx

source_name: METFLOX+canertinib_liver_D7 PHx

value: at d7 PHx MET flox +canertinib


title: Liver tissue  from METKO+canertinib mice at D2 Phx

source_name: METKO+canertinib_liver_d2 PHx

value: at d2 PHx METKO+canertinib


title: Liver tissue  from METKO mice at D2 Phx

source_name: METKO_liver_D2 PHx

value: at d2 PHx METKO


title: gastrocnemius from transgenic mice, biological rep2


title: Liver tissue  from MET flox mice at D14 Phx

source_name: met flox_liver_D14 PHx

value: Metff/ff:ERCre+/+ mice

value: at d14 PHx MET flox


title: T20 control vec rep3

value: Colorectal cancer patient-derived sphere cultures


title: Liver tissue  from METKO+canertinib mice at D14 Phx

source_name: METKO+canertinib_liver_D14 PHx

value: at d14 PHx METKO+canertinib

value: liver


title: Liver tissue  from MET flox + canertinib  mice at D2 Phx

source_name: METFLOX+canertinib_liver_D2 PHx

value: at d2 PHx MET flox +canertinib


title: Liver tissue  from MET flox+canertinib  mice at D0 Phx

source_name: METFLOX+canertinib_liver_D0 PHx

value: at d0 PHx MET flox +canertinib


title: Liver tissue  from METKO mice at D0 Phx

source_name: METKO_liver_D0 PHx

value: at d0 PHx METKO


title: Liver tissue  from METKO+canertinib mice at D0 Phx

source_name: METKO+canertinib_liver_d0 Phx

value: at d0 PHx METKO+canertinib


title: Liver tissue  from METKO+canertinib mice at D7 Phx

source_name: METKO+canertinib_liver_D7 PHx

value: at d7  PHx METKO+canertinib


title: T20 control vec rep2


title: Control larve at 10 dpf, biological rep2

city: Tianjin

first: Xudan

last: Lei

address: Weijin Road 94

department: Medical College

institute: nankai University

description: Gene expression data from control 2 zebrafish

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip2 Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G

organism: Danio rerio

source_name: zebrafish larve at 10dpf

growth_protocol: Tg (mbp:nfsB-egfp) larvae were collected after natural spawning, housed at 28.5C, and staged by hours post fertilization (hpf) or days post fertilization (dpf)

treatment_protocol: Metronidazole (Sigma M3761) was dissolved in 0.2% dimethyl sulfoxide (DMSO, Sigma V900090) in  E3 medium (5 mmol/L NaCl, 0.17 mmol/L KCl, 0.33 mmol/L CaCl2, 0.33 mmol/L MgSO4, pH 7.2) with vigorous shaking in the dark. 5dpf Tg (mbp:nfsB-egfp) fish were treated continuously with 5mM metronidazole-0.2% DMSO-system water for 5 days in the dark as the experimental group.

value: 10 dpf zebrafish

tag: genotype

value: Tg (mbp:nfsB-egfp) larvae

tag: medium

value: 0.2% DMSO-E3 medium


title: Mtz treatment 1 larve at 10 dpf, biological rep1

description: Gene expression data from Mtz treatment 1 zebrafsih

value: 5mM metronidazole-0.2% DMSO-E3 medium


title: Control larve at 10 dpf, biological rep3

description: Gene expression data from control 3 zebrafish


title: Mtz treatment 1 larve at 10 dpf, biological rep3

description: Gene expression data from Mtz treatment 3 zebrafsih


title: T34_glioblastoma

status: Public on Oct 26 2016

city: Heidelberg

first: Christel

last: Herold-Mende

address: Im Neuenheimer Feld 400

department: Department of Neurosurgery

institute: Heidelberg University Hospital

description:
location group 4
8136640004_H

data_processing: Raw-intensity data were obtained after image analysis of the fluorescent spot intensity reads. All preprocessing and normalization steps were performed in the R programming environment [www.r-project.org]. Inter-array normalization was conducted using qspline normalization in the affy package. Probe sets belonging to one gene were median summarized leading to a reduced number of probes in the normalized data set. Next, a linear model was fitted to account for different batches (limma package). Lastly, intra-array normalization was performed by means of median-centering data and followed by log2 transformation.

source_name: glioblastoma tissue

label_protocol: Standard labeling protocol of Genomic Core Facility of the German Cancer Research Center (DKFZ, Heidelberg, Germany)

extract_protocol: Total RNA was extracted from tissue using the AllPrep Kit (Qiagen) according to manufacturer's instructions. RNA integrity was assessed by the Agilent 2100 Bioanalyzer.

value: glioblastoma

tag: brain location

value: infiltrating neither subventricular zone nor cortex

tag: batch


title: T31_glioblastoma

description:
location group 4
8136640006_H


title: T32_glioblastoma

description:
location group 4
8136640006_I


title: T29_glioblastoma

description:
location group 4
8136640005_I


title: pancreasRNA_PDAC_rep2

city: Chengdu

first: Shikai

last: Zhu

address: No.32 West Second Section First Ring Road

institute: Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital

description: lncRNA expression data from PDAC

hyb_protocol: Sample array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.Briefly, 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven,and then the hybridized arrays were washed and fixed.

scan_protocol: The hybridized arrays were scanned with the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: pancreasRNA, PDAC

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

treatment_protocol: PDAC tissue samples and their matched adjacent non-tumor samples  were taken during surgery, immediately frozen in liquid nitrogen, and stored at -80˚C for microarry analysis.

tag: individual

value: patient 2

value: PDAC

tag: gender

value: Female


title: T28_glioblastoma

description:
location group 4
8136640005_H


title: T33_glioblastoma

description:
location group 4
8981561095_H


title: pancreasRNA_control_rep1

description: lncRNA expression data from pancreatic tissue

source_name: pancreasRNA, control

value: patient 1

value: pancreas, matched adjacent non-tumor

value: Male


title: NO-NH-IA-CK-AB 0.5-0.5-1-1-1-rep2

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

department: Biology

country: France

institute: CNRS

description: SAMPLE 64

hyb_protocol: Affymetrix recommendation

scan_protocol: Affymetrix recommendation

data_processing: Mas5 [R]

organism: Arabidopsis thaliana

label_protocol: Affymetrix recommendation

growth_protocol: Hydroponic media consisted of 1X Murashige and Skoog basal medium containing no nitrogen or sucrose (custom-ordered, GibcoBRL, Gaithersburg, MD, USA) supplemented with: 3mM sucrose, 0.5mM ammonium succinate, MES buffered at pH 5.7 (0.5 g.l-1). Plants were grown for 14-16 days in day/night cycles (16/8hr) (150 µmol photons m-2.s-1) (Percival Scientific Inc., Perry, IA, USA), at 22°C. 24 hours before the treatments plants were transferred toward an equivalent fresh N-free medium.

extract_protocol: Trizol

treatment_protocol: Treatments are then applied with combinations of IAA, CK, ABA, NO3-, NH4+

value: Roots

tag: treated with

value: after 4 hours of treatment


title: T35_glioblastoma

description:
location group 4
8136640004_I

tag: tissue


title: Control larve at 10 dpf, biological rep1

description: Gene expression data from control 1 zebrafish


title: pancreasRNA_control_rep2


title: T27_glioblastoma

description:
location group 3
8981561102_H

value: infiltrating cortex


title: T26_glioblastoma

description:
location group 3
8136640006_G


title: T25_glioblastoma

description:
location group 3
8136640006_F


title: T24_glioblastoma

description:
location group 3
8136640006_E


title: pancreasRNA_PDAC_rep3

description: lncRNA expression data from PDAC

value: patient 3


title: pancreasRNA_control_rep3


title: NO-NH-IA-CK-AB 0.5-0.5-1-1-1-rep1

description: SAMPLE 63


title: T23_glioblastoma

description:
location group 3
8136640005_G


title: T36_glioblastoma

description:
location group 4
8136640004_J


title: Mtz treatment 1 larve at 10 dpf, biological rep2

description: Gene expression data from Mtz treatment 2 zebrafsih


title: T30_glioblastoma

description:
location group 4
8136640005_J


title: NO-NH-IA-CK-AB 0.5-0.5-1-1-0-rep2

description: SAMPLE 62


title: pancreasRNA_PDAC_rep1

description: lncRNA expression data from PDAC


title: NO-NH-IA-CK-AB 0.5-0.5-1-0-1-rep2

description: SAMPLE 60


title: T20_glioblastoma

description:
location group 3
8136640004_G


title: NO-NH-IA-CK-AB 0.5-0.5-1-1-0-rep1

description: SAMPLE 61


title: T22_glioblastoma

description:
location group 3
8136640005_F


title: T21_glioblastoma

description:
location group 3
8136640005_E


title: T19_glioblastoma

description:
location group 3
8136640004_F


title: NO-NH-IA-CK-AB 0.5-0.5-0-1-1-rep1

description: SAMPLE 55


title: T15_glioblastoma

description:
location group 2
8136640006_D

value: infiltrating subventricular zone


title: T16_glioblastoma

description:
location group 2
8136640005_C


title: NO-NH-IA-CK-AB 0.5-0.5-0-0-1-rep2

description: SAMPLE 52


title: NO-NH-IA-CK-AB 0.5-0.5-0-1-0-rep2

description: SAMPLE 54


title: NO-NH-IA-CK-AB 1-0-1-1-1-rep2

description: SAMPLE 48


title: NO-NH-IA-CK-AB 0.5-0.5-1-0-1-rep1

description: SAMPLE 59


title: T11_glioblastoma

description:
location group 1
8986302004_G

value: infiltrating subventricular zone and cortex


title: T13_glioblastoma

description:
location group 2
8136640004_D


title: T14_glioblastoma

description:
location group 2
8136640006_C


title: NO-NH-IA-CK-AB 0.5-0.5-0-1-0-rep1

description: SAMPLE 53


title: NO-NH-IA-CK-AB 0.5-0.5-0-0-0-rep2

description: SAMPLE 50


title: T18_glioblastoma

description:
location group 3
8136640004_E


title: NO-NH-IA-CK-AB 0.5-0.5-0-0-0-rep1

description: SAMPLE 49


title: T9_glioblastoma

description:
location group 1
8986302004_C


title: T8_glioblastoma

description:
location group 1
8981561093_H


title: NO-NH-IA-CK-AB 0.5-0.5-0-1-1-rep2

description: SAMPLE 56


title: NO-NH-IA-CK-AB 0.5-0.5-0-0-1-rep1

description: SAMPLE 51


title: NO-NH-IA-CK-AB 0.5-0.5-1-0-0-rep2

description: SAMPLE 58


title: NO-NH-IA-CK-AB 0.5-0.5-1-0-0-rep1

description: SAMPLE 57


title: T12_glioblastoma

description:
location group 2
8136640004_C


title: T17_glioblastoma

description:
location group 2
8136640005_D


title: T10_glioblastoma

description:
location group 1
8986302004_D


title: T7_glioblastoma

description:
location group 1
8981561093_B


title: T6_glioblastoma

description:
location group 1
8136640006_B


title: NO-NH-IA-CK-AB 1-0-1-1-1-rep1

description: SAMPLE 47


title: NO-NH-IA-CK-AB 1-0-1-1-0-rep2

description: SAMPLE 46


title: NO-NH-IA-CK-AB 1-0-1-1-0-rep1

description: SAMPLE 45


title: NO-NH-IA-CK-AB 1-0-1-0-0-rep2

description: SAMPLE 42


title: Pax7-/- MEFs, biological rep 2

city: Warsaw

first: Areta

middle: Magda

last: Czerwinska

address: Krakowskie Przedmiescie 26/28

department: Faculty of Biology

country: Poland

institute: University of Warsaw

description: Gene expression data

hyb_protocol: According to manufacturer's protocol.

scan_protocol: The chips were scanned using the Affymetrix GeneAtlas scanner according to manufacturer's protocol.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

source_name: fibroblasts, Pax7ko

label_protocol: According to manufacturer's protocol.

growth_protocol: MEFs were cultured under standard conditions, DMEM containing FBS and antibiotics.

extract_protocol: Total RNA was extracted using High Pure RNA isolation kit (Roche) according to manufacturer's protocol.

treatment_protocol: Material was collected at confluence. Cells were washed with PBS and frozen in -80C.

tag: strain

tag: cell type

value: ESCs


title: T1_glioblastoma

description:
location group 1
8136640004_A


title: Pax7+/+ MEFs, biological rep 3

description: Gene expression data

source_name: fibroblasts, Pax7wt


title: Pax7-/- MEFs, biological rep 3

description: Gene expression data


title: NO-NH-IA-CK-AB 1-0-0-1-1-rep2

description: SAMPLE 40


title: NO-NH-IA-CK-AB 1-0-1-0-1-rep1

description: SAMPLE 43


title: NO-NH-IA-CK-AB 1-0-1-0-0-rep1

description: SAMPLE 41


title: Pax7+/+ MEFs, biological rep 1

description: Gene expression data


title: NO-NH-IA-CK-AB 1-0-1-0-1-rep2

description: SAMPLE 44


title: T4_glioblastoma

description:
location group 1
8136640005_B


title: Pax7+/+ MEFs, biological rep 2

description: Gene expression data


title: Pax7-/- MEFs, biological rep 1

description: Gene expression data


title: T3_glioblastoma

description:
location group 1
8136640005_A


title: NO-NH-IA-CK-AB 1-0-0-1-1-rep1

description: SAMPLE 39


title: NO-NH-IA-CK-AB 1-0-0-1-0-rep2

description: SAMPLE 38


title: NO-NH-IA-CK-AB 1-0-0-0-1-rep1

description: SAMPLE 35


title: siETV5_REP1

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina) was background-subtracted and quantile-normalized using the lumi package within R

growth_protocol: hADSC cells were purchased from Invitrogen and maintained in in Complete MesenPRO RS™ Medium (Invitrogen).

extract_protocol: RNA was extracted and prepared using Aurum Total RNA kit (Bio-Rad) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Cells were plated in 6-well plates and transfected with TRα, TRβ, ETV5 or scramble siRNA. After two days cells RNA was collected.

value: human adipose derived stem cells (hADSC)

tag: transfected with

value: 2 days after transfection


title: siETV5_REP3


title: NO-NH-IA-CK-AB 1-0-0-0-0-rep2

description: SAMPLE 34


title: T2_glioblastoma

description:
location group 1
8136640004_B

value: glioblastoma


title: T5_glioblastoma

description:
location group 1
8136640006_A


title: NO-NH-IA-CK-AB 1-0-0-0-1-rep2

description: SAMPLE 36


title: NO-NH-IA-CK-AB 1-0-0-1-0-rep1

description: SAMPLE 37


title: siTRβ_REP3

value: siTRβ


title: siETV5_REP2


title: siTRβ_REP1


title: siTRβ_REP2


title: siTRα_REP3

value: siTRα


title: NO-NH-IA-CK-AB 0-1-1-1-0-rep1

description: SAMPLE 29


title: NO-NH-IA-CK-AB 0-1-1-1-1-rep1

description: SAMPLE 31


title: X89

city: Toronto

first: Ming

last: Tsao

state: Ontario

address: 610 University Avenue

department: Ontario Cancer Institute

country: Canada

institute: University of Toronto

description: xenograft

hyb_protocol: Standard Illumina hybridization protocol, labeled cRNA were hybridized into 4 Human HT-12 v4.0 BeadChips

data_processing:
The data files were quantified in GenomeStudio Version 2009.2 (Illumina) or Version 2011.1 (Illumina). Probes to be outputed from the GGenomeStudio must have the bead types present in all samples. No imputation was done.
Pre-processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: xenograft

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit/DASL Assay kit for Illumina arrays

growth_protocol: piece of primary tumor was implanted subcutaneously into SCID mouse to form xenograft tumors

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: no treatment

tag: type

value: xenograft

tag: histology

value: large cell carcinoma of the lung

tag: array used

value: Dasl


title: NO-NH-IA-CK-AB 0-1-1-1-1-rep2

description: SAMPLE 32


title: NO-NH-IA-CK-AB 1-0-0-0-0-rep1

description: SAMPLE 33


title: X81

description: xenograft

value: Adenocarcinoma of the lung


title: NO-NH-IA-CK-AB 0-1-1-0-0-rep2

description: SAMPLE 26


title: X86

description: xenograft

value: Squamous cell carcinoma of the lung


title: X77

description: xenograft


title: X193

description: xenograft


title: siTRα_REP1


title: siCTRL_REP3

value: scramble siRNA


title: siCTRL_REP2


title: NO-NH-IA-CK-AB 0-1-1-1-0-rep2

description: SAMPLE 30

value: Roots

value: after 4 hours of treatment


title: NO-NH-IA-CK-AB 0-1-1-0-1-rep2

description: SAMPLE 28


title: osteo T3_18h_REP3 = osteo_T3

description: replicate 3

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina), probes determined to align to a single gene transcript (as defined by Ensembl) was background-subtracted and quantile-normalized using the lumi package within R

source_name: hADSC-derived osteoblasts

growth_protocol: hADSC cells were purchased from Invitrogen and maintained in in Complete MesenPRO RS™ Medium (Invitrogen). ADSC were induced to differentiate towards chondrocytes, osteoblasts or adipocytes using  STEMPRO® Chondrogenesis, Osteogenesis or Adipogenes Differentiation Kit (Invitrogen) respectively.

treatment_protocol: Cells were plated in 6-well plates and treated with 100 nM T3 for 0 or 18 h.

value: hADSC-derived osteoblasts

tag: treatment


title: X62

description: xenograft


title: siTRα_REP2

tag: time point


title: X191

description: xenograft


title: osteo T3_18h_REP2 = osteo_T2

description: replicate 2


title: X83

description: xenograft


title: X178

description: xenograft


title: NO-NH-IA-CK-AB 0-1-1-0-1-rep1

description: SAMPLE 27


title: NO-NH-IA-CK-AB 0-1-0-1-1-rep2

description: SAMPLE 24


title: osteo T3_18h_REP1 = osteo_T1

description: replicate 1


title: X82

description: xenograft


title: osteo ctrl_REP3 = osteo_C3

description: replicate 3

value: T3 0 h


title: osteo ctrl_REP2 = osteo_C2

description: replicate 2


title: X169

description: xenograft


title: NO-NH-IA-CK-AB 0-1-0-1-0-rep1

description: SAMPLE 21


title: NO-NH-IA-CK-AB 0-1-0-1-1-rep1

description: SAMPLE 23


title: osteo ctrl_REP1 = osteo_C1

description: replicate 1


title: NO-NH-IA-CK-AB 0-1-0-1-0-rep2

description: SAMPLE 22


title: X139

description: xenograft


title: X137

description: xenograft


title: chondro T3_18h_REP3 = chondro_3w_T3

description: replicate 3

source_name: hADSC-derived chondrocytes

value: hADSC-derived chondrocytes


title: X148

description: xenograft


title: chondro ctrl_REP3 = chondro_3w_C3

description: replicate 3


title: NO-NH-IA-CK-AB 0-1-0-0-0-rep1

description: SAMPLE 17


title: chondro T3_18h_REP1 = chondro_3w_T1

description: replicate 1


title: X134

description: xenograft

value: Sarcomatoid


title: chondro ctrl_REP1 = chondro_3w_C1

description: replicate 1


title: X149

description: xenograft


title: chondro T3_18h_REP2 = chondro_3w_T2

description: replicate 2


title: NO-NH-IA-CK-AB 0-1-0-0-1-rep1

description: SAMPLE 19


title: NO-NH-IA-CK-AB 0-1-0-0-0-rep2

description: SAMPLE 18


title: liver tissues from mice were treated with CCl4 in combination with injection of Lenti-shLFAR1, biological rep3

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

description: lenti-shRNA-lncLFAR1+CCl4 3

hyb_protocol: Following fragmentation, double-stranded cDNA were hybridized for 16 hr at 45℃ on Affymetrix Mouse Gene ST 1.0 array (Affymetrix, SantaClara, CA, USA). GeneChips were washed and stained in the GeneChip2 Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G.

data_processing: Tiff images generated by the GeneChip2 Scanner 3000 7G were processed by the Genepix 6 microarray analysis software (Molecular Devices). Gene array analysis was performed according to the manufacturer’s instructions (GeneChip 430 2.0 and 230 2.0; Affymetrix, Santa Clara, CA).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA ( The Ambion® WT Expression Kit  For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 2009, Affymetrix).

growth_protocol: All Balb/c mice aged at 8 weeks obtained from institute of laboratory animal sciences, CAMS & PUMC (Beijing , China), weighting about 20g. Mice were maintained in a 12-h light/dark cycle at 22- 25°C with free access to food and water. All protocols were approved by the Ethical Committee of Tianjin Medical University.

treatment_protocol: After acclimatization for one week, Forty Balb/c mice were randomly divided into four groups: Mice were treated with oil in combination with injection of Lenti-NC (NC, n=10), CCl4 in combination with injection of Lenti-NC (NC+CCl4, n=10), oil in combination with injection of Lenti-shLFAR1 (shLFAR1, n=10) and CCl4 in combination with injection of Lenti-shLFAR1 (shLFAR1+CCl4, n=10). The lentvirus was injected via the tail vein 2 weeks after the first injection of CCl4 .Mice in the NC+CCl4 group and the shLFAR1+CCl4 group, separately, were administered 5% CCl4 (v/v) dissolved in olive oil (0.3 ml/kg body weight) thrice per week for additional 4 weeks via intraperitoneal (ip) injection after the lentivirus was injected. NC and shLFAR1 group animals were injected with an equivalent volume of olive oil.

value: Male

value: Balb/c

value: liver


title: X154

description: xenograft


title: X133

description: xenograft


title: NO-NH-IA-CK-AB 0-0-1-1-1-rep2

description: SAMPLE 16


title: X132

description: xenograft


title: siCTRL_REP1

value: human adipose derived stem cells (hADSC)

value: 2 days after transfection


title: chondro ctrl_REP2 = chondro_3w_C2

description: replicate 2


title: liver tissues from mice were treated with CCl4 in combination with injection of Lenti-shLFAR1, biological rep1

description: lenti-shRNA-lncLFAR1+CCl4 1


title: NO-NH-IA-CK-AB 0-0-1-1-0-rep2

description: SAMPLE 14


title: adipo T3_18h_REP3 = Ax_T3

description: replicate 3

source_name: hADSC-derived adipocytes

value: hADSC-derived adipocytes


title: X12

description: xenograft

value: xenograft


title: adipo T3_18h_REP2 = Ax_T2

description: replicate 2


title: NO-NH-IA-CK-AB 0-1-1-0-0-rep1

description: SAMPLE 25


title: X108

description: xenograft

value: Dasl


title: NO-NH-IA-CK-AB 0-0-1-1-1-rep1

description: SAMPLE 15


title: adipo ctrl_REP2 = Ax_C2

description: replicate 2


title: adipo T3_18h_REP1 = Ax_T1

description: replicate 1


title: X119

description: xenograft

value: Adenocarcinoma of the lung


title: NO-NH-IA-CK-AB 0-0-1-0-1-rep2

description: SAMPLE 12


title: liver tissues from mice were treated with CCl4 in combination with injection of Lenti-NC, biological rep2

description: NC+CCl4 2


title: NO-NH-IA-CK-AB 0-0-1-0-0-rep2

description: SAMPLE 10


title: liver tissues from mice were treated with oil in combination with injection of Lenti-shLFAR1, biological rep3

description: lenti-shRNA-lncLFAR1 3


title: X106

description: xenograft

value: Squamous cell carcinoma of the lung


title: adipo ctrl_REP1 = Ax_C1

description: replicate 1


title: liver tissues from mice were treated with CCl4 in combination with injection of Lenti-NC, biological rep3

description: NC+CCl4 3


title: NO-NH-IA-CK-AB 0-0-1-1-0-rep1

description: SAMPLE 13


title: adipo ctrl_REP3 = Ax_C3

description: replicate 3


title: liver tissues from mice were treated with oil in combination with injection of Lenti-NC, biological rep3

description: Lenti-NC 3


title: RV infected cells T24h, biological rep2

city: Moscow

first: James

middle: Theodore

last: Van Leuven

state: ID

address: 709 S Deakin St

department: Center for Modeling Complex Interactions

institute: University of Idaho

hyb_protocol: Samples were hybridized to the Roche Nimblegen 12x135k MM9 Microarray (Design 100718_MM9_EXP).

scan_protocol: Scan protocol not provided.

data_processing: The data were processed with the 'oligo' and 'pdInfoBuilder' packages in R using Robust Multichip Average (rma) preprocessing methodology. This strategy allows background subtraction, quantile normalization and summarization (via median-polish).

source_name: ATCC (VR-1645) infected

label_protocol: Microarray analysis was done on RNA samples submitted to the Genomics Resources Core Laboratory at The Institute for Bioinformatics and Evolutionary Studies at the University of Idaho, Moscow, ID

growth_protocol: PR8 (A/Puerto Rico/8/1934 (H1N1)), obtained from BEI Resources (NR-3169), was grown and titrated by plaque assay in MDCK (ATCC: CCL-34) cells. MHV, obtained from ATCC (VR-261), was grown and titrated by plaque assay in 17Cl.1 cells (Sturman and Takemoto, 1972) (provided by Dr. Kathryn Holmes, University of Colorado Denver School of Medicine). RV, obtained from ATCC (VR-1645), was grown and titrated by tissue culture infectious dose 50% (TCID50) assay in HeLa cells (ATCC: CCL-2). LA4 (ATCC: CCL-196), a murine lung epithelial cell line, was cultured in Ham's F12K medium (Mediatech, Manassas, VA).

extract_protocol: RNA was isolated from cell cultures using an RNAeasy Plus kit (QIAGEN)

treatment_protocol: Our experimental approach was to infect LA4 cells with the three viruses at times t=0 h and t=12 h and harvest RNA for microarray analysis at t=24 h. Controls were mock-inoculated at both time points. Preliminary experiments were done to establish a multiplicity of infection (MOI) for each virus that resulted in comparable numbers of cells positive for viral antigen at 24 h post-infection (Figure S1). Based on this, LA4 cells were inoculated with 3 TCID50/cell RV, 1 PFU/cell PR8, or 3 PFU/cell MHV. Triplicate wells of LA4 cells in 6-well plates were inoculated with each virus diluted in serum-free medium or were mock-inoculated with serum-free medium for 1 h at 37C. Viral inocula were removed and the cells were rinsed twice with serum-free medium. The cells were incubated in Ham's F12K medium with 2% FBS for 12 or 24 h, at which time RNA was isolated. For the 24 h samples, the media were removed and replaced with fresh media 12 h after inoculation.

tag: cell line

tag: viral infection

value: ATCC (VR-1645) infected

tag: hours post infection


title: liver tissues from mice were treated with oil in combination with injection of Lenti-shLFAR1, biological rep2

description: lenti-shRNA-lncLFAR1 2


title: NO-NH-IA-CK-AB 0-0-1-0-0-rep1

description: SAMPLE 9

value: Roots


title: T3_18h_REP3 = stem_T3

description: replicate 3

source_name: hADSC

value: hADSC


title: NO-NH-IA-CK-AB 0-0-1-0-1-rep1

description: SAMPLE 11

value: after 4 hours of treatment


title: liver tissues from mice were treated with CCl4 in combination with injection of Lenti-NC, biological rep1

description: NC+CCl4 1


title: T3_18h_REP2 = stem_T2

description: replicate 2


title: RV infected cells T24h, biological rep3


title: NO-NH-IA-CK-AB 0-0-0-1-1-rep2

description: SAMPLE 8


title: RV infected cells T12h, biological rep3


title: liver tissues from mice were treated with CCl4 in combination with injection of Lenti-shLFAR1, biological rep2

description: lenti-shRNA-lncLFAR1+CCl4 2


title: liver tissues from mice were treated with oil in combination with injection of Lenti-NC, biological rep2

description: Lenti-NC 2


title: T3_18h_REP1 = stem_T1

description: replicate 1


title: RV infected cells T12h, biological rep2


title: ctrl_REP3 = stem_C3

description: replicate 3

value: T3 0 h


title: liver tissues from mice were treated with oil in combination with injection of Lenti-NC, biological rep1

description: Lenti-NC 1


title: NO-NH-IA-CK-AB 0-0-0-1-1-rep1

description: SAMPLE 7


title: RV infected cells T12h, biological rep1


title: X88

description: xenograft

value: large cell carcinoma of the lung

value: DirHyb


title: NO-NH-IA-CK-AB 0-0-0-0-1-rep2

description: SAMPLE 4


title: PR8 infected cells T24h, biological rep2

source_name: A/Puerto Rico/8/1934 (H1N1) infected

value: A/Puerto Rico/8/1934 (H1N1) infected


title: ctrl_REP1 = stem_C1

description: replicate 1


title: X85

description: xenograft


title: X57

description: xenograft


title: NO-NH-IA-CK-AB 0-0-0-1-0-rep1

description: SAMPLE 5


title: X55

description: xenograft


title: RV infected cells T24h, biological rep1


title: PR8 infected cells T24h, biological rep1


title: NO-NH-IA-CK-AB 0-0-0-0-1-rep1

description: SAMPLE 3


title: PR8 infected cells T12h, biological rep2


title: NO-NH-IA-CK-AB 0-0-0-0-0-rep1

description: SAMPLE 1


title: MEF_MSK1_rep3

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: Gene expression data following knockdown of KMT2A or MSK1 in mouse embryonic fibroblasts

hyb_protocol: Samples were hybridised using a Nimblegen Hybridisation Kit (05 583 934 001), including Sample Tracking Controls (05 223 512 001)

scan_protocol: Slides were scanned on a Nimblegen MS200 microarray scanner at a resolution of 2µm with balanced Speed/Sensitivity and 100% laser intensity using autogain

data_processing: Data were extracted using DEVA (Roche Nimblegen) and normalised by robust multichip average in R.

source_name: MEF, MSK1 shRNA

label_protocol: Samples were labelled with Cy3 using a Nimblegen One Colour Labeling Kit (Roche Nimblegen, 06 370 438 001)

growth_protocol: Mouse embryonic fibroblasts (MEFs) were generated in house, via isolation from Balb/c wild-type mouse embryos between day 12-15 of gestation and cultured in DMEM, 100 µg/ml streptomycin, 100 U/ml penicillin, 1/100 MEM non-essential amino acids, 1/1000 2-mercaptoethanol and 10% FBS at 37oC, 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was converted to double-stranded cDNA using cDNA synthesis kit (Roche Nimblegen, 11 117 831 001)

treatment_protocol: shRNA vectors were purchased from Origene (Msk1: TR504795; MLL1: TR517798) and transfected into MEFs by  electroporation (GenePulser XCell, Biorad). MEFs were brought into a single cell suspension by trypsination and washed with ice-cold PBS. 4x106 cells per transfection were resuspended in 400μl electroporation buffer (10mM Hepes, pH7.5, 135mM KCl, 2mM MgCl2, 5mM EGTA, 25% FBS) and transferred to a 4mm electroporation cuvette (Biorad). 20μg of vector DNA was added to the cells immediately before transfection and incubated on ice for 1 minute. Cells were transfected with one pulse (300V, 600μF, 1000Ω), and allowed to recover (RT, 1min), before addition of 10ml pre-warmed MEF medium and incubation at 37°C, 5% CO2 for 6 hours. Non-transfected cells were removed by puromycin treatment (10μg/ml, 14 hrs).  After 20 hours cells were harvested.

value: Balb/c


title: X50

description: xenograft


title: PR8 infected cells T12h, biological rep3


title: X207

description: xenograft


title: PR8 infected cells T12h, biological rep1


title: NO-NH-IA-CK-AB 0-0-0-0-0-rep2

description: SAMPLE 2


title: MEF_MSK1_rep2


title: MHV infected cells T24h, biological rep3

source_name: ATCC (VR-261) infected

value: ATCC (VR-261) infected


title: ctrl_REP2 = stem_C2

description: replicate 2


title: X162

description: xenograft


title: MHV infected cells T24h, biological rep2


title: MEF_MSK1_rep1


title: PR8 infected cells T24h, biological rep3


title: MHV infected cells T24h, biological rep1


title: X142

description: xenograft


title: MHV infected cells T12h, biological rep3


title: NO-NH-IA-CK-AB 0-1-0-0-1-rep2

description: SAMPLE 20


title: MEF_KMT2A_rep3

source_name: MEF, KMT2A shRNA


title: MHV infected cells T12h, biological rep2


title: MHV infected cells T12h, biological rep1


title: MEF_KMT2A_rep2


title: MEF_KMT2A_rep4


title: X152

description: xenograft


title: X123

description: xenograft


title: control T24h, biological rep2

source_name: not infected

value: not infected

value: 24 after mock inoculation


title: control T24h, biological rep3


title: MEF_control_rep3

source_name: MEF, mock transfected


title: MEF_KMT2A_rep1


title: NO-NH-IA-CK-AB 0-0-0-1-0-rep2

description: SAMPLE 6


title: MEF_control_rep1


title: X110

description: xenograft


title: X140

description: xenograft


title: X113

description: xenograft


title: MEF_control_rep2


title: control T24h, biological rep1


title: liver tissues from mice were treated with oil in combination with injection of Lenti-shLFAR1, biological rep1

description: lenti-shRNA-lncLFAR1 1

value: Male

value: liver


title: 4156

status: Public on Oct 25 2016

type: genomic

city: Seattle

first: William

middle: M

last: Grady

state: WASHINGTON

address: 1100 Fairview N.Ave

department: Department of Clinical Research

institute: Fred Hutchinson Cancer Research Center

description: esophagus sample

hyb_protocol: per Illumina Infinium protocol

scan_protocol: per Illumina Infinium protocol

data_processing:
Filtered out probes with detection p-value > 0.05, probes on the X chromosome, and probes containing at least one SNP with low minor allele frequency (MAF=0) in the probe body. The background noise is corrected and SWAN normalization is performed by using the functions provided by the Bioconductor minfi package. Batch effects across three batch runs are corrected using the Combat algorithm from the R sva package.
MatrixSignalIntensities.csv: Unmethylated and methylated signal intensities and detection p-value

label: Cy5 and Cy3

molecule: genomic DNA

source_name: esophagus

label_protocol: per Illumina Infinium protocol

extract_protocol: formalin-fixed, paraffin-embedded samples were extracted using the DNAeasy blood and tissue kit (Qiagen)

tag: run

value: FBE

tag: age

value: M

tag: bmi

tag: smokecigarettes

value: Yes

tag: alcoholicrinksperweek

value: Less than one drink a week

tag: be status


title: 4157

description: esophagus sample

tag: gender

value: 6 to 10 drinks a week


title: 4155

description: esophagus sample

value: More than 10 drinks a week


title: 4146

description: esophagus sample

value: EAC

value: 1 to 5 drinks a week


title: 4147

description: esophagus sample

value: SQ


title: 4139

description: esophagus sample

value: BE

tag: Stage


title: 4126

description: esophagus sample


title: 4150

description: esophagus sample

value: F


title: 4124

description: esophagus sample

value: HGD


title: 4131

description: esophagus sample

value: No


title: 4130

description: esophagus sample


title: 4129

description: esophagus sample

value: Cardia


title: 4134

description: esophagus sample

value: LGD


title: 4138

description: esophagus sample


title: 4127

description: esophagus sample


title: 4141

description: esophagus sample

value: III


title: 4149

description: esophagus sample


title: 4133

description: esophagus sample

value: I


title: 4137

description: esophagus sample


title: 4121

description: esophagus sample


title: 4148

description: esophagus sample

value: Fundus

value: II


title: 4125

description: esophagus sample

value: M


title: 4123

description: esophagus sample

value: Yes


title: 4128

description: esophagus sample


title: 4122

description: esophagus sample


title: 4119

description: esophagus sample


title: 4120

description: esophagus sample


title: 4140

description: esophagus sample


title: 4132

description: esophagus sample


title: 4116

description: esophagus sample


title: 4117

description: esophagus sample


title: 4118

description: esophagus sample


title: 4115

description: esophagus sample


title: 4110

description: esophagus sample


title: 4111

description: esophagus sample


title: 4136

description: esophagus sample


title: 4112

description: esophagus sample


title: yFR1636vsFR762_Med15-9MYCvsNoTag_WT_20160715_rep2

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

description:
Biological replicate 1 of 2. Med15 occupancy in WT cells. Med15 ChIP sample (Cy5-labeled) was performed from a 9xMYC-tagged Med15 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED15 gene is not tagged (Cy3-labeled).
A genome browser-ready file for  Med15 occupancy in WT cells
processed data file: SmthBED_yFR1636vsFR762_Med15-9MYCvsNoTag_WT_20160715_rep1-2__S.cerevisiaeApr11_24536.bed

hyb_protocol: Hybridization: Resuspend colored pellet in 110uL hybridization buffer (100uL DIGEasy Buffer, 5uL 10mg/mL Salmon Sperm DNA, 5uL 8mg/mL yeast tRNA). Put at 95?C for 5 minutes. Put at 42?C for 10 min (Keep samples at 42?C while waiting for hybridization). Follow standard Agilent chamber hybridization protocols. Incubate overnight (16-24h) at 42?C in Agilent hybridization oven at 20 rpm rotation speed.  Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Stripping: Stripping is done in 1L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. 1. Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations.  Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 5 ml of this 1M solution in 1L Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180K  Set the scan as follow:  pixel size = 2Âµm;  speed = 20;  Scan Mode = Normal;  Acquisition Mode = Simultaneous;  Focus = Auto.    Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing:
Correction = Foreground-Background  Normalisation = limma loess (subgrid)
Bed files: The ChIP-chip data from individual replicates were normalized using the Limma Loess method and replicates were combined as described previously (Jeronimo and Robert, 2014, Nat Struct Mol Biol 21(5):449-55). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10 bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C.    Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly.    Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C.    Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.    Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O).  PCR cycling conditions:  1) 5:00 at 55C  2) 5:00 at 72C  3) 2:00 at 95C  4) 0:30 at 95C  5) 0:30 at 55C  6) 1:00 at 72C  7) Repeat steps 4-6 31 more times.  8) 4:00 at 72C  9) Forever at 4C    Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness.    Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour.    Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness.      Phosphate Wash Buffer (100mL):  0.5mL 1M KPO4, pH 8.5  15.25mL ddH2O  84.25mL 95% EtOH  Solution will be cloudy upon mixing.    Phosphate Elution Buffer (10mL):  0.04mL 1M KPO4, pH 8.5  9.96mL ddH2O    1M KPO4, pH 8.5 (10mL):  9.5mL 1M K2HPO4  0.5mL 1M KH2PO4    1M Sodium Carbonate Buffer, pH 9.0 (100mL):  10.8g Na2CO3  80mL ddH2O  pH to 9.0 with concentrated HCl  Adjust volume to 100mL with ddH2O  DILUTE 1:10 WHEN USING!  Solution will change composition over time. Use only if less than a month old.

growth_protocol: YEP+2% Glucose containing about 15 glass beads of 4mm-diameter is inoculated at OD600 0.1 from an overnight preculture in the appropriate media, agitated at 330rpm and allowed to grow until it reaches OD600 0.6-0.8. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (optional). Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C. To reduce floculation, this protocol was adapted from van de Peppel et al., Molecular Cell 2005 (Holstege lab).

extract_protocol: Cells are thawed on ice, and resuspended in 700uL lysis buffer with protease inhibitors (solution composition detailed at the end). 500uL of acid-washed glass beads (Sigma) are added, and the cells are lysed using the bead-beater (4x5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x 20sec at output 7 Watts, with a 1 minute break between sonication cycles. The sonicated lysates is centrifuge for 5 min at 4'C max speed and supernatant used immediately for ChIP (or saved and frozen at -80'C). Lysis buffer: 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL Pepstatin.

treatment_protocol:
null
IP protocol: anti-MYCtag (9E10 lab stock 2015). Anti-mouse Dynabeads (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared, 2015)  is added (2.5uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Lysis buffer: 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL. Pepstatin.

tag: strain

tag: genotype

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 MED15-9xMYC::klTRP1

tag: antibody

value: 9E10 (lab stock prepared by Pierre, 2015)


title: yFR2492vsFR2491_Med15-9MYCvsNoTag_cdk8D290A_20160715_rep2

description:
Biological replicate 1 of 2. Med15 occupancy in cdk8D290A mutant cells. Med15 ChIP sample (Cy5-labeled) was performed from a 9xMYC-tagged Med15 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED15 gene is not tagged (Cy3-labeled).
A genome browser-ready file for  Med15 occupancy in cdk8D290A mutant cells
processed data file: SmthBED_yFR2492vsFR2491_Med15-9MYCvsNoTag_cdk8D290A_20160715_rep1-2__S.cerevisiaeApr11_543849.bed

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 MED15-9xMYC::klTRP1 cdk8D290A

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 cdk8D290A


description:
Biological replicate 1 of 2. TFIIB occupancy in med3Dmed15D cells. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in med3Dmed15D cells
processed data file: SmthBED_yFR2200_TailD_TFIIBvsInput_EtOH_20160314_rep1-2__S.cerevisiaeApr11_474653.bed;

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice. Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.    Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O).  PCR cycling conditions:  1) 5:00 at 55C  2) 5:00 at 72C  3) 2:00 at 95C  4) 0:30 at 95C  5) 0:30 at 55C  6) 1:00 at 72C  7) Repeat steps 4-6 31 more times.  8) 4:00 at 72C  9) Forever at 4C    Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness.    Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour.    Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness.      Phosphate Wash Buffer (100mL):  0.5mL 1M KPO4, pH 8.5  15.25mL ddH2O  84.25mL 95% EtOH  Solution will be cloudy upon mixing.    Phosphate Elution Buffer (10mL):  0.04mL 1M KPO4, pH 8.5  9.96mL ddH2O    1M KPO4, pH 8.5 (10mL):  9.5mL 1M K2HPO4  0.5mL 1M KH2PO4    1M Sodium Carbonate Buffer, pH 9.0 (100mL):  10.8g Na2CO3  80mL ddH2O  pH to 9.0 with concentrated HCl  Adjust volume to 100mL with ddH2O  DILUTE 1:10 WHEN USING!  Solution will change composition over time. Use only if less than a month old.

growth_protocol: 60mL YEP+2% Glucose containing about 15 glass beads of 4mm-diameter is inoculated at OD600 0.15 from an overnight preculture in the appropriate media, agitated at 330rpm and allowed to grow until it reaches OD600 0.6-0.8. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (optional). Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C. Ref: Holstege lab, van de Peppel et al., Molecular Cell 2005.

treatment_protocol:
null
IP protocol: ChIP_TFIIB. Protein G Dynabeads (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 2mL PBS + 0.5% BSA. Anti-yTFIIB (from Richard Young) antibody is added (2uL / ChIP), and incubated overnight at 4C in haematological mixer. Beads are washed twice with Lysis buffer, and resuspended in 30uL Lysis buffer / ChIP. 30uL of resuspended beads/antibody is added to 400-600 uL of lysate, and incubated overnight at 4C in haematological mixer. Beads are then washed using the Dynal magnet system twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4'C, and 50uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65'C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate Wash Buffer: 10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA.

tag: strain information

value: MATα his3Δ1 leu2Δ0 lys2Δ0 met15Δ0 ura3Δ0 med3Δ::kanMX4 med15Δ::kanMX4

value: TFIIB


description:
Biological replicate 2 of 2. Med15 occupancy in cdk8D290A mutant cells. Med15 ChIP sample (Cy5-labeled) was performed from a 9xMYC-tagged Med15 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED15 gene is not tagged (Cy3-labeled).
A genome browser-ready file for  Med15 occupancy in cdk8D290A mutant cells
processed data file: SmthBED_yFR2492vsFR2491_Med15-9MYCvsNoTag_cdk8D290A_20160715_rep1-2__S.cerevisiaeApr11_543849.bed


title: 4027

description: esophagus sample

tag: histology

value: SQ

value: F


title: yFR1325_Srb5-AA_90minRapamycin_TFIIBvsInput_20160208_rep2

description:
Biological replicate 2 of 2. TFIIB occupancy in med18-AA cells treated 90 minutes with 1 microg/ml of Rapamycin. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in med18-AA cells treated 90 minutes with 1 microg/ml of Rapamycin
processed data file: SmthBED_yFR1325_Srb5-AA_90minRapamycin_TFIIBvsInput_20160208_rep1-2__S.cerevisiaeApr11_404980.bed;

growth_protocol: YEP+2%Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reachs OD600=0.5-0.6. Cell cultures are treated with 1 microg/ml of Rapamycin and allowed to grow for additional 90 min. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min.  Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.

treatment_protocol:
1 microg/ml of Rapamycin for 90 min
IP protocol: ChIP_TFIIB. Protein G Dynabeads (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 2mL PBS + 0.5% BSA. Anti-yTFIIB (from Richard Young) antibody is added (2uL / ChIP), and incubated overnight at 4C in haematological mixer. Beads are washed twice with Lysis buffer, and resuspended in 30uL Lysis buffer / ChIP. 30uL of resuspended beads/antibody is added to 400-600 uL of lysate, and incubated overnight at 4C in haematological mixer. Beads are then washed using the Dynal magnet system twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4'C, and 50uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65'C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65'C to reverse the crosslinks with the ChIP samples. Lysis Buffer (no protease inhibitors): 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate Wash Buffer: 10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA.

value: MATα ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1 MED18-FRB::kanMX6

treatment_protocol: 1 microg/ml of Rapamycin for 90 min


description:
Biological replicate 1 of 2. TFIIB occupancy in WT cells. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in WT cells
processed data file: SmthBED_yFR117_WT_TFIIBvsInput_EtOH_20160314_rep1-2__S.cerevisiaeApr11_353805.bed;

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


description:
Biological replicate 1 of 2. TFIIB occupancy in med18-AA cells treated 90 minutes with 1 microg/ml of Rapamycin. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in med18-AA cells treated 90 minutes with 1 microg/ml of Rapamycin
processed data file: SmthBED_yFR1325_Srb5-AA_90minRapamycin_TFIIBvsInput_20160208_rep1-2__S.cerevisiaeApr11_404980.bed;


title: yFR117_WT_TFIIBvsInput_EtOH_20160314_rep2

description:
Biological replicate 2 of 2. TFIIB occupancy in WT cells. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in WT cells
processed data file: SmthBED_yFR117_WT_TFIIBvsInput_EtOH_20160314_rep1-2__S.cerevisiaeApr11_353805.bed;


title: 3991

description: esophagus sample

value: IV

value: 1 to 5 drinks a week


title: 3997

description: esophagus sample

value: I

value: No


title: 3998

description: esophagus sample

value: Fundus


title: 3988

description: esophagus sample

value: Less than one drink a week


title: 3995

description: esophagus sample

value: EAC

value: M


title: yFR2200_TailD_TFIIBvsInput_EtOH_20160314_rep2

description:
Biological replicate 2 of 2. TFIIB occupancy in med3Dmed15D cells. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in med3Dmed15D cells
processed data file: SmthBED_yFR2200_TailD_TFIIBvsInput_EtOH_20160314_rep1-2__S.cerevisiaeApr11_474653.bed;


title: 3989

description: esophagus sample

value: HGD/Ca


description:
Biological replicate 1 of 2. Med7 occupancy in kin28asmed3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes. Med7 ChIP sample (Cy5-labeled) was performed from a 13xMYC-tagged Med7 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED7 gene is not tagged (Cy3-labeled).
genome browser-ready file for Med7 occupancy in kin28asmed3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes
processed data file: SmthBED_yFR2269vsFR2275_kin28as-deltaTail_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep1-2__S.cerevisiaeApr11_840812.bed;

growth_protocol: YEP+2% Glucose is inoculated at OD600 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reach OD600 0.6-0.8. NA-PP1 is added at final concentration 6uM and cultures allowed to grow for an additional 15 min. Culture is poured/divided in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C

treatment_protocol:
6microM NA-PP1 for 15 min
IP protocol: anti-MYCtag (9E10 lab stock 2015). Anti-mouse Dynabeads (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared, 2015)  is added (2.5uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. Lysis buffer: 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL. Pepstatin.

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 kin28::kin28as (L83G) [pSH579, CEN URA3 kin28as (L83G)] med3Δ::LEU2 med15Δ::KanMX4 MED7-13xMYC::HPHr

value: 9E10 (lab stock prepared by Pierre, 2015)

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 kin28::kin28as (L83G) [pSH579, CEN URA3 kin28as (L83G)] med3Δ::LEU2 med15Δ::KanMX4 MED7::HIS3


description:
Biological replicate 1 of 2. TFIIB occupancy in WT cells treated 90 minutes with 1 microg/ml of Rapamycin. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in WT cells treated 90 minutes with 1 microg/ml of Rapamycin
processed data file: SmthBED_yFR1321_WT-AA_90minRapamycin_TFIIBvsInput_20160208_rep1-2__S.cerevisiaeApr11_589437.bed;

value: MATα ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1

value: TFIIB


title: 3996

description: esophagus sample

value: BE


title: yFR2269vsFR2275_kin28as-deltaTail_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep2

description:
Biological replicate 2 of 2. Med7 occupancy in kin28asmed3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes. Med7 ChIP sample (Cy5-labeled) was performed from a 13xMYC-tagged Med7 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED7 gene is not tagged (Cy3-labeled).
genome browser-ready file for Med7 occupancy in kin28asmed3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes
processed data file: SmthBED_yFR2269vsFR2275_kin28as-deltaTail_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep1-2__S.cerevisiaeApr11_840812.bed;


title: 3992

description: esophagus sample

value: Yes


title: yFR2264vsFR2274_KIN28-deltaTail_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep2

description:
Biological replicate 2 of 2. Med7 occupancy in med3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes. Med7 ChIP sample (Cy5-labeled) was performed from a 13xMYC-tagged Med7 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED7 gene is not tagged (Cy3-labeled).
genome browser-ready file for Med7 occupancy in med3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes
processed data file: SmthBED_yFR2264vsFR2274_KIN28-deltaTail_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep1-2__S.cerevisiaeApr11_251333.bed;

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 med3Δ::LEU2 med15Δ::kanMX4 MED7-13xMYC::HPHr

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 med3Δ::LEU2 med15Δ::kanMX4 MED7::HIS3


title: 4114

description: esophagus sample


title: 3993

description: esophagus sample

value: carditis


description:
Biological replicate 1 of 2. Med7 occupancy in med3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes. Med7 ChIP sample (Cy5-labeled) was performed from a 13xMYC-tagged Med7 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED7 gene is not tagged (Cy3-labeled).
genome browser-ready file for Med7 occupancy in med3Dmed15D cells treated with 6 microM NAPP1 for 15 minutes
processed data file: SmthBED_yFR2264vsFR2274_KIN28-deltaTail_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep1-2__S.cerevisiaeApr11_251333.bed;


description:
Biological replicate 2 of 2. Med15 occupancy in WT cells. Med15 ChIP sample (Cy5-labeled) was performed from a 9xMYC-tagged Med15 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED15 gene is not tagged (Cy3-labeled).
A genome browser-ready file for  Med15 occupancy in WT cells
processed data file: SmthBED_yFR1636vsFR762_Med15-9MYCvsNoTag_WT_20160715_rep1-2__S.cerevisiaeApr11_24536.bed

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 MED15-9xMYC::klTRP1


title: yFR1321_WT-AA_90minRapamycin_TFIIBvsInput_20160208_rep2

description:
Biological replicate 2 of 2. TFIIB occupancy in WT cells treated 90 minutes with 1 microg/ml of Rapamycin. TFIIB ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against TFIIB and hybridized against Input DNA (Cy3-labeled).
genome browser-ready file for TFIIB occupancy in WT cells treated 90 minutes with 1 microg/ml of Rapamycin
processed data file: SmthBED_yFR1321_WT-AA_90minRapamycin_TFIIBvsInput_20160208_rep1-2__S.cerevisiaeApr11_589437.bed;


title: 3994

description: esophagus sample

value: HGD

value: I

value: No


title: yFR1900vsFR762-KIN28_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep2

description:
Biological replicate 2 of 2. Med7 occupancy in WT cells treated with 6 microM NAPP1 for 15 minutes. Med7 ChIP sample (Cy5-labeled) was performed from a 13xMYC-tagged Med7 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED7 gene is not tagged (Cy3-labeled).
genome browser-ready file for Med7 occupancy in WT cells treated with 6 microM NAPP1 for 15 minutes
processed data file: SmthBED_yFR1900vsFR762-KIN28_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep1-2__S.cerevisiaeApr11_131621.bed;

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 MED7-13xMYC::HPHr


description:
Biological replicate 1 of 2. Med7 occupancy in kin28as cells treated with 6 microM NAPP1 for 15 minutes. Med7 ChIP sample (Cy5-labeled) was performed from a 13xMYC-tagged Med7 strain using the anti-MYC antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the MED7 gene is not tagged (Cy3-labeled).
genome browser-ready file for Med7 occupancy in kin28as cells treated with 6 microM NAPP1 for 15 minutes
processed data file: SmthBED_yFR1902vsFR763-kin28as_Med7-13MYCvsUntagged_15minNAPP1_20160129_rep1-2__S.cerevisiaeApr11_407586.bed;

value: MATα ade2::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 kin28::kin28as (L83G) [pSH579, CEN URA3 kin28as (L83G)] MED7-13xMYC::HPHr