title: T2S_9467_M01ZH09_TD_PREV


title: T2_2397

status: Public on Sep 02 2019

type: RNA

city: Oxford

first: Amber

last: Barton

address: Centre for Clinical Vaccinology and Tropical Medicine

country: United Kingdom

institute: Oxford Vaccine Group

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was quantile normalized, background subtracted and log2 transformed using neqc() in R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: Standard Illumina TotalPrep RNA Amplification kits.

growth_protocol: NA - whole blood samples from clinical trial

extract_protocol: Tempus tube RNA isolation kit.

tag: group

value: CTRL

tag: tissue

value: Whole blood


title: T2S_4476_M01ZH09_nonTD_Va

status: Public on Oct 12 2017

data_processing: Data was quantile normalised, background subtracted and log2 transformed using neqc() in R.

growth_protocol: NA - whole blood samples from clinical trial.

tag: condition

value: nonTD

tag: date

tag: timepoint

value: Va


title: T2S_9880_M01ZH09_nonTD_Va


title: T2S_6953_M01ZH09_TD_Va

value: TD


title: T2S_4030_M01ZH09_nonTD_Va


title: T2S_3020_M01ZH09_nonTD_Va


title: T2S_1729_M01ZH09_nonTD_Va


title: T2S_6696_M01ZH09_TD_PREV

value: PREV


title: T2S_870_M01ZH09_TD_PREV


title: T2S_2280_M01ZH09_TD_Va


title: T2S_422_Ty21a_nonTD_Va


title: T2S_8509_M01ZH09_nonTD_Va


title: T2S_9194_M01ZH09_TD_PREV


title: T2S_1203_M01ZH09_nonTD_Va


title: T2S_3514_M01ZH09_nonTD_PREV


title: T2S_382_M01ZH09_nonTD_PREV


title: T2S_7301_M01ZH09_nonTD_PREV


title: T2S_5512_M01ZH09_TD_Va


title: T2S_7520_M01ZH09_nonTD_PREV


title: T2S_6616_M01ZH09_TD_Va


title: T2S_2133_M01ZH09_TD_Va


title: T2S_2528_M01ZH09_TD_PREV


title: T2S_7895_M01ZH09_TD_PREV


title: T2S_991_M01ZH09_TD_Va


title: T2S_6871_M01ZH09_nonTD_Va


title: T2S_4026_Ty21a_nonTD_Va


title: T2S_9064_M01ZH09_TD_PREV


title: T2S_2867_Ty21a_nonTD_Va


title: T2S_6666_M01ZH09_nonTD_Va


title: T2S_2570_M01ZH09_nonTD_PREV


title: T2S_4772_Ty21a_nonTD_Va


title: T2S_7085_Ty21a_nonTD_PREV


title: T2S_7867_Ty21a_nonTD_PREV


title: T2S_485_Ty21a_nonTD_PREV


title: T2S_7212_Ty21a_nonTD_Va


title: T2S_3702_Ty21a_TD_PREV


title: T2S_6430_Ty21a_nonTD_Va


title: T2S_6610_Ty21a_TD_PREV


title: T2S_6502_Placebo_nonTD_PREV

value: Placebo


title: T2S_389_Ty21a_TD_Va


title: T2S_3511_Ty21a_nonTD_PREV


title: T2S_4341_Ty21a_nonTD_Va


title: T2S_494_Ty21a_nonTD_PREV


title: T2S_3981_Ty21a_TD_Va


title: T2S_7424_Placebo_nonTD_Va


title: T2S_6920_Placebo_nonTD_FG2


title: T2S_5967_Ty21a_TD_FG2


title: T2S_2746_M01ZH09_nonTD_PREV


title: T2S_4205_Ty21a_nonTD_PREV


title: T2S_3918_M01ZH09_nonTD_Va


title: T2S_2961_Ty21a_TD_FG2


title: T2S_2553_Ty21a_TD_FG3


title: T2S_8544_Ty21a_TD_FG3


title: T2S_6876_Ty21a_nonTD_PREV


title: T2S_1441_Ty21a_TD_PREV


title: T2S_3379_Ty21a_nonTD_Va


title: T2S_9692_Ty21a_TD_PREV


title: T2S_6897_M01ZH09_nonTD_FG2


title: T2S_7868_Ty21a_TD_FG2


title: T2S_3490_Ty21a_TD_FG3


title: T2S_24_Ty21a_TD_FG2


title: T2S_9623_Placebo_nonTD_PREV


title: T2S_3374_M01ZH09_TD_PREV


title: T2S_1636_M01ZH09_nonTD_FG2


title: T2S_3917_Placebo_nonTD_FG2


title: T2S_9737_Placebo_nonTD_Va


title: T2S_3847_M01ZH09_TD_FG2


title: T2S_3012_Placebo_nonTD_FG2


title: T2S_5823_M01ZH09_nonTD_PREV


title: T2S_1878_Placebo_nonTD_Va


title: T2S_2821_M01ZH09_nonTD_Va


title: T2S_1049_Ty21a_nonTD_PREV


title: T2S_2303_Ty21a_nonTD_FG2


title: T2S_8052_M01ZH09_TD_FG2


title: T2S_1909_M01ZH09_TD_Va


title: T2S_7621_Placebo_TD_PREV


title: T2S_4689_M01ZH09_TD_FG2


title: T2S_1977_Placebo_TD_FG2


title: T2S_4557_Placebo_TD_Va


title: T2S_6173_M01ZH09_TD_PREV


title: T2S_5552_M01ZH09_TD_FG2


title: T2S_8400_Placebo_TD_Va


title: T2S_5976_Ty21a_nonTD_FG3


title: T2S_4091_M01ZH09_TD_Va


title: T2S_9962_M01ZH09_TD_Va


title: T2S_5276_M01ZH09_TD_Va


title: T2S_1930_M01ZH09_TD_PREV


title: T2S_469_M01ZH09_TD_FG2


title: T2S_2490_Placebo_TD_FG2


title: T2S_8362_M01ZH09_TD_PREV


title: T2S_636_M01ZH09_TD_Va


title: T2S_7683_Ty21a_nonTD_PREV


title: T2S_1138_Ty21a_nonTD_FG2


title: T2S_4928_M01ZH09_TD_FG2


title: T2S_8147_Ty21a_nonTD_PREV


title: T2S_9939_M01ZH09_TD_PREV


title: T2S_7354_Placebo_TD_Va


title: T2S_4289_Ty21a_nonTD_FG3


title: T2S_3612_Ty21a_nonTD_FG3


title: T2S_1157_Ty21a_TD_FG3


title: T2S_1350_Ty21a_nonTD_FG3


title: T2S_8979_Ty21a_TD_PREV


title: T2S_3601_Placebo_TD_FG2


title: T2S_131_Ty21a_nonTD_PREV


title: T2S_4058_Ty21a_nonTD_FG3


title: T2S_6434_Ty21a_nonTD_PREV


title: T2S_7967_Placebo_TD_PREV


title: T2S_2541_M01ZH09_nonTD_FG2


title: T2S_1674_Ty21a_nonTD_FG2


title: MDA-MB-231-control rep

status: Public on Jun 30 2016

type: SRA

city: Brighton

first: Leandro

last: Castellano

address: Falmer, JMS Building

institute: University of Sussex

description: duplicated GSM929913 Sample records to enable the retrieval of the complete raw data from SRA.

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were mapped to the hg19 genome assembly using Partek flow (Partek incorporated)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genomic Suite (Partek Incorporated)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Cell lines were maintained in DMEM supplemented with 10% FCS, 1% penicillin/streptomycin, and 2% glutamine

extract_protocol: Total RNA has been extracted using TRIzol (invitrigen). Libraries were prepared using the True-seq RNA preparation kit (Illumina) following the manufacturer instructions

treatment_protocol: MCF-7 cell lines were transiently transfected with either miR-23b or miR-26a mimic using hiperfect transfection reagent (Qiagen).

tag: cell line

tag: cell type

value: mesenchymal-like breast cancer cells

tag: genotype/variation

value: control


title: MCF-7-miR-nc rep

description: duplicated GSM929910 Sample records to enable the retrieval of the complete raw data from SRA.

value: epithelial breast cancer cells


title: MDA-MB-231-sp-26a rep

value: reduced miR-26a activity

tag: stably transfected with

value: miR-26a with specific sponge vector


title: T2S_6769_Placebo_TD_FG2


title: T2S_9076_Ty21a_TD_FG2


title: T2S_6912_Placebo_nonTD_PREV


title: T2S_8078_Placebo_nonTD_PREV


title: T2S_7206_Placebo_TD_Va


title: T2S_3557_M01ZH09_TD_FG2


title: T2S_5199_Placebo_nonTD_FG2


title: T2S_8098_M01ZH09_nonTD_Va


title: T2S_5527_M01ZH09_nonTD_PREV


title: T2S_785_Placebo_nonTD_FG2


title: T2S_7075_M01ZH09_TD_PREV


title: T2S_2828_Placebo_nonTD_Va


title: T2S_2627_Ty21a_nonTD_FG2


title: T2S_5799_Placebo_TD_PREV


title: MCF-7-miR-26a_rep

value: overexpression of miR-26a

tag: transiently transfected with


title: PTCL.22 - mAdbID:126543

status: Public on Jun 01 2015

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

country: USA

institute: University of Nebraska Medical Center

description: mAdb experiment ID: 126543

hyb_protocol: Affymetrix Hybridization Protocol Other: The labeled cRNAs were hybridized to HG-U133 plus 2.0 Affymetrix GeneChip arrays (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scannning Protocol Other: The chips were scanned with an Affymetrix GeneChip Scanner 3000 and subsequent images analyzed by the use of GCOS 1.4 (Affymetrix).

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol:
Affymetrix Labeling Protocol
Other: The total RNAs (1 ug) were amplified and labeled following the one-cycle target labeling protocol (Affymetrix).

extract_protocol:
AllPrep DNA/RNA/isolation Kit
Other: Total RNA was extracted with AllPrep DNA/RNA/isolation Kit (Qiagen), according to the manufacturer's instructions.

value: lymph node

tag: disease state

value: Peripheral T-cell lymphoma (PTCL)

tag: individual

tag: clinical info

value: Follow up status:alive

value: Follow up years:0.72


title: AITL.72 - mAdbID:126572

description: mAdb experiment ID: 126572

value: Follow up years:7.151666667


title: NKt.61 - mAdbID:126562

description: mAdb experiment ID: 126562

value: Follow up status:dead

value: Follow up years:1.141666667


title: AITL.62 - mAdbID:126524

description: mAdb experiment ID: 126524

value: Follow up years:2.239166667


title: AITL.65 - mAdbID:126571

description: mAdb experiment ID: 126571

value: Follow up years:0.4025


title: PTCL.29 - mAdbID:126570

description: mAdb experiment ID: 126570

value: Follow up years:0.194166667


title: PTCL.5 - mAdbID:126556

description: mAdb experiment ID: 126556

value: Follow up years:3.414166667


title: 3223 - mAdbID:99519

description: mAdb experiment ID: 99519

tag: gender

value: male

tag: age


title: PTCL.30 - mAdbID:126564

description: mAdb experiment ID: 126564

value: Follow up years:3.033333333


title: AITL.16 - mAdbID:126555

description: mAdb experiment ID: 126555

value: Follow up years:1.12


title: ALCL.15 - mAdbID:126535

description: mAdb experiment ID: 126535

value: Follow up years:2.76


title: 3225 - mAdbID:99520

description: mAdb experiment ID: 99520

value: Follow up years:0.632443532


title: ALCL.31 - mAdbID:126567

description: mAdb experiment ID: 126567

value: Follow up years:0.898333333


title: PTCL.58 - mAdbID:126552

description: mAdb experiment ID: 126552

value: lymph node

value: Follow up years:0.3425


title: ALCL.28 - mAdbID:126523

description: mAdb experiment ID: 126523

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.990833333


title: 3234 - mAdbID:99625

description: mAdb experiment ID: 99625

value: Follow up status:alive

value: Follow up years:1.368925394


title: ALCL.56 - mAdbID:126545

description: mAdb experiment ID: 126545

value: Follow up status:dead

value: Follow up years:7.22


title: AITL.69 - mAdbID:126531

description: mAdb experiment ID: 126531

value: Follow up years:1.2375


title: PTCL.51 - mAdbID:126563

description: mAdb experiment ID: 126563


title: PTCL.63 - mAdbID:126548

description: mAdb experiment ID: 126548

value: Follow up years:0.815833333


title: 3295 - mAdbID:99990

description: mAdb experiment ID: 99990


title: AITL.18 - mAdbID:126519

description: mAdb experiment ID: 126519

value: Follow up years:0.0025


title: T2S_7604_Placebo_nonTD_PREV

value: Whole blood

value: Placebo

value: nonTD

value: PREV


title: PTCL.6 - mAdbID:126544

description: mAdb experiment ID: 126544


title: NKt.70 - mAdbID:126518

description: mAdb experiment ID: 126518

value: Follow up years:0.870833333


title: AITL.64 - mAdbID:126525

description: mAdb experiment ID: 126525

value: Follow up years:0.051666667


title: PTCL.68 - mAdbID:126520

description: mAdb experiment ID: 126520

value: lymph node

value: Follow up years:0.355833333


title: PTCL.3 - mAdbID:126536

description: mAdb experiment ID: 126536

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:15.09083333


title: ALCL.40 - mAdbID:126538

description: mAdb experiment ID: 126538


title: ALCL.4 - mAdbID:126559

description: mAdb experiment ID: 126559

value: Follow up years:0.0875


title: ALCL.50 - mAdbID:126501

description: mAdb experiment ID: 126501


title: AITL.25 - mAdbID:126517

description: mAdb experiment ID: 126517

value: Follow up status:alive

value: Follow up years:1.231666667


title: ALCL.17 - mAdbID:126516

description: mAdb experiment ID: 126516


title: 3349 - mAdbID:105922

description: mAdb experiment ID: 105922

value: male

value: Follow up status:dead

value: Follow up years:0.030116359


title: AITL.59 - mAdbID:126502

description: mAdb experiment ID: 126502

value: Follow up years:1.806666667


title: 3347 - mAdbID:105920

description: mAdb experiment ID: 105920

value: female

value: Follow up years:0.774811773


title: AITL.20 - mAdbID:126506

description: mAdb experiment ID: 126506

value: Follow up years:0.180833333


title: NKt.1 - mAdbID:126498

description: mAdb experiment ID: 126498

value: Follow up years:7.293333333


title: ALCL.8 - mAdbID:126511

description: mAdb experiment ID: 126511

value: Follow up years:5.741666667


title: 3381 - mAdbID:101832

description: mAdb experiment ID: 101832

value: Follow up years:0.589364035


title: 3338 - mAdbID:105964

description: mAdb experiment ID: 105964

value: lymph node

value: Follow up years:4.271047228


title: AITL.14 - mAdbID:126504

description: mAdb experiment ID: 126504

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:1.12


title: 3389 - mAdbID:101842

description: mAdb experiment ID: 101842

value: Follow up years:0.035635965


title: 3388 - mAdbID:101849

description: mAdb experiment ID: 101849

value: Follow up status:alive

value: Follow up years:9.799890351


title: AITL.27 - mAdbID:126503

description: mAdb experiment ID: 126503

value: Follow up years:0.164166667


title: 3254 - mAdbID:101245

description: mAdb experiment ID: 101245

value: male

value: Follow up status:dead

value: Follow up years:2.250513347


title: AITL.33 - mAdbID:126515

description: mAdb experiment ID: 126515

value: Follow up years:0.076666667


title: 3261 - mAdbID:101241

description: mAdb experiment ID: 101241

value: Follow up years:0.095824778


title: 3258 - mAdbID:101243

description: mAdb experiment ID: 101243

value: female

value: Follow up years:0.97467488


title: 3337 - mAdbID:105963

description: mAdb experiment ID: 105963

value: Follow up years:0.090349076


title: 3379 - mAdbID:101823

description: mAdb experiment ID: 101823

value: Follow up years:8.697916667


title: 3267 - mAdbID:101235

description: mAdb experiment ID: 101235

value: lymph node

value: Follow up years:7.923340178


title: 3342 - mAdbID:105967

description: mAdb experiment ID: 105967

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.621492129


title: 3262 - mAdbID:101240

description: mAdb experiment ID: 101240

value: Follow up years:0.323066393


title: 3392 - mAdbID:101843

description: mAdb experiment ID: 101843

value: Follow up years:1.461074561


title: 3273 - mAdbID:101229

description: mAdb experiment ID: 101229

value: Follow up years:18.39561944


title: 3387 - mAdbID:101840

description: mAdb experiment ID: 101840

value: Follow up status:alive

value: Follow up years:14.96436404


title: 3328 - mAdbID:101213

description: mAdb experiment ID: 101213

value: male

value: Follow up status:dead

value: Follow up years:2.46954141


title: 3329 - mAdbID:101212

description: mAdb experiment ID: 101212

value: Follow up years:3.06091718


title: 3330 - mAdbID:101211

description: mAdb experiment ID: 101211

value: Follow up years:4.840520192


title: 3393 - mAdbID:101853

description: mAdb experiment ID: 101853

value: Follow up years:4.281798246


title: 3303 - mAdbID:101220

description: mAdb experiment ID: 101220

value: Follow up years:2.450376454


title: 3305 - mAdbID:101219

description: mAdb experiment ID: 101219

value: Follow up years:5.56605065


title: 3321 - mAdbID:100225

description: mAdb experiment ID: 100225

value: lymph node

value: Follow up years:0.511978097


title: 3316 - mAdbID:100218

description: mAdb experiment ID: 100218

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:7.972621492


title: FoxD3 injections WT replicate 3

status: Public on Dec 31 2013

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

country: Germany

institute: University of Freiburg

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_3.txt
FoxD3 injections WT replicate 3

hyb_protocol: Agilent Gene Expression Hybridization Kit was used . Micorarrays were hybridized in the Agilent 2545A hybridization oven according Agilent Two-color Microarray based gene expression analysis protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing:
Data were extracted using Agilent Feature Extraction Software and GE2-107_95_Sep09_QC protocol.
Further Normalisation and processing of the data was done using Genedata Expressionist and Analyst software. Cy3 and Cy5 channels of each microarray were normalized using quantile normalization.

organism: Danio rerio

source_name: WT whole embryo

label_protocol: Samples were processed by Agilent Technologies Two-Color Microarray-Based Gene Expression Analysis kit according to Agilent Two-color Microarray based gene expression analysis protocol.

growth_protocol: WT (wild type) or MZ(MZspg) embryos carrying the m793 allele of the spg mutation were used.

extract_protocol: 60-100 embryos per sample were snap-frozen in liquid nitrogen, and total RNA was isolated using the RNA Easy kit (Qiagen). Sample quality was assessed in an Agilent Bioanalyzer 2100, using the RNA 6000 nano Assay Kit.

treatment_protocol: Embryos of the genotypes indicated were injected with 50-100 pg/embryo of Klf4 mRNA, FoxD3 mRNA, or Nanog-like mRNA  or left uninjected. When indicated (CHX) at 1.5 hpf, the embryos were placed into 15 mkg/ml Cycloheximide solution (Calbiochem)  until 4.7 hpf.  Embryos were frozen at 4.7 hpf for RNA isolation.

tag: hours post fertilization

tag: chx treatment

value: no

tag: microinjection


title: FoxD3 injections MZ CHX replicate 3

description:
US90900275_251506410537_S01_GE2_107_Sep09_QC_1_4.txt
FoxD3 injections MZ CHX replicate 3

source_name: MZ whole embryo

value: yes


title: Nanog-like injections MZ replicate 2

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_4.txt
HACP injections MZ replicate 2

value: HACP


title: Nanog-like injections MZ replicate 3

description:
US90900275_251506410440_S01_GE2_107_Sep09_QC_1_4.txt
HACP injections MZ replicate 3


title: FoxD3 injections MZ replicate 2

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_2.txt
FoxD3 injections MZ replicate 2


title: FoxD3 injections MZ CHX replicate 1

description:
US90900275_251506410534_S01_GE2_107_Sep09_QC_1_4.txt
FoxD3 injections MZ CHX replicate 1


title: Nanog-like injections MZ replicate 1

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_4.txt
HACP injections MZ replicate 1


title: FoxD3 injections MZ replicate 3

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_3.txt
FoxD3 injections MZ replicate 3


title: Klf4 injections MZ CHX replicate 2

description:
US90900275_251506410534_S01_GE2_107_Sep09_QC_1_2.txt
Klf4 injections MZ CHX replicate 2


title: FoxD3 injections MZ replicate 1

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_1.txt
FoxD3 injections MZ replicate 1


title: Klf4 injections MZ CHX replicate 1

description:
US90900275_251506410534_S01_GE2_107_Sep09_QC_1_1.txt
Klf4 injections MZ CHX replicate 1


title: FoxD3 injections MZ CHX replicate 2

description:
US90900275_251506410536_S01_GE2_107_Sep09_QC_1_4.txt
FoxD3 injections MZ CHX replicate 2


title: FoxD3 injections WT replicate 2

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_2.txt
FoxD3 injections WT replicate 2


title: 3331 - mAdbID:101210

description: mAdb experiment ID: 101210

value: female

tag: tissue

value: Follow up years:0.254620123


title: FoxD3 injections WT replicate 1

description:
US90900275_251506410439_S01_GE2_107_Sep09_QC_1_1.txt
FoxD3 injections WT replicate 1


title: MZ CHX Control replicate 3

description:
US90900275_251506410534_S01_GE2_107_Sep09_QC_1_3.txt
MZ CHX Control replicate 3


title: Klf4 injections WT replicate 2

description:
US90900275_251506410438_S01_GE2_107_Sep09_QC_1_2.txt
Klf4 injections WT replicate 2


title: WT Control replicate 3

description:
US90900275_251506410438_S01_GE2_107_Sep09_QC_1_3.txt
WT Control replicate 3


title: Klf4 injections WT replicate 3

description:
US90900275_251506410438_S01_GE2_107_Sep09_QC_1_3.txt
Klf4 injections WT replicate 3


title: MZ CHX Control replicate 2

description:
US90900275_251506410534_S01_GE2_107_Sep09_QC_1_2.txt
MZ CHX Control replicate 2


title: MZ CHX Control replicate 1

description:
US90900275_251506410534_S01_GE2_107_Sep09_QC_1_1.txt
MZ CHX Control replicate 1


title: Klf4 injections WT replicate 1

description:
US90900275_251506410438_S01_GE2_107_Sep09_QC_1_1.txt
Klf4 injections WT replicate 1


title: 3039 - mAdbID:100065

description: mAdb experiment ID: 100065

value: Follow up years:0.076712329


title: WT Control replicate 2

description:
US90900275_251506410438_S01_GE2_107_Sep09_QC_1_2.txt
WT Control replicate 2


title: WT Control replicate 1

description:
US90900275_251506410438_S01_GE2_107_Sep09_QC_1_1.txt
WT Control replicate 1


title: Klf4 injections MZ replicate 1

description:
US90900275_251506410440_S01_GE2_107_Sep09_QC_1_1.txt
Klf4 injections MZ replicate 1


title: Klf4 injections MZ replicate 3

description:
US90900275_251506410440_S01_GE2_107_Sep09_QC_1_3.txt
Klf4 injections MZ replicate 3


title: MZ Control replicate 1

description:
US90900275_251506410440_S01_GE2_107_Sep09_QC_1_1.txt
MZ Control replicate 1


title: MZ Control replicate 2

description:
US90900275_251506410440_S01_GE2_107_Sep09_QC_1_2.txt
MZ Control replicate 2


title: Klf4 injections MZ replicate 2

description:
US90900275_251506410440_S01_GE2_107_Sep09_QC_1_2.txt
Klf4 injections MZ replicate 2


title: FoxD5 Morpholino injection replicate 3

description: US90900275_252643710068_S01_GE2_107_Sep09_QC_1_4.txt: Cy5

hyb_protocol: Agilent Gene Expression Hybridization Kit was used . Micorarrays were hybridized in the Agilent 2545A hybridization oven according Agilent Two-color Microarray based gene expression analysis protocoll

data_processing:
Data were extracted using Agilent Feature Extraction Software and GE2_107_Sep09_QC protocol.
Further Normalisation and processing of the data was done using Genedata Expressionist and Analyst software. Cy3 and Cy5 channels of each microarray were normalized using quantile normalization

source_name: FoxD5 Morpholino injection

label_protocol: Samples were processed by Agilent Technologies Two-Color Microarray-Based Gene Expression Analysis kit according to Agilent Two-color Microarray based gene expression analysis protocoll

growth_protocol: WT (wild type)  were used

extract_protocol: 60-100 embryos per sample were snap-frozen in liquid nitrogen, and total RNA was isolated using the RNA Easy kit (Qiagen). Sample quality was assessed in an Agilent Bioanalyzer 2100, using the RNA 6000 nano Assay Kit

treatment_protocol: Embryos  were injected with 4 ng/embryo of Klf4 Morpholino (MO), 8 ng/embryo of  Standard Control MO, FoxD5 MO or FoxD3 MO,  or 4ng/embryo of FoxD3MO+4ng/embryo of FoxD5MO.  Embryos were frozen at 4,7 hpf for RNA isolation

value: whole embryo

value: wild type

value: FoxD5 Morpholino


title: FoxD3 Morpholino injection replicate 3

description: US90900275_252643710066_S01_GE2_107_Sep09_QC_1_3.txt: Cy3

source_name: FoxD3 Morpholino injection

value: FoxD3 Morpholino


title: FoxD5 Morpholino injection replicate 2

description: US90900275_252643710067_S01_GE2_107_Sep09_QC_1_4.txt: Cy3


title: FoxD5 Morpholino injection replicate 1

description: US90900275_252643710066_S01_GE2_107_Sep09_QC_1_4.txt: Cy5


title: Klf4 Morpholino injection replicate 1

description: US90900275_252643710068_S01_GE2_107_Sep09_QC_1_1.txt: Cy3

source_name: Klf4 Morpholino injection

value: Klf4 Morpholino


title: FoxD3+FoxD5 Morpholino injection replicate 3

description: US90900275_252643710066_S01_GE2_107_Sep09_QC_1_3.txt: Cy5

source_name: FoxD3+FoxD5 Morpholino injection

value: FoxD3 and FoxD5Morpholino


title: Control Morpholino injection replicate 2

description: US90900275_252643710068_S01_GE2_107_Sep09_QC_1_3.txt: Cy5

source_name: Control Morpholino injection

value: Standard Control Morpholino


title: Klf2b Morpholino injection replicate 1

description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_3.txt: Cy3

source_name: Klf2b Morpholino injection

treatment_protocol: Embryos  were injected with 4 ng/embryo of Klf2a, Klf2b or Standard Control Morpholino (MO) or 2ng/embryo of Klf2aMO+2ng/embryo of Klf2bMO.  Embryos were frozen at 4,7 hpf for RNA isolation

value: Klf2b Morpholino


title: FoxD3 Morpholino injection replicate 2

description: US90900275_252643710066_S01_GE2_107_Sep09_QC_1_2.txt: Cy5


title: Control Morpholino injection replicate 1

description: US90900275_252643710068_S01_GE2_107_Sep09_QC_1_1.txt: Cy5


title: MZ Control replicate 3

description:
US90900275_251506410440_S01_GE2_107_Sep09_QC_1_3.txt
MZ Control replicate 3


title: Klf2a+Klf2b Morpholino injection replicate 1

description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_1.txt: Cy5

source_name: Klf2a+Klf2b Morpholino injection

value: Klf2a-Klf2b Morpholino


title: FoxD3+FoxD5 Morpholino injection replicate 2

description: US90900275_252643710066_S01_GE2_107_Sep09_QC_1_2.txt: Cy3


title: FoxD3+FoxD5 Morpholino injection replicate 1

description: US90900275_252643710066_S01_GE2_107_Sep09_QC_1_1.txt: Cy5


title: Klf2a+Klf2b Morpholino injection replicate 2

description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_2.txt: Cy3


title: Klf4 Morpholino injection replicate 2

description: US90900275_252643710068_S01_GE2_107_Sep09_QC_1_3.txt: Cy3


title: FoxD3 injected WT CHX replicate 2

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_2.txt: Cy3

source_name: FoxD3 injected WT CHX

growth_protocol: WT (wild type) or MZ(MZspg) embryos carrying the m793 allele of the spg mutation were used

treatment_protocol: Embryos of the genotypes indicated were injected with 50-100 pg/embryo of Klf2a, Klf2b or FoxD3 mRNA or left uninjected.When indicated (CHX) at 1,5 hpf, the embryos were placed into 15 mkg/ml Cycloheximide solution (Calbiochem)  until 4.7 hpf. Embryos were frozen at 4,7 hpf for RNA isolation


title: FoxD3 Morpholino injection replicate 1

description: US90900275_252643710066_S01_GE2_107_Sep09_QC_1_1.txt: Cy3


title: Klf2a Morpholino injection replicate 1

description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_1.txt: Cy3

source_name: Klf2a Morpholino injection

value: Klf2a Morpholino


title: Klf2b injected WT CHX replicate 1

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_3.txt: Cy5

source_name: Klf2b injected WT CHX


title: FoxD3 injected WT CHX replicate 1

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_1.txt: Cy5


title: Klf2b Morpholino injection replicate 2

description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_4.txt: Cy5


description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_4.txt: Cy3


title: Klf2a Morpholino injection replicate 2

description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_2.txt: Cy5


title: Klf2a injected WT CHX replicate 2

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_4.txt: Cy5

source_name: Klf2a injected WT CHX


description: US90900275_252643710189_S01_GE2_107_Sep09_QC_1_3.txt: Cy5


title: Klf2b injected WT CHX replicate 2

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_4.txt: Cy3


title: GFP injected WT CHX replicate 2

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_4.txt: Cy5

source_name: GFP injected WT CHX

value: GFP


title: Klf2a injected WT CHX replicate 1

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_3.txt: Cy3


title: GFP injected WT CHX replicate 1

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_3.txt: Cy3


title: FoxD3 injected MZ CHX replicate 1

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_1.txt: Cy3

source_name: FoxD3 injected MZ CHX

value: MZspg


title: Klf2a injected MZ CHX replicate 2

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_2.txt: Cy5

source_name: Klf2a injected MZ CHX

value: yes


title: Klf2b injected MZ CHX replicate 2

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_2.txt: Cy3

source_name: Klf2b injected MZ CHX


title: Klf2a injected WT replicate 2

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_2.txt: Cy5

source_name: Klf2a injected WT

value: no


title: GFP injected WT control replicate 2

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_4.txt: Cy5

source_name: GFP injected WT control


title: Klf2b injected MZ replicate 1

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_1.txt: Cy5

source_name: Klf2b injected MZ


title: GFP injected MZ CHX replicate 1

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_3.txt: Cy5

source_name: GFP injected MZ CHX


title: GFP injected MZ control replicate 1

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_3.txt: Cy5

source_name: GFP injected MZ control


title: GFP injected MZ CHX replicate 2

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_4.txt: Cy3


title: FoxD3 injected WT replicate 2

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_4.txt: Cy5

source_name: FoxD3 injected WT


title: GFP injected MZ control replicate 2

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_4.txt: Cy3


title: Klf2b injected WT replicate 1

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_1.txt: Cy5

source_name: Klf2b injected WT


title: Klf2b injected WT replicate 2

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_2.txt: Cy3


title: Klf2a injected MZ CHX replicate 1

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_1.txt: Cy3


title: Klf2a injected MZ replicate 2

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_2.txt: Cy5

source_name: Klf2a injected MZ


title: FoxD3 injected MZ replicate 2

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_4.txt: Cy3

source_name: FoxD3 injected MZ


title: FoxD3 injected MZ replicate 1

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_3.txt: Cy5


title: FoxD3 injected WT replicate 1

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_3.txt: Cy3


title: GFP injected WT control replicate 1

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_3.txt: Cy3


title: Klf2b injected MZ CHX replicate 1

description: US90900275_252643710193_S01_GE2_107_Sep09_QC_1_1.txt: Cy5


title: FoxD3 injected MZ CHX replicate 2

description: US90900275_252643710191_S01_GE2_107_Sep09_QC_1_2.txt: Cy5


title: Klf2a injected WT replicate 1

description: US90900275_252643710190_S01_GE2_107_Sep09_QC_1_1.txt: Cy3


title: Klf2b injected MZ replicate 2

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_2.txt: Cy3


title: Klf2a injected MZ replicate 1

description: US90900275_252643710192_S01_GE2_107_Sep09_QC_1_1.txt: Cy3


title: Klf4 injections MZ CHX replicate 3

description:
US90900275_251506410534_S01_GE2_107_Sep09_QC_1_3.txt
Klf4 injections MZ CHX replicate 3

source_name: MZ whole embryo


title: WT CHX replicate_2

status: Public on Jul 31 2013

description: A_PCRstudy_251506410375_S01_Green_GE2_107_Sep09_QC_1G

data_processing:
Data were extracted using Agilent Feature Extraction Software and GE2-107_95_Sep09_QC protocoll.
Further Normalisation and processing of the data was done using Genedata Expressionist and Analyst software. Cy3 and Cy5 channels of each microarray were normalized using quantile normalization

source_name: WT CHX

growth_protocol: WT (wild type) or MZ embryos carrying the m793 allele of the spg mutation were used

treatment_protocol: Embryos of the genotypes indicated were injected with 100 pg/embryo Pou5f1 mRNA, 50 pg/embryo Sox2 mRNA or left uninjected. At 1.5 hpf, the embryos were placed into 15 mkg/ml Cycloheximide solution (Calbiochem), until the embryos were frozen at 4.7 hpf for RNA isolation


title: Pou5f1 injections MZ CHX replicate_3

description: US45103001_251506410374_S01_GE2_107_Sep09_QC_3R

source_name: Pou5f1 injections MZ CHX

value: MZ mutant


title: MZ CHX replicate_1

description: A_PCRstudy_251506410375_S01_Green_GE2_107_Sep09_QC_1R

source_name: MZ CHX


title: MZ CHX replicate_3

description: US45103001_251506410374_S01_GE2_107_Sep09_QC_4G


title: MZ CHX replicate_2

description: A_PCRstudy_251506410375_S01_Green_GE2_107_Sep09_QC_2R


title: WT CHX replicate_3

description: A_PCRstudy_251506410375_S01_Green_GE2_107_Sep09_QC_2G


title: Sox2 injections MZ CHX replicate_4

description: US45103001_251506410447_S01_GE2_107_Sep09_QC_3G

source_name: Sox2 injections MZ CHX


title: Pou5f1 injections MZ CHX replicate_1

description: US45103001_251506410374_S01_GE2_107_Sep09_QC_1R


title: WT CHX replicate_1

description: US45103001_251506410374_S01_GE2_107_Sep09_QC_4R


title: MDA-MB-231-sp-23b

status: Public on May 01 2013

value: mesenchymal-like breast cancer cells

value: reduced miR-23b activity

value: miR-23b with specific sponge vector


title: MCF-7-miR-23b

value: epithelial breast cancer cells

value: overexpression of miR-23b


title: MCF-7-miR-nc

value: control


title: Sox2 injections WT CHX replicate_3

description: rebeecca_270508_251506410445_S01_GE2_107_Sep09_QC_4R

source_name: Sox2 injections WT CHX

value: wild type

value: whole embryo


title: Sox2 injections MZ CHX replicate_2

description: US45103001_251506410447_S01_GE2_107_Sep09_QC_1G


title: Sox2 injections WT CHX replicate_2

description: rebeecca_270508_251506410445_S01_GE2_107_Sep09_QC_3G


title: Sox2 injections MZ CHX replicate_3

description: US45103001_251506410447_S01_GE2_107_Sep09_QC_2G


title: Sox2 injections MZ CHX replicate_1

description: rebeecca_270508_251506410445_S01_GE2_107_Sep09_QC_1R


title: Pou5f1 injections MZ CHX replicate_2

description: US45103001_251506410374_S01_GE2_107_Sep09_QC_2G


title: MDA-MB-231-control


title: Sox2 injections WT CHX replicate_1

description: rebeecca_270508_251506410445_S01_GE2_107_Sep09_QC_2G


title: WT 60% epiboly stage replicate2

status: Public on Mar 01 2010

description: WT of MZ to WT comparison 60% epiboly stage  Replicate 2

hyb_protocol: Agilent Gene Expression Hybridization Kit was used . Micorarrays were hybridized in the Agilent 2545A hybridization oven according Agilent Two-color Microarray based gene expression analysis protocol

scan_protocol: Microarrays were scanned on a GeneChip scanner 3000.

data_processing: CEL files were loaded to the Refiner Array module of Genedata Expressionist software, submitted to quality inspection, classified and condensed using the MAS5 Affymetrix statistical algorithm.

source_name: wild-type whole embryo

label_protocol: cRNA was amplified using the Ambion MessageAmp™ RNA Amplification Kit. Sample fragmentation, hybridization, washing and staining were performed according to Affymetrix Gene Chip Expression Analysis Technical Manual

growth_protocol: WT embryos of AB x TÜB strain crosses (www.ZFIN.org) and MZ  embryos carrying the m793 allele of the spg mutation were used

extract_protocol: 120 embryos per sample were snap-frozen in liquid nitrogen, and total RNA was isolated using the RNA Easy kit (Qiagen). Sample quality was assessed in an Agilent Bioanalyzer 2100, using the RNA 6000 nano Assay Kit

treatment_protocol: Embryos of the genotypes indicated were precisely staged either following in vitro fertilization (t=0 hpf), or using natural crosses and staging at the 4-cell stage (t=1 hpf)

value: 7 hpf

tag: stage

value: 60% epiboly


title: MZspg 60% epiboly stage replicate1

description: MZ of MZ to WT comparison 60% epiboly stage  Replicate 1

source_name: MZspg whole embryo


title: MZspg 60% epiboly stage replicate2

description: MZ of MZ to WT comparison 60% epiboly stage  Replicate 2


title: WT 60% epiboly stage replicate1

description: WT of MZ to WT comparison 60% epiboly stage  Replicate 1


title: WT 30% epiboly stage replicate2

description: WT of MZ to WT comparison 30% epiboly stage  Replicate 2

value: 4,7 hpf

value: 30% epiboly


title: MZspg 30% epiboly stage replicate2

description: MZ of MZ to WT comparison 30% epiboly stage  Replicate 2


title: MZspg 30% epiboly stage replicate1

description: MZ of MZ to WT comparison 30% epiboly stage  Replicate 1


title: Quadriceps Early cachexia rep3

status: Public on Aug 30 2011

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in Genespring GX software (version 7.3)

organism: Mus musculus

source_name: Mouse quadriceps

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX) according to the manufacturer's instructions, starting with 400 ng total quadriceps RNA.  Successful cRNA generation was checked using the Bioanalyzer 2100.

extract_protocol: Total RNA was extracted from flash frozen quadriceps using TRIzol. Quality control was by Agilent Bioanalyzer 2100 using the RNA 6000 Nano kit.

tag: strain

tag: vendor

value: Harlan

value: 5-6 weeks

value: quadriceps

tag: Sex

value: female


title: MZ at 8 hpf  replicate 3

description: MZ to WT comparison 75p  Replicate 3

data_processing: Data were extracted using Agilent Feature Extraction Software and GE2-v5_95_Feb07 protocoll.

label_protocol: Samples were processed by Agilent Technologies Two-Color Microarray-Based Gene Expression Analysis kit according to Agilent Two-color Microarray based gene expression analysis protocol

value: 75% epiboly


title: MZ at 8 hpf  replicate 2

description: MZ to WT comparison 75p  Replicate 2


title: Quadriceps severe cachexia rep1


title: MZ at 7 hpf  replicate 3

description: MZ to WT comparison 60p  Replicate 3


title: Quadriceps severe cachexia rep2


title: M sphere replicate 2

description: M and MZ_sphere replicate 2

source_name: M whole embryo

growth_protocol: M and MZ  embryos carrying the m793 allele of the spg mutation were used

treatment_protocol: Embryos of the genotypes indicated were  were frozen for RNA isolation  at the indicated stages

value: sphere


title: MZ sphere replicate 1

description: M and MZ_sphere replicate 1


title: MZ sphere replicate 3

description: M and MZ_sphere replicate 3


title: M sphere replicate 1

description: M and MZ_sphere replicate 1


title: WT at 8 hpf  replicate 3

description: MZ to WT comparison 75p  Replicate 3

source_name: WT whole embryo


title: MZ at 8 hpf  replicate 1

description: MZ to WT comparison 75p  Replicate 1


title: MZ at 7 hpf replicate 1

description: MZ to WT comparison 60p  Replicate 1


title: WT at 8 hpf  replicate 1

description: MZ to WT comparison 75p  Replicate 1


title: MZ at 7 hpf replicate 2

description: MZ to WT comparison 60p  Replicate 2


title: WT at 8 hpf  replicate 2

description: MZ to WT comparison 75p  Replicate 2


title: MZ at 6 hpf  replicate 3

description: MZ to WT comparison shield  Replicate 3

value: shield


title: WT at 7 hpf replicate 1

description: MZ to WT comparison 60p  Replicate 1


title: WT at 7 hpf  replicate 3

description: MZ to WT comparison 60p  Replicate 3


title: Wt at 6 hpf  replicate 2

description: MZ to WT comparison shield  Replicate 2


title: WT at 7 hpf replicate 2

description: MZ to WT comparison 60p  Replicate 2


title: MZ at 5 hpf replicate 2

description: MZ to WT comparison 40p Replicate 2

value: 40% epiboly


title: WT at 6 hpf  replicate 1

description: MZ to WT comparison shield  Replicate 1


title: WT at 6 hpf  replicate 3

description: MZ to WT comparison shield  Replicate 3


title: Wt at 5 hpf replicate 3

description: MZ to WT comparison 40p Replicate 3


title: MZ at 6 hpf  replicate 2

description: MZ to WT comparison shield  Replicate 2


title: WT at 5 hpf replicate 1

description: MZ to WT comparison 40p Replicate 1


title: MZ at 5 hpf replicate 1

description: MZ to WT comparison 40p Replicate 1


title: MZ at 6 hpf  replicate 1

description: MZ to WT comparison shield  Replicate 1


title: WT at 4,7 hpf replicate 2

description: MZ to WT comparison 30p Replicate 2


title: MZ at 4,7 hpf  replicate 1

description: MZ to WT comparison 30p Replicate 1


title: MZ at 5 hpf replicate 3

description: MZ to WT comparison 40p Replicate 3


title: WT at 4,7 hpf  replicate 1

description: MZ to WT comparison 30p Replicate 1


title: MZ at 4,7 hpf replicate 2

description: MZ to WT comparison 30p Replicate 2


title: MZ sphere replicate 2

description: M and MZ_sphere replicate 2


title: MZ at 4,7 hpf replicate 3

description: MZ to WT comparison 30p Replicate 3


title: WT at 4,7 hpf replicate 3

description: MZ to WT comparison 30p Replicate 3


title: MZ at 4 hpf  replicate 1

description: MZ to WT comparison sphere Replicate 1


title: WT at 4 hpf  replicate 1

description: MZ to WT comparison sphere Replicate 1


title: WT at 4 hpf  replicate 3

description: MZ to WT comparison sphere Replicate 3


title: MZ at 4 hpf  replicate 2

description: MZ to WT comparison sphere Replicate 2


title: MZ at 4 hpf  replicate 3

description: MZ to WT comparison sphere Replicate 3


title: WT at 4 hpf  replicate 2

description: MZ to WT comparison sphere Replicate 2


title: WT at 5 hpf replicate 2

description: MZ to WT comparison 40p Replicate 2


title: MZ at 3 hpf  replicate 2

description: MZ to WT comparison 1K Replicate 2

value: 1 K


title: MZ at 2,5 hpf  replicate 3

description: MZ to WT comparison 256 cell Replicate 3

value: 256 cell


title: MZ at 3 hpf  replicate 1

description: MZ to WT comparison 1K Replicate 1


title: WT at 3 hpf  replicate 3

description: MZ to WT comparison 1K Replicate 3


title: WT at 3 hpf  replicate 2

description: MZ to WT comparison 1K Replicate 2


title: MZ at 3 hpf  replicate 3

description: MZ to WT comparison 1K Replicate 3


title: WT at 3 hpf  replicate 1

description: MZ to WT comparison 1K Replicate 1


title: WT at 2,5 hpf  replicate 1

description: MZ to WT comparison 256 cell Replicate 1


title: MZ at 1 hpf  replicate 2

description: MZ to WT comparison 4 cell Replicate 2

value: 4 cell


title: MZ at 2,5 hpf  replicate 1


title: WT at 2,5 hpf  replicate 3


title: MZ at 2,5 hpf  replicate 2

description: MZ to WT comparison 256 cell Replicate 2


title: MZ at 1 hpf replicate 1

description: MZ to WT comparison 4 cell Replicate 1


title: WT at 1 hpf replicate 1

description: MZ to WT comparison 4 cell Replicate 1


title: WT at 2,5 hpf  replicate 2


title: WT at 1 hpf  replicate 2

description: MZ to WT comparison 4 cell Replicate 2


title: WT in ovary replicate 3

description: MZ to WT comparison ovary Replicate 3

value: ovary


title: WT in ovary replicate 1

description: MZ to WT comparison ovary Replicate 1


title: Sox2 injections WT CHX replicate 3

description: Sox2_injections_WT_CHX replicate 3

growth_protocol: , WT embryos of AB x TÜB strain crosses (www.ZFIN.org) and MZ  embryos carrying the m793 allele of the spg mutation were used

treatment_protocol: Embryos of the genotypes indicated were injected with 100 pg/embryo Pou5f1 mRNA, 50 pg/embryo Sox2 mRNA or left uninjected. At 1,5 hpf, the embryos were placed into 15 mkg/ml Cycloheximide solution (Calbiochem), until the embryos were frozen for RNA isolation

tag: cycloheximide treatment at 1,5 hpf

value: YES

value: Sox2 50 pg/embryo


title: Pou5f1 injections MZ CHX replicate 1

description: Pou5f1 injections MZ CHX replicate 1

value: Pou5f1 100 pg/embryo


title: Pou5f1 injections MZ CHX replicate 2

description: Pou5f1 injections MZ CHX replicate 2


title: MZ CHX treated replicate 3

description: MZ  CHX treated replicate 3

value: NO


title: Sox2 injections WT CHX replicate 1

description: Sox2_injections_WT_CHX replicate 1


title: Sox2 injections WT CHX replicate 2

description: Sox2_injections_WT_CHX replicate 2


title: MZ in ovary replicate 3

description: MZ to WT comparison ovary Replicate 3


title: MZ CHX treated replicate 2

description: MZ CHX treated replicate 2


title: WT in ovary replicate 2

description: MZ to WT comparison ovary Replicate 2


title: MZ in ovary replicate 2

description: MZ to WT comparison ovary Replicate 2


title: MZ in ovary replicate 1

description: MZ to WT comparison ovary Replicate 1


title: Pou5f1 injections MZ CHX replicate 3

description: Pou5f1 injections MZ CHX  replicate 3


title: MZ CHX treated replicate 1

description: MZ CHX treated replicate 1


title: WT CHX treated replicate 1

description: WT  CHX treated replicate 1


title: Pou5f1 injections MZ replicate 3

description: Pou5f1 injections MZ  replicate 3


title: WT CHX treated replicate 2

description: WT  CHX treated replicate 2


title: Pou5f1 injections MZ replicate 2

description: Pou5f1 injections MZ  replicate 2


title: Pou5f1 injections MZ replicate 1

description: Pou5f1 injections MZ  replicate 1


title: 4,7hpf MZ replicate 1

description: 4,7hpf__MZ_replicate 1


title: 4,7hpf MZ replicate 2

description: 4,7hpf__MZ_replicate 2


title: 4,7hpf MZ replicate 3

description: 4,7hpf__MZ_replicate 3


title: MZ 40% epiboly  replicate 2

description: M and MZ_40%epiboly  replicate 2


title: MZ 40% epiboly  replicate 1

description: M and MZ_40%epiboly  replicate 1


title: M 40% epiboly  replicate 3

description: M and MZ_40%epiboly  replicate 3


title: MZ 40% epiboly  replicate 3

description: M and MZ_40%epiboly  replicate 3


title: M 40% epiboly  replicate 1

description: M and MZ_40%epiboly  replicate 1


title: M 40% epiboly  replicate 2

description: M and MZ_40%epiboly  replicate 2


title: M sphere replicate 3

description: M and MZ_sphere replicate 3


title: WT CHX treated replicate 3

description: WT CHX treated replicate 3


title: WT 30% epiboly stage replicate1

description: WT of MZ to WT comparison 30% epiboly stage  Replicate 1

value: 4,7 hpf

value: 30% epiboly


title: Angioimmunoblastic T-cell lymphoma 2

status: Public on Feb 08 2010

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-137

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Scanning Protocol.

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. Further analysis (e.g., clustering, classification) was carried using BRB-ArrayTools version (3.7.0).

source_name: Pre-treated fresh frozen biopsy, PTCL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All the tissues used in the study were fresh frozen and stored below -70 degree C.

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

tag: cell type

value: PTCL


title: Anapalstic Large cell lymphoma ALK-POS16

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-51

value: male


title: Peripheral T-Cell lymphoma, unspecified 25

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-86

value: female


title: Peripheral T-Cell lymphoma, unspecified 24

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-85


title: Peripheral T-Cell lymphoma, unspecified 42

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-157


title: Angioimmunoblastic T-cell lymphoma 1

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-127


title: Adult T-cell leukemia/lymphoma-12

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-73


title: Anapalstic Large cell lymphoma ALK-POS13

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-39


title: Anapalstic Large cell lymphoma ALK-NEG8

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-38


title: Peripheral T-Cell lymphoma, unspecified 38

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-136


title: Peripheral T-Cell lymphoma, unspecified 37

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-134


title: Anapalstic Large cell lymphoma ALK-POS10

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-128


title: Peripheral T-Cell lymphoma, unspecified 32

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-124


title: Angioimmunoblastic T-cell lymphoma 3

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-138


title: Peripheral T-Cell lymphoma, unspecified 7

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-11


title: Adult T-cell leukemia/lymphoma-8

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-66


title: Peripheral T-Cell lymphoma, unspecified 36

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-133


title: Adult T-cell leukemia/lymphoma-11

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-71


title: Anapalstic Large cell lymphoma ALK-POS12

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-23


title: Peripheral T-Cell lymphoma, unspecified 35

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-132


title: Adult T-cell leukemia/lymphoma-10

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-69


title: Peripheral T-Cell lymphoma, unspecified 26

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-90


title: Adult T-cell leukemia/lymphoma-6

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-64


title: Peripheral T-Cell lymphoma, unspecified 45

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-05