title: P008895-10062013-TD4-01

description: sample

value: M

value: HL


title: P009005.06112013.TTC4.01

status: Public on Nov 13 2016

type: RNA

city: Edinburgh

first: Nichols

last: Ventham

address: Western General Hospital

department: CGEM

country: United Kingdom

institute: Univerisity of Edinburgh

description:
Sample 236
P009005.06112013.TTC4.01

hyb_protocol: Standard Illumina hybridization protocol,18 hour

scan_protocol: Standard Illumina scanning protocol,iScan NO660

data_processing: Data read into R using lumi, background adjusted, variance stabilzed and quantile normalized.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: For the whole blood PAXgene samples (WB), sample concentration and cleanup was performed using the MinElute RNA cleanup kit (Qiagen), globin mRNA transcripts were depleted using GlobinClear (Ambion, Life Technologies USA). All RNA was subsequently amplified and biotylated using the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Life Technology).

extract_protocol: Separated cell RNA was extracted using the Allprep DNA/RNA miRNA universal kit (Qiagen). Whole blood RNA was extracted from PAXgene tubes using the PAXgene blood miRNA kit (PreAnalytix®, Switzerland). The RNA was quantified and assessed for quality using the Agilent BioAnalyzer with only samples with a RNA-integrity number of >7 being used for downstream analyses.

tag: age

tag: Sex

value: F

tag: disease state (diagnosisfull)

value: CD (Crohn's disease)

tag: smoking status

value: Ex

tag: disease state (simplediagnosis)

value: CD

tag: cell type

tag: scandate

tag: samplenumber

tag: sentrixbarcode

tag: samplesection

value: H


title: X8997.PAX.GC

description:
Sample 250
X8997.PAX.GC

source_name: WB

value: UC (Ulcerative colitis)

value: UC

value: WB

value: J


title: P008891.07082013.TTC14.01

description:
Sample 237
P008891.07082013.TTC14.01

value: Never

value: I


title: P008915.10072013.TTC8.01

description:
Sample 235
P008915.10072013.TTC8.01

value: G


title: 0311HC [Whole blood]

type: genomic

description: sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: HiScan H166

data_processing:
Data were processed using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed.The processed data matrix (ProcessedMethWb.txt) represents beta values following background adjustment and correction for dye colour bias. For the final analysis in the published paper additional whole blood DNA samples were added from GSE87640.
Whole blood DNA methylation samples were processed separately using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. Probes were background adjusted, corrected from dye colour bias, and quantile normalised.  Whole blood samples from two datasets were combined at this stage. Subsequently, intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ) and inter-array batch effects were corrected for using ComBat. The data matrix can be found on the SuperSeries GSE87650 record.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Whole blood

label_protocol: DNA was bisulphite converted using the EZ-96 DNA Methylation kit (Zymo Research, Irving CA). Standard Illumina Protocol

extract_protocol: DNA was extracted using the QIAGEN Allprep kit according to instructions

value: Whole blood


title: P009054.14012014.TTCgP.01

description:
Sample 232
P009054.14012014.TTCgP.01

value: HL (Healthy control (Lab volunteer))

value: HC

value: D


title: P009005.06112013.TTC8.01

description:
Sample 231
P009005.06112013.TTC8.01

value: C


title: P009091.20032014.TTCgP.01

description:
Sample 234
P009091.20032014.TTCgP.01

value: F


title: P008918.22072013.TTC4.01

description:
Sample 230
P008918.22072013.TTC4.01

value: M

value: B


title: P009003.05112013.TTC4.01

description:
Sample 233
P009003.05112013.TTC4.01

value: E


title: P009026.04122013.TTC8.01

description:
Sample 227
P009026.04122013.TTC8.01

value: Ex

value: K


title: P009003.25062014.TTC14.02

description:
Sample 228
P009003.25062014.TTC14.02

value: L


title: P009080.05032014.TTC14.01

description:
Sample 229
P009080.05032014.TTC14.01

value: CD (Crohn's disease)

value: Current

value: CD

value: A


title: P008970-24102013-TD8-01

description: sample

data_processing:
Data were processed using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. In methylumi, probes were background adjusted, corrected from dye colour bias, and quantile normalised. Intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ). Inter-array batch effects were corrected for using ComBat.
Whole blood DNA methylation samples were processed separately using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. Probes were background adjusted, corrected from dye colour bias, and quantile normalised.  Whole blood samples from two datasets were combined at this stage. Subsequently, intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ) and inter-array batch effects were corrected for using ComBat. The data matrix can be found on the SuperSeries GSE87650 record.

tag: age at sample


title: P009070.12022014.TTCgP.01

description:
Sample 226
P009070.12022014.TTCgP.01

value: Never

value: WB

value: J


title: P008882-21052013-TB-01

description: sample

source_name: wh blood

value: wh blood

value: UC


title: P009011-13112013-TB-02

description: sample

value: IB

value: HC


title: P008896.12062013.TTC14.01

description:
Sample 225
P008896.12062013.TTC14.01

value: F

value: UC (Ulcerative colitis)

value: I


title: P008918.22072013.TTC8.01

description:
Sample 224
P008918.22072013.TTC8.01

value: M

value: Ex

value: H


title: P008926-08082013-TD4-01

description: sample

value: HL


title: P008915-10072013-TD4-01

description: sample


title: P008903-19062013-TDM-01

description: sample

source_name: monocytes

value: monocytes


title: P008916-16072013-TD8-01

description: sample


title: P009005-06112013-TD4-01

description: sample


title: P008872-08052013-TDM-01

description: sample

value: CD


title: P008862-16042013-TD8-01

description: sample


title: P009026.04122013.TTC14.01

description:
Sample 220
P009026.04122013.TTC14.01

value: D


title: P008946-28082013-TDM-01

description: sample


title: P008998-23102013-TB-01

description: sample


title: P008927-08082013-TB-01

description: sample


title: P008902-19062013-TB-01

description: sample


title: P008888-29052013-TDM-01

description: sample


title: P008874-13052013-TB-01

description: sample


title: P008886.27052013.TTC14.01

description:
Sample 223
P008886.27052013.TTC14.01

value: CD (Crohn's disease)

value: Current

value: G


title: P008948.28082013.TTC14.01

description:
Sample 222
P008948.28082013.TTC14.01

value: IB (IBS)

value: Never


title: P008995-17102013-TB-01

description: sample

value: wh blood

value: IB


title: P008816.12062013.TTC4.01

description:
Sample 219
P008816.12062013.TTC4.01

value: UC

value: C


title: P008918-22072013-TD4-01

description: sample


title: P009034.16122013.TTC4.01

description:
Sample 218
P009034.16122013.TTC4.01

value: UC (Ulcerative colitis)

value: B


title: P008998.23102013.TTC14.01

description:
Sample 216
P008998.23102013.TTC14.01

value: M

value: L


title: P008994-16102013-TB-01

description: sample

value: F


title: P008916.16072013.TTC14.01

description:
Sample 217
P008916.16072013.TTC14.01

value: HL (Healthy control (Lab volunteer))

value: HC

value: A


title: P008911-08072013-TD8-01

description: sample

value: CD


title: P008801.22052013.TTC8.01

description:
Sample 213
P008801.22052013.TTC8.01

value: CD (Crohn's disease)

value: I


title: P008868.24042013.TTC4.01

description:
Sample 212
P008868.24042013.TTC4.01

value: H


title: P008940-24082013-TDM-01

description: sample

value: monocytes


title: P009028.09122013.TTC4.01

description:
Sample 214
P009028.09122013.TTC4.01

value: HC (Healthy control)

value: Never

value: J


title: P009049-09012014-TD4-01

description: sample

value: HL


title: P008998.23102013.TTC8.01

description:
Sample 211
P008998.23102013.TTC8.01

value: UC (Ulcerative colitis)

value: UC

value: G


title: P008822-02042013-TD4-01

description: sample

value: IB


title: P009015-18112013-TDM-01

description: sample

value: M


title: P008862.16042013.TTC4.01

description:
Sample 215
P008862.16042013.TTC4.01

value: F

value: Ex

value: K


title: P009049.09012014.TTC4.01

description:
Sample 210
P009049.09012014.TTC4.01

value: HL (Healthy control (Lab volunteer))

value: HC


title: P008895.10062013.TTCgP.01

description:
Sample 208
P008895.10062013.TTCgP.01

value: WB

value: D


title: P008975-02102013-TB-01

description: sample

value: wh blood


title: P009055.25062014.TTC14.02

description:
Sample 207
P009055.25062014.TTC14.02

value: IB (IBS)

value: C


title: P008954.04092013.TTC14.01

description:
Sample 221
P008954.04092013.TTC14.01

value: CD (Crohn's disease)

value: Current

value: CD

value: E


title: P009049-09012014-TB-01

description: sample

value: HL


title: P009054.14012014.TTC14.01

description:
Sample 203
P009054.14012014.TTC14.01


title: P008970-23092013-TB-01

description: sample


title: P008985-09102013-TD4-01

description: sample

value: UC


title: P009088.19032014.TTC8.01

description:
Sample 206
P009088.19032014.TTC8.01

value: UC (Ulcerative colitis)

value: B


title: P008867-24042013-TD4-01

description: sample

value: M


title: P008891-05062013-TB-01

description: sample


title: P008902-19062013-TDM-01

description: sample

value: monocytes


title: P008961-10092013-TB-01

description: sample


title: P008948-28082013-TDM-01

description: sample

value: IB


title: P008929-09082013-TDM-01

description: sample

value: F

value: HC


title: P009013.13112013.TTC4.01

description:
Sample 200
P009013.13112013.TTC4.01

value: Never

value: H


title: P007821-10102013-TB-01

description: sample

value: wh blood


title: P008929-09082013-TD4-01

description: sample


title: P008946-28082013-TD4-01

description: sample


title: P009005.06112013.TTCgP.01

description:
Sample 198
P009005.06112013.TTCgP.01

value: Ex

value: WB


title: P008916.16072013.TTC4.01

description:
Sample 199
P008916.16072013.TTC4.01

value: HL (Healthy control (Lab volunteer))

value: G


title: P008903-19062013-TB-01

description: sample

value: CD


title: P008931.TTC4.01

description:
Sample 204
P008931.TTC4.01

value: CD (Crohn's disease)

value: L


title: P009050.TTCgP.01.Px

description:
Sample 197
P009050.TTCgP.01.Px

value: E


title: P008940-24082013-TD8-01

description: sample


title: P008897.12062013.TTCgP.01

description:
Sample 201
P008897.12062013.TTCgP.01

value: DI (Diverticular disease)

value: Current

value: I


title: P008862.TTC8.01

description:
Sample 209
P008862.TTC8.01


title: P008961-10092013-TDM-01

description: sample

value: M

value: monocytes

value: UC


title: P008954-04092013-TB-01

description: sample

value: F


title: P009014.13112013.TTCgP.01

description:
Sample 196
P009014.13112013.TTCgP.01

value: UC (Ulcerative colitis)

value: D


title: P008926.08082013.TTC4.01

description:
Sample 195
P008926.08082013.TTC4.01

value: Never

value: HC

value: C


title: P008930.14082013.TTC4.01

description:
Sample 193
P008930.14082013.TTC4.01

value: A


title: P008908-02072013-TDM-01

description: sample

value: CD


title: P008895-10062013-TDM-01

description: sample

value: HL


title: P008999-24102013-TD4-01

description: sample


title: X9001.PAX.GC

description:
Sample 192
X9001.PAX.GC

value: CD (Crohn's disease)

value: WB

value: L


title: P008872.08052013.TTC14.01

description:
Sample 194
P008872.08052013.TTC14.01

value: Ex

value: B


title: P008868-24042013-TDM-01

description: sample

value: M


title: P008868-24042013-TD4-01

description: sample


title: P008999.25062014.TTC14.02

description:
Sample 205
P008999.25062014.TTC14.02

value: HL (Healthy control (Lab volunteer))


title: P008902-19062013-TD8-01

description: sample

value: UC


title: P008891-07082013-TD8-01

description: sample


title: P009051.12012014.TTCgP.01

description:
Sample 202
P009051.12012014.TTCgP.01

value: F

value: J


title: P008908-02072013-TD4-01

description: sample


title: P008822-02042013-TD8-01

description: sample

value: IB


title: P008847.22042013.TTC8.01

description:
Sample 184
P008847.22042013.TTC8.01

value: Never

value: D


title: P008895.10062013.TTC8.01

description:
Sample 185
P008895.10062013.TTC8.01

value: HC

value: E


title: P008946.28082013.TTC4.01

description:
Sample 191
P008946.28082013.TTC4.01

value: UC (Ulcerative colitis)

value: Don't know

value: K


title: P008006-15102013-TD8-01

description: sample

value: HL


title: P009015.18112013.TTC4.01

description:
Sample 188
P009015.18112013.TTC4.01

value: H


title: P008954.04092013.TTC8.01

description:
Sample 187
P008954.04092013.TTC8.01

value: CD (Crohn's disease)

value: Current

value: CD

value: G


title: P008916.16072013.TTCgP.01

description:
Sample 189
P008916.16072013.TTCgP.01

value: HL (Healthy control (Lab volunteer))

value: WB

value: I


title: P008946.28082013.TTC14.01

description:
Sample 183
P008946.28082013.TTC14.01

value: M

value: UC

value: C


title: P008985.09102013.TTC14.01

description:
Sample 186
P008985.09102013.TTC14.01

value: Ex

value: F


title: P008867-24042013-TB-01

description: sample

value: wh blood


title: P008816.12062013.TTC8.01

description:
Sample 190
P008816.12062013.TTC8.01

value: UC (Ulcerative colitis)

value: Never

value: J


title: P009051.12012014.TTC4.01

description:
Sample 181
P009051.12012014.TTC4.01

value: A


title: P009122.21052014.TTCgP.01

description:
Sample 182
P009122.21052014.TTCgP.01

value: B


title: P008896-12062013-TDM-01

description: sample

value: monocytes


title: P008847-20032013-TB-01

description: sample

value: CD


title: P008801-22052013-TD8-01

description: sample


title: P009080.05032014.TTCgP.01

description:
Sample 178
P009080.05032014.TTCgP.01

value: CD (Crohn's disease)

value: Current


title: P008886-27052013-TD8-01

description: sample


title: P008006.15102013.TTCPx.01

description:
Sample 179
P008006.15102013.TTCPx.01

value: HL (Healthy control (Lab volunteer))

value: HC

value: WB

value: K


title: P009034.16122013.TTCgP.01

description:
Sample 177
P009034.16122013.TTCgP.01

value: M

value: UC

value: I


title: P009088.19032014.TTCgP.01

description:
Sample 176
P009088.19032014.TTCgP.01

value: F

value: Ex

value: H


title: P009110.24042014.TTCgP.01

description:
Sample 180
P009110.24042014.TTCgP.01

value: L


title: P009039.18122013.TTCgP.01

description:
Sample 175
P009039.18122013.TTCgP.01

value: G


title: P009050.10012014.TTC8.01

description:
Sample 174
P009050.10012014.TTC8.01

value: Never


title: P008998-23102013-TD8-01

description: sample


title: P008822-27022013-TB-01

description: sample

value: wh blood

value: IB


title: P009085.17032014.TTC14.01

description:
Sample 172
P009085.17032014.TTC14.01

value: CD (Crohn's disease)

value: CD

value: D


title: P009014.13112013.TTC14.01

description:
Sample 173
P009014.13112013.TTC14.01

value: UC (Ulcerative colitis)

value: E


title: P008911-08072013-TD4-01

description: sample


title: P008926-08082013-TB-01

description: sample

value: HL

value: HC


title: P008931.19082013.TTC8.01

description:
Sample 170
P008931.19082013.TTC8.01

value: B


title: P008983-08102013-TD4-01

description: sample

value: M


title: P008847.TTC14.01

description:
Sample 167
P008847.TTC14.01

value: K


title: P009032.11122013.TTC14.01

description:
Sample 168
P009032.11122013.TTC14.01

value: F

value: UC


title: P009039-18122013-TD8-01

description: sample


title: P008975.02102013.TTC14.01

description:
Sample 169
P008975.02102013.TTC14.01

value: ID (IBD-U)

value: A


title: P008868-24042013-TB-01

description: sample


title: P009054-14012014-TB-01

description: sample


title: P009034-16122013-TB-01

description: sample


title: P008006-15102013-TD4-01

description: sample


title: P009021.TTC14.01

description:
Sample 166
P009021.TTC14.01

value: HC (Healthy control)

value: Current

value: J


title: P008888-29052013-TB-01

description: sample

value: wh blood


title: P009055-15012014-TD4-01

description: sample

value: IB


title: P008841.11042013.TTC8.01

description:
Sample 165
P008841.11042013.TTC8.01

value: Ex

value: I


title: P008948.28082013.TTC8.01

description:
Sample 164
P008948.28082013.TTC8.01

value: IB (IBS)

value: Never

value: H


title: P009039-18122013-TD4-01

description: sample

value: CD


title: P008867-24042013-TDM-01

description: sample

value: M

value: monocytes


title: P009146.30062014.TTCgP.01

description:
Sample 162
P009146.30062014.TTCgP.01

value: F

value: UC (Ulcerative colitis)

value: WB


title: P009050-10012014-TB-01_R4

description: replicate

value: HL

value: HC


title: P008975-02102013-TD4-01

description: sample

value: UC


title: P008841-11042013-TDM-01

description: sample


title: P008867.24042013.TTC4.01

description:
Sample 159
P008867.24042013.TTC4.01

value: CD (Crohn's disease)

value: C


title: P008903.19062013.TTCgP.01

description:
Sample 161
P008903.19062013.TTCgP.01

value: E


title: P009003-05112013-TDM-01

description: sample


title: P008998.23102013.TTC4.01

description:
Sample 160
P008998.23102013.TTC4.01

value: D


title: P009028.09122013.TTC14.01

description:
Sample 163
P009028.09122013.TTC14.01

value: HC (Healthy control)

value: G


title: P008816-12062013-TD4-01

description: sample


title: P008999-24102013-TB-01

description: sample

value: wh blood


title: P009095.24032014.TTC4.01

description:
Sample 171
P009095.24032014.TTC4.01

value: Current


title: P009095.24032014.TTC14.01

description:
Sample 156
P009095.24032014.TTC14.01

value: CD

value: L


title: P008918-22072013-TDM-01

description: sample

value: M

value: monocytes


title: P008801.22052013.TTC4.01

description:
Sample 158
P008801.22052013.TTC4.01

value: F

value: Never

value: B


title: P009026-04122013-TDM-01

description: sample


title: P009054-14012014-TD4-01

description: sample

value: HL

value: HC


title: P008862-16042013-TD4-01

description: sample


title: P008994.16102013.TTC4.01

description:
Sample 153
P008994.16102013.TTC4.01

value: CD (Crohn's disease)

value: I


title: P008930.14082013.TTC8.01

description:
Sample 157
P008930.14082013.TTC8.01

value: A


title: P009003-05112013-TB-01

description: sample


title: P008940-24082013-TD4-01

description: sample


title: P009013-13112013-TD4-01

description: sample


title: P008896-12062013-TD4-01

description: sample

value: UC


title: P009005-06112013-TB-01

description: sample


title: P007821-10102013-TD8-01

description: sample


title: P008816-12062013-TD8-01

description: sample


title: P009029-09122013-TB-01

description: sample

value: OT


title: P008970.24102013.TTC4.01

description:
Sample 154
P008970.24102013.TTC4.01

value: J


title: P009029.09122013.TTC14.01

description:
Sample 149
P009029.09122013.TTC14.01

value: OT (Other)

value: E


title: P008998.23102013.TTCgP.01

description:
Sample 155
P008998.23102013.TTCgP.01

value: UC (Ulcerative colitis)

value: WB

value: K


title: P008902-19062013-TD4-01

description: sample

value: M


title: P009055-15012014-TB-01

description: sample

value: wh blood

value: IB


title: P008983-08102013-TDM-01

description: sample

value: monocytes


title: P009055.15012014.TTC4.01

description:
Sample 147
P009055.15012014.TTC4.01

value: IB (IBS)

value: C


title: P008999.24102013.TTC4.01

description:
Sample 151
P008999.24102013.TTC4.01

value: F

value: HL (Healthy control (Lab volunteer))

value: Ex

value: HC

value: G


title: P009091.20032014.TTC14.01

description:
Sample 150
P009091.20032014.TTC14.01

value: CD (Crohn's disease)

value: Never

value: CD


title: P008969.23092013.TTCgP.01

description:
Sample 145
P008969.23092013.TTCgP.01

value: Current

value: A


title: P008902.19062013.TTC4.01

description:
Sample 148
P008902.19062013.TTC4.01

value: UC (Ulcerative colitis)

value: UC

value: D


title: X8946.TTC8.01

description:
Sample 143
X8946.TTC8.01

value: M

value: Don't know

value: K


title: P009049-09012014-TDM-01

description: sample

value: monocytes

value: HL


title: P008896.12062013.TTC8.01

description:
Sample 144
P008896.12062013.TTC8.01

value: F

value: L


title: P009030-09122013-TD4-01

description: sample

value: HC


title: P008948-28082013-TD4-01

description: sample

value: IB


title: P008911-08072013-TDM-01

description: sample


title: P008970.24102013.TTC14.01

description:
Sample 146
P008970.24102013.TTC14.01

value: CD (Crohn's disease)

value: B


title: P008902.19062013.TTC14.01

description:
Sample 140
P008902.19062013.TTC14.01

value: Ex

value: H


title: P009013-13112013-TB-01

description: sample

value: wh blood

value: CD


title: P008918-22072013-TD8-01

description: sample

value: UC


title: P008969.23092013.TTC4.01

description:
Sample 137
P008969.23092013.TTC4.01

value: Current

value: E


title: P008948.28082013.TTCgP.01

description:
Sample 152
P008948.28082013.TTCgP.01

value: M

value: IB (IBS)

value: Never

value: WB


title: P009085.17032014.TTCgP.01

description:
Sample 138
P009085.17032014.TTCgP.01

value: F


title: P009013-13112013-TDM-01

description: sample

value: monocytes


title: P008989.14102013.TTCgP.01

description:
Sample 141
P008989.14102013.TTCgP.01

value: HC

value: I


title: P008816.18092013.TTCgP.01

description:
Sample 142
P008816.18092013.TTCgP.01

value: UC (Ulcerative colitis)

value: J


title: P009091.20032014.TTCV.01

description:
Sample 139
P009091.20032014.TTCV.01

value: CD (Crohn's disease)

value: G


title: P008985.09102013.TTC4.01

description:
Sample 136
P008985.09102013.TTC4.01

value: Ex

value: D


title: P008931-19082013-TB-01

description: sample

value: wh blood

value: CD


title: P008801-22052013-TD4-01

description: sample


title: P007821-10102013-TDM-01

description: sample

value: HL


title: P008891-07082013-TDM-01

description: sample

value: M

value: UC


title: P008930.14082013.TTCgP.01

description:
Sample 133
P008930.14082013.TTCgP.01

value: Never

value: A


title: P008985.09102013.TTC8.01

description:
Sample 130
P008985.09102013.TTC8.01


title: P008915.10072013.TTC14.01

description:
Sample 132
P008915.10072013.TTC14.01

value: L


title: P008872.08052013.TTC4.01

description:
Sample 129
P008872.08052013.TTC4.01

value: F


title: P008874.13052013.TTCgP.01

description:
Sample 128
P008874.13052013.TTCgP.01

value: WB

value: H


title: P008994-16102013-TD4-01

description: sample


title: P008970.23092013.TTCgP.01

description:
Sample 126
P008970.23092013.TTCgP.01

value: Current


title: P009021-02122013-TDM-01

description: sample

value: monocytes

value: HC


title: P009013-13112013-TD8-01

description: sample


title: P008908-02072013-TD8-01

description: sample


title: P008983-08102013-TD8-01

description: sample


title: P009003.05112013.TTCgP.01

description:
Sample 131
P009003.05112013.TTCgP.01

value: HL (Healthy control (Lab volunteer))

value: K


title: P008954-04092013-TD8-01

description: sample


title: P008895-10062013-TD8-01

description: sample


title: P008874.TTC8.01

description:
Sample 135
P008874.TTC8.01

value: CD (Crohn's disease)

value: C


title: P008006-15102013-TDM-01

description: sample


title: P008961.10092013.TTC8.01

description:
Sample 127
P008961.10092013.TTC8.01

value: UC (Ulcerative colitis)

value: G


title: P009032-11122013-TB-01

description: sample

value: wh blood


title: P008918.22072013.TTCgP.01

description:
Sample 124
P008918.22072013.TTCgP.01

value: M

value: Ex

value: UC

value: D


title: P008006.15102013.TTC4.01

description:
Sample 123
P008006.15102013.TTC4.01

value: Never


title: P008896-12062013-TB-01

description: sample

value: F


title: P008891-07082013-TD4-01

description: sample


title: P008999.24102013.TTCgP.01

description:
Sample 125
P008999.24102013.TTCgP.01

value: WB

value: E


title: P009055.15012014.TTC8.01

description:
Sample 120
P009055.15012014.TTC8.01

value: IB (IBS)

value: L


title: P008911.08072013.TTCgP.01

description:
Sample 122
P008911.08072013.TTCgP.01

value: CD

value: B


title: P008948-28082013-TD8-01

description: sample

value: IB

value: HC


title: P009054.25062014.TTC4.02

description:
Sample 134
P009054.25062014.TTC4.02

value: HL (Healthy control (Lab volunteer))


title: P008896.12062013.TTCgP.01

description:
Sample 118
P008896.12062013.TTCgP.01

value: UC (Ulcerative colitis)

value: J


title: P009029.09122013.TTCgP.01

description:
Sample 121
P009029.09122013.TTCgP.01

value: M

value: OT (Other)

value: Current

value: A


title: P009039-18122013-TDM-01

description: sample

value: monocytes


title: P008999.24102013.TTC8.01

description:
Sample 115
P008999.24102013.TTC8.01

value: F

value: Ex

value: G


title: P008975.02102013.TTCgP.01

description:
Sample 117
P008975.02102013.TTCgP.01

value: ID (IBD-U)

value: Never

value: UC

value: WB

value: I


title: P008930-14082013-TB-01

description: sample

value: wh blood

value: CD


title: P009014-13112013-TB-01

description: sample


title: P008801.22052013.TTCgP.01

description:
Sample 113
P008801.22052013.TTCgP.01

value: CD (Crohn's disease)

value: E


title: P008926-08082013-TD8-01

description: sample

value: HL

value: HC


title: P008841-19032013-TB-01

description: sample


title: P009091.20032014.TTC4.01

description:
Sample 116
P009091.20032014.TTC4.01

value: H


title: P009028-09122013-TD8-01

description: sample

value: M


title: P008961.10092013.TTC4.01

description:
Sample 110
P008961.10092013.TTC4.01

value: UC (Ulcerative colitis)

value: Current

value: B


title: P009051-12012014-TDM-01

description: sample

value: F

value: monocytes


title: P008915-10072013-TD8-01

description: sample


title: P008891.07082013.TTC4.01

description:
Sample 111
P008891.07082013.TTC4.01

value: Never

value: C


title: P009050-10012014-TDM-01

description: sample


title: P008911.08072013.TTC14.01

description:
Sample 107
P008911.08072013.TTC14.01

value: Ex

value: K


title: P009085.17032014.TTC4.01

description:
Sample 108
P009085.17032014.TTC4.01

value: L


title: P009050-10012014-TB-01_R3

description: replicate

value: wh blood


title: P009030.09122013.TTC8.01

description:
Sample 109
P009030.09122013.TTC8.01

value: IB (IBS)

value: A


title: P009088.19032014.TTC14.01

description:
Sample 112
P009088.19032014.TTC14.01

value: UC

value: D


title: P008006.15102013.TTC14.01

description:
Sample 119
P008006.15102013.TTC14.01

value: HL (Healthy control (Lab volunteer))

value: HC


title: P008946-28082013-TB-01

description: sample

value: M


title: P008931-19082013-TD8-01

description: sample

value: CD


title: P008862-16042013-TB-01

description: sample


title: P008874-13052013-TDM-01

description: sample


title: P008908.02072013.TTC14.01

description:
Sample 104
P008908.02072013.TTC14.01

value: CD (Crohn's disease)

value: Current

value: H


title: P009029-09122013-TDM-01

description: sample

value: monocytes

value: OT


title: P008868.24042013.TTC14.01

description:
Sample 106
P008868.24042013.TTC14.01

value: UC (Ulcerative colitis)

value: Never

value: J


title: P009183.10092014.TTCgP.01

description:
Sample 114
P009183.10092014.TTCgP.01

value: WB

value: F


title: P008929.09082013.TTC14.01

description:
Sample 102
P008929.09082013.TTC14.01

value: Ex


title: P008954-04092013-TD4-01

description: sample


title: P009030-09122013-TD8-01

description: sample


title: P008948-28082013-TB-01

description: sample

value: wh blood

value: IB


title: P009029-09122013-TD8-01

description: sample


title: P009049.09012014.TTCgP.01

description:
Sample 105
P009049.09012014.TTCgP.01

value: HL (Healthy control (Lab volunteer))

value: I


title: P008975.02102013.TTC8.01

description:
Sample 100
P008975.02102013.TTC8.01

value: ID (IBD-U)

value: UC

value: D


title: P008929-09082013-TB-01

description: sample

value: HL

value: HC


title: P008888-29052013-TD8-01

description: sample

value: M


title: P008969-23092013-TD4-01

description: sample

value: CD


title: P009051.12012014.TTC14.01

description:
Sample 101
P009051.12012014.TTC14.01

value: UC (Ulcerative colitis)

value: E


title: P008995.17102013.TTCgP.01

description:
Sample 99
P008995.17102013.TTCgP.01

value: IB (IBS)

value: Never

value: C


title: P009051-12012014-TD4-01

description: sample

value: F


title: P008927-08082013-TD8-01

description: sample


title: P008896-12062013-TD8-01

description: sample


title: P008868.24042013.TTC8.01

description:
Sample 96
P008868.24042013.TTC8.01

value: L


title: P008903.19062013.TTC14.01

description:
Sample 98
P008903.19062013.TTC14.01

value: CD (Crohn's disease)

value: B


title: P009015.18112013.TTCgP.01

description:
Sample 95
P009015.18112013.TTCgP.01

value: Ex

value: WB

value: K


title: P009075.26022014.TTCgP.01

description:
Sample 94
P009075.26022014.TTCgP.01

value: Current

value: J


title: P008918-22072013-TB-01

description: sample

value: wh blood

value: UC


title: P009014.13112013.TTC8.01

description:
Sample 97
P009014.13112013.TTC8.01

value: M

value: A


title: P008902.19062013.TTC8.01

description:
Sample 103
P008902.19062013.TTC8.01

value: UC (Ulcerative colitis)

value: G


title: P008916-16072013-TD4-01

description: sample

value: HL

value: HC


title: P008874-13052013-TD8-01

description: sample

value: CD


title: P009026-04122013-TD4-01

description: sample


title: P009015.25062014.TTC8.01

description:
Sample 93
P009015.25062014.TTC8.01

value: I


title: P008896.12062013.TTC4.01

description:
Sample 89
P008896.12062013.TTC4.01

value: F

value: Never

value: E


title: P008940.24082013.TTC14.01

description:
Sample 88
P008940.24082013.TTC14.01

value: CD (Crohn's disease)

value: D


title: P008886.27052013.TTC8.01

description:
Sample 91
P008886.27052013.TTC8.01

value: Current


title: P009143.25062014.TTCgP.01

description:
Sample 92
P009143.25062014.TTCgP.01

value: IB (IBS)

value: WB

value: H


title: P009021-02122013-TD8-01

description: sample

value: M


title: P008872.08052013.TTC8.01

description:
Sample 87
P008872.08052013.TTC8.01

value: Ex

value: C


title: P008927-08082013-TDM-01

description: sample

value: monocytes


title: P008847-22042013-TD8-01

description: sample


title: P008874-13052013-TD4-01

description: sample


title: P008985-09102013-TDM-01

description: sample

value: UC


title: P008903-19062013-TD8-01

description: sample


title: P008895.10062013.TTC14.01

description:
Sample 84
P008895.10062013.TTC14.01

value: HL (Healthy control (Lab volunteer))

value: HC

value: L


title: P009050-10012014-TD4-01

description: sample

value: HL


title: P009050.10012014.TTC4.01

description:
Sample 85
P009050.10012014.TTC4.01

value: Never

value: A


title: P009051-12012014-TD8-01

description: sample

value: F


title: P009032.04122013.TTC4.01

description:
Sample 83
P009032.04122013.TTC4.01

value: UC (Ulcerative colitis)

value: K


title: P009034-16122013-TD4-01

description: sample


title: P008994-16102013-TD8-01

description: sample

value: CD


title: P008961-10092013-TD8-01

description: sample


title: P009014-13112013-TDM-01

description: sample


title: P009015-18112013-TD4-01

description: sample


title: P009055-15012014-TDM-01

description: sample

value: IB


title: P008994.16102013.TTCgP.01

description:
Sample 81
P008994.16102013.TTCgP.01

value: CD (Crohn's disease)

value: WB

value: I


title: P009029-09122013-TD4-01

description: sample

value: M

value: OT


title: P008888.29052013.TTC14.01

description:
Sample 82
P008888.29052013.TTC14.01

value: UC

value: J


title: P009095.24032014.TTCgP.01

description:
Sample 80
P009095.24032014.TTCgP.01

value: Current

value: H


title: P008801.22052013.TTC14.01

description:
Sample 86
P008801.22052013.TTC14.01

value: B


title: P007821.10102013.TTC4.01

description:
Sample 79
P007821.10102013.TTC4.01

value: HL (Healthy control (Lab volunteer))

value: Never

value: HC

value: G


title: P009075.26022014.TTC14.01

description:
Sample 77
P009075.26022014.TTC14.01

value: E


title: P008969-23092013-TD8-01

description: sample

value: CD


title: P008886-27052013-TB-01

description: sample

value: wh blood


title: P009026.04122013.TTCgP.01

description:
Sample 90
P009026.04122013.TTCgP.01

value: UC (Ulcerative colitis)

value: Ex

value: F


title: P009075.26022014.TTC4.01

description:
Sample 78
P009075.26022014.TTC4.01

value: M

value: CD (Crohn's disease)


title: P009030-09122013-TDM-01

description: sample

value: monocytes


title: P008006-15102013-TB-01

description: sample

value: HL


title: P009054.14012014.TTC8.01

description:
Sample 75
P009054.14012014.TTC8.01

value: C


title: P009032-11122013-TDM-01

description: sample

value: UC


title: P008903-19062013-TD4-01

description: sample


title: P008888.29052013.TTC8.01

description:
Sample 76
P008888.29052013.TTC8.01

value: D


title: P009080.05032014.TTCV.01

description:
Sample 72
P009080.05032014.TTCV.01

value: Current

value: L


title: P008969.23092013.TTC14.01

description:
Sample 74
P008969.23092013.TTC14.01

value: B


title: P008994.16102013.TTC8.01

description:
Sample 70
P008994.16102013.TTC8.01

value: Never

value: J


title: P009054-14012014-TDM-01

description: sample

value: HC


title: P008931.19082013.TTC14.01

description:
Sample 73
P008931.19082013.TTC14.01

value: CD

value: A


title: P008822.02042013.TTC8.01

description:
Sample 69
P008822.02042013.TTC8.01

value: IB (IBS)

value: Ex

value: I


title: P008891.CgP.Px

description:
Sample 67
P008891.CgP.Px

value: M

value: UC (Ulcerative colitis)

value: WB

value: G


title: P008888.29052013.TTCgP.01

description:
Sample 68
P008888.29052013.TTCgP.01

value: UC

value: H


title: P008006.25062014.TTC8.01

description:
Sample 71
P008006.25062014.TTC8.01

value: HL (Healthy control (Lab volunteer))

value: K


title: P008954-04092013-TDM-01

description: sample

value: F

value: monocytes


title: P008916-16072013-TB-01

description: sample

value: wh blood

value: HL


title: P008903.19062013.TTC4.01

description:
Sample 64
P008903.19062013.TTC4.01

value: CD (Crohn's disease)

value: Never

value: CD

value: D


title: P009028-09122013-TDM-01

description: sample

value: HC


title: P008985-09102013-TB-01

description: sample

value: M


title: P008801-22052013-TDM-01

description: sample


title: P008888.29052013.TTC4.01

description:
Sample 62
P008888.29052013.TTC4.01

value: UC (Ulcerative colitis)

value: B


title: P009128.04062014.TTCgP.01

description:
Sample 61
P009128.04062014.TTCgP.01

value: Current

value: WB

value: A


title: P008985.09102013.TTCgP.01

description:
Sample 60
P008985.09102013.TTCgP.01

value: Ex

value: UC

value: L


title: P009049.09012014.TTC14.01

description:
Sample 66
P009049.09012014.TTC14.01

value: HL (Healthy control (Lab volunteer))

value: F


title: P009118.14052014.TTCgP.01

description:
Sample 65
P009118.14052014.TTCgP.01

value: E


title: P008847-22042013-TDM-01

description: sample

value: monocytes


title: P009095.24032014.TTCV.01

description:
Sample 59
P009095.24032014.TTCV.01

value: CD (Crohn's disease)

value: K


title: P008969.23092013.TTC8.01

description:
Sample 58
P008969.23092013.TTC8.01

value: CD

value: J


title: P008801-06022013-TB-01

description: sample

value: wh blood


title: P008927-08082013-TD4-01

description: sample

value: HL

value: HC


title: P008999-24102013-TD8-01

description: sample


title: P008816-12062013-TB-01

description: sample

value: M


title: P008961-10092013-TD4-01

description: sample


title: P009015-18112013-TB-01

description: sample


title: P009028.09122013.TTC8.01

description:
Sample 54
P009028.09122013.TTC8.01

value: HC (Healthy control)

value: Never


title: P008915-10072013-TB-01

description: sample


title: P009051-12012014-TB-01

description: sample


title: P009072.12022014.TTCgP.01

description:
Sample 57
P009072.12022014.TTCgP.01

value: UC (Ulcerative colitis)

value: Current

value: WB

value: I


title: P009075.26022014.TTCV.01

description:
Sample 63
P009075.26022014.TTCV.01

value: C


title: P008998-23102013-TD4-01

description: sample

value: UC


title: P009054-14012014-TD8-01

description: sample


title: P009021.02122013.TTCgP.01

description:
Sample 52
P009021.02122013.TTCgP.01

value: D


title: P009080.05032014.TTC8.01

description:
Sample 55
P009080.05032014.TTC8.01

value: CD (Crohn's disease)

value: G


title: P008872-08052013-TD8-01

description: sample

value: F

value: CD


title: P008886-27052013-TDM-01

description: sample

value: monocytes


title: P008954.04092013.TTCgP.01

description:
Sample 50
P008954.04092013.TTCgP.01

value: B


title: P009039.18122013.TTC14.01

description:
Sample 51
P009039.18122013.TTC14.01


title: P008916.16072013.TTC8.01

description:
Sample 53
P008916.16072013.TTC8.01

value: HL (Healthy control (Lab volunteer))

value: HC

value: E


title: P008886-27052013-TD4-01

description: sample

value: M


title: P009030.09122013.TTC14.01

description:
Sample 56
P009030.09122013.TTC14.01

value: IB (IBS)

value: Never

value: H


title: P009021-02122013-TD4-01

description: sample


title: P008822.02042013.TTC14.01

description:
Sample 49
P008822.02042013.TTC14.01

value: Ex

value: A


title: P008930.14082013.TTC14.01

description:
Sample 48
P008930.14082013.TTC14.01

value: L


title: P008862-16042013-TDM-01

description: sample


title: P008895-10062013-TB-01

description: sample

value: wh blood

value: HL


title: P009028-09122013-TD4-01

description: sample


title: P009032-11122013-TD4-01

description: sample

value: UC


title: P009014.13112013.TTC4.01

description:
Sample 45
P009014.13112013.TTC4.01

value: UC (Ulcerative colitis)

value: I


title: P008915-10072013-TDM-01

description: sample

value: monocytes

value: CD


title: P009112.28042014.TTCgP.01

description:
Sample 47
P009112.28042014.TTCgP.01

value: F

value: WB

value: K


title: P008948.28082013.TTC4.01

description:
Sample 46
P008948.28082013.TTC4.01

value: M

value: HC

value: J


title: P009049-09012014-TD8-01

description: sample


title: P008868-24042013-TD8-01

description: sample


title: P009034-16122013-TDM-01

description: sample


title: P009050-10012014-TB-01_R2

description: replicate


title: P009088.19032014.TTC4.01

description:
Sample 40
P009088.19032014.TTC4.01

value: D


title: P008847.22042013.TTC4.01

description:
Sample 41
P008847.22042013.TTC4.01

value: CD (Crohn's disease)

value: Never

value: E


title: P008940.24082013.TTCgP.01

description:
Sample 42
P008940.24082013.TTCgP.01

value: Current


title: P009088.19032014.TTCV.01

description:
Sample 39
P009088.19032014.TTCV.01

value: Ex

value: C


title: P008862.16042013.TTC14.01

description:
Sample 38
P008862.16042013.TTC14.01

value: B


title: P009013.13112013.TTC8.01

description:
Sample 37
P009013.13112013.TTC8.01

value: A


title: P009014-13112013-TD4-01

description: sample

value: UC


title: P008918.22072013.TTC14.01

description:
Sample 44
P008918.22072013.TTC14.01

value: UC (Ulcerative colitis)

value: H


title: P009029.09122013.TTC8.01

description:
Sample 35
P009029.09122013.TTC8.01

value: OT (Other)


title: P008930-14082013-TDM-01

description: sample

value: monocytes

value: CD


title: P009013.13112013.TTCgP.01

description:
Sample 43
P009013.13112013.TTCgP.01

value: M

value: WB

value: G


title: P008886.27052013.TTC4.01

description:
Sample 36
P008886.27052013.TTC4.01

value: CD (Crohn's disease)

value: L


title: P009030-09122013-TB-02

description: sample

value: F

value: wh blood

value: HC


title: P009026-04122013-TD8-01

description: sample


title: P007821-10102013-TD4-01

description: sample

value: HL


title: P009005-06112013-TDM-01

description: sample


title: P007821.10102013.TTC14.01

description:
Sample 34
P007821.10102013.TTC14.01

value: HL (Healthy control (Lab volunteer))

value: Never

value: J


title: P008999-24102013-TDM-01

description: sample


title: P009032-11122013-TD8-01

description: sample

value: UC


title: P008926.08082013.TTC14.01

description:
Sample 33
P008926.08082013.TTC14.01

value: I


title: P009015.18112013.TTC14.01

description:
Sample 32
P009015.18112013.TTC14.01

value: UC (Ulcerative colitis)

value: Ex

value: H


title: P008961.10092013.TTCgP.01

description:
Sample 30
P008961.10092013.TTCgP.01

value: M

value: Current


title: P009085.17032014.TTCV.01

description:
Sample 29
P009085.17032014.TTCV.01

value: CD

value: E


title: P008946-28082013-TD8-01

description: sample


title: P008961.10092013.TTC14.01

description:
Sample 28
P008961.10092013.TTC14.01

value: D


title: NYU1306

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

country: Japan

institute: Hyogo College of Medicine

description: DNA copy number change of

hyb_protocol: Genomic DNAs from MM and paired PBL, each 250 ng, were fluorescently labeled with Cy5 (test) and Cy3 (reference) with a Genomic DNA ULS Labeling Kit  (Agilent Technologies). Labeled DNAs from tumor and paired normal were combined, denatured, pre-annealed with Cot-1 DNA (Invitrogen) and blocking agent, and then hybridized to each of the arrays.

scan_protocol: Hybridization was performed for 24 hr in a rotating oven at 65°C and 20 rpm in accordance to the protocol of Agilent Technologies.

data_processing:
After hybridization and washes, the arrays were scanned using an Agilent G2505C scanner at 3 μm resolution .
Images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies), in accordance to the CGH_107_Sep09 protocol for background subtraction and normalization.

label_protocol: Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. Genomic DNA from peripheral blood was isolated with a QIAamp DNA Blood Mini Kit (Qiagen).

treatment_protocol: After centrifugation, primary cells in pleural effusions or ascites were cultured in α-MEM (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS (Equitech-Bio, Ingram, TX, USA). Surgically resected tumors were cut into small pieces. These pieces were plated on culture dishes and gently overlaid with culture medium. Primary outgrowth cells were cultured in α-MEM–10% FBS. Adherent cells were expanded by several passages for several weeks or months.

tag: tissue

value: malignant mesothelioma tissue

value: Normal tissue


title: P009095.24032014.TTC8.01

description:
Sample 26
P009095.24032014.TTC8.01

value: CD (Crohn's disease)

value: B


title: P008816.12062013.TTC14.01

description:
Sample 27
P008816.12062013.TTC14.01

value: C


title: P008975.02102013.TTC4.01

description:
Sample 31
P008975.02102013.TTC4.01

value: F

value: ID (IBD-U)

value: Never

value: G


title: NYU1937

description: DNA copy number change of


title: P008970-24102013-TDM-01

description: sample

value: monocytes


title: P009026-04122013-TB-01

description: sample

value: wh blood

value: UC


title: NYU1353

description: DNA copy number change of

value: PBL


title: P008975-02102013-TD8-01

description: sample


title: NYU1373

description: DNA copy number change of


title: P008847-22042013-TD4-01

description: sample

value: M


title: P008816-12062013-TDM-01

description: sample


title: P009003-05112013-TD8-01

description: sample

value: HL

value: HC


title: P009085.17032014.TTC8.01

description:
Sample 25
P009085.17032014.TTC8.01

value: Current

value: CD

value: A


title: P008969-23092013-TB-01

description: sample


title: P009050-10012014-TD8-01

description: sample


title: P008915.10072013.TTC4.01

description:
Sample 24
P008915.10072013.TTC4.01

value: CD (Crohn's disease)

value: Ex

value: L


title: P009055-15012014-TD8-01

description: sample

value: IB


title: NYU1744

description: DNA copy number change of

value: malignant mesothelioma tissue

value: Normal tissue


title: P008888-29052013-TD4-01

description: sample


title: P008891.07082013.TTC8.02

description:
Sample 23
P008891.07082013.TTC8.02

value: UC (Ulcerative colitis)

value: Never

value: K


title: NYU1633

description: DNA copy number change of


title: NYU1861

description: DNA copy number change of


title: P009075.26022014.TTC8.01

description:
Sample 22
P009075.26022014.TTC8.01

value: J


title: NYU1250

description: DNA copy number change of


title: P009021-02122013-TB-01

description: sample

value: wh blood


title: P008822-02042013-TDM-01

description: sample

value: F

value: monocytes


title: P008983.08102013.TTC8.01

description:
Sample 20
P008983.08102013.TTC8.01

value: M

value: HL (Healthy control (Lab volunteer))

value: HC

value: H


title: P008822.02042013.TTC4.01

description:
Sample 21
P008822.02042013.TTC4.01

value: IB (IBS)

value: I


title: P009014-13112013-TD8-01

description: sample

value: UC


title: NYU0966

description: DNA copy number change of

value: PBL


title: NYU0851

description: DNA copy number change of

value: malignant mesothelioma tissue


title: P008874.13052013.TTC14.01

description:
Sample 19
P008874.13052013.TTC14.01

value: CD (Crohn's disease)

value: CD

value: G


title: P008911-08072013-TB-01

description: sample


title: P008969-23092013-TDM-01

description: sample


title: P008841.11042013.TTC14.01

description:
Sample 18
P008841.11042013.TTC14.01

value: UC (Ulcerative colitis)

value: Ex


title: NYU0207

description: DNA copy number change of


title: P008970-24102013-TD4-01

description: sample


title: P008926-08082013-TDM-01

description: sample

value: HL


title: P008867.24042013.TTC8.01

description:
Sample 17
P008867.24042013.TTC8.01

value: Never

value: E


title: P009013.13112013.TTC14.01

description:
Sample 16
P009013.13112013.TTC14.01

value: M

value: D


title: P009005-06112013-TD8-01

description: sample

value: F


title: NYU1017

description: DNA copy number change of


title: P008872-08052013-TB-01

description: sample

value: wh blood


title: NYU0559

description: DNA copy number change of


title: NYU0093

description: DNA copy number change of


title: P009028-09122013-TB-01

description: sample

value: HC


title: P009055.15012014.TTCgP.01

description:
Sample 15
P009055.15012014.TTCgP.01

value: IB (IBS)

value: WB

value: C


title: P009015-18112013-TD8-01

description: sample

value: UC


title: P008985-09102013-TD8-01

description: sample


title: P008929.09082013.TTC4.01

description:
Sample 14
P008929.09082013.TTC4.01

value: HL (Healthy control (Lab volunteer))

value: B


title: P008998-23102013-TDM-01

description: sample

value: monocytes


title: NYU1419

description: DNA copy number change of

value: malignant mesothelioma tissue

value: PBL


title: NYU0866

description: DNA copy number change of


title: NYU0871

description: DNA copy number change of


title: P008867.24042013.TTC14.01

description:
Sample 13
P008867.24042013.TTC14.01

value: CD (Crohn's disease)

value: CD

value: A


title: P008916-16072013-TDM-01

description: sample

value: HL


title: NYU1755

description: DNA copy number change of


title: NYU0809

description: DNA copy number change of


title: P008895.10062013.TTC4.01

description:
Sample 11
P008895.10062013.TTC4.01

value: M

value: Never

value: K


title: P009021.02122013.TTC4.01

description:
Sample 12
P009021.02122013.TTC4.01

value: HC (Healthy control)

value: Current

value: HC

value: L


title: NYU0937

description: DNA copy number change of


title: P009003-05112013-TD4-01

description: sample


title: P008841.11042013.TTC4.01

description:
Sample 9
P008841.11042013.TTC4.01

value: F

value: UC (Ulcerative colitis)

value: Ex

value: UC

value: I


title: NYU0754

description: DNA copy number change of

value: malignant mesothelioma tissue

value: PBL


title: P008946.28082013.TTCgP.01

description:
Sample 10
P008946.28082013.TTCgP.01

value: Don't know

value: WB

value: J


title: P009026.04122013.TTC4.01

description:
Sample 8
P009026.04122013.TTC4.01

value: M

value: H


title: P009034-16122013-TD8-01

description: sample


title: NYU0517

description: DNA copy number change of


title: Young_51_rep3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Young_51
Gene expression data from heart, Young mice, untreated

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (HiScan)

data_processing:
Data processing with the GenomeStudioV2011.1 software
Normalization method: cubic spline algorithm.

label: Biotin

organism: Mus musculus

source_name: Heart, Young mice, untreated

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Midi Kit (Qiagen) using Trizol Reagent (Sigma)

treatment_protocol: As described in the paper. Briefly, mice were housed in a 12h light/dark cycle in IVC cages (type 3) in groups of 4-5 individuals with access to food and water ad libitum. Autoclaved nest material and paper houses served as cage enrichment. Spermidine was applied orally via drinking water. Supplementation was conducted life-long (starting at age 4 month) using 3 mM spermidine. Food (standard chow, Ssniff V1534) and water consumption was recorded twice a week during indicated time periods (averaged over a time period of 4 weeks) by weighing water bottles and food pellets. Generally, animal cages were always randomly assigned to treatment or control groups.

value: 6 months

tag: strain

tag: treatment

value: untreated

value: heart


title: NYU0217

description: DNA copy number change of


title: Young_50_rep2

description:
Young_50
Gene expression data from heart, Young mice, untreated


title: P008872-08052013-TD4-01

description: sample

value: CD


title: P008930-14082013-TD4-01

description: sample


title: Young_49_rep1

description:
Young_49
Gene expression data from heart, Young mice, untreated


title: NYU0647

description: DNA copy number change of


title: P008983-08102013-TB-01

description: sample

value: wh blood

value: HL

value: HC


title: Self vs self experiment

description: negative control

hyb_protocol: Hybridization was performed for 24 hr in a rotating oven at 65°C and 20 rpm in accordance to the protocol of Agilent Technologies.

scan_protocol: After hybridization and washes, the arrays were scanned using an Agilent G2505C scanner at 3 μm resolution .

data_processing: Images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies), in accordance to the CGH_107_Sep09 protocol for background subtraction and normalization.

source_name: Reference DNA in SureTag DNA Labeling Kit (Agilent Technologies)

label_protocol: Genomic DNAs from MM and paired PBL, each 250 ng, were fluorescently labeled with Cy5 (test) and Cy3 (reference) with a Genomic DNA ULS Labeling Kit  (Agilent Technologies). Labeled DNAs from tumor and paired normal were combined, denatured, pre-annealed with Cot-1 DNA (Invitrogen) and blocking agent, and then hybridized to each of the arrays.

growth_protocol: After centrifugation, primary cells in pleural effusions or ascites were cultured in α-MEM (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS (Equitech-Bio, Ingram, TX, USA). Surgically resected tumors were cut into small pieces. These pieces were plated on culture dishes and gently overlaid with culture medium. Primary outgrowth cells were cultured in α-MEM–10% FBS. Adherent cells were expanded by several passages for several weeks or months.

extract_protocol: Genomic DNA from cultured cells were isolated with an AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. Genomic DNA from peripheral blood was isolated with a QIAamp DNA Blood Mini Kit (Qiagen).

tag: control type

value: negative


title: Endometrial samples from sub clinical endometritis cows (SE) rep 3

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

description:
Endometrial gene expression from cows classified as affected by sub clinical endometritis (SE)
s3

hyb_protocol: After fragmentation, amplified RNA was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA).

scan_protocol: After washing and staining using the Fluidics Station 450/250 integrated following the recommendation of GeneChip® expression wash, stain, arrays were scanned using affymetrix®GeneChip™3000 slide scanner (Affymetrix, CA, USA).

data_processing: The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Guanine cytosine robust multi-array analysis (gcrma) method was used for array normalization and background correction . Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA) in software, (www.r-project.org) by integrating the bioconductor packages (www.bioconductor.org).

organism: Bos taurus

source_name: Endometrial biopsy samples collected from Holstein Friesian cows at 42-60 days postpartum and the biopsies were classified as sub clinical endometritis (SE) based on clinical examination of the animal and histological evaluation of the biopsies

label_protocol: After RNA amplification, cRNA labeling was performed using GeneChip®3’ IVT Express Kit according to the protocol described in GeneChip®3’ IVT Express Kit user manual (Affymetrix Inc).

extract_protocol: Total RNA was isolated from 15 mg samples of HE, CE and SE using miRNeasy mini kit (QIAGEN GmbH, Hilden, Germany).

tag: breed

value: Holstein Friesian

value: Endometrial biopsy

tag: biopsy classification

value: sub clinical endometritis (SE)


title: Aged_Spermidine_76_rep3

description:
Aged_Spermidine_76
Gene expression data from heart, Aged mice, treated with 3 mM spermidine

source_name: Heart, Aged mice, treated with 3 mM spermidine

tag: age

value: 30-32 months

value: treated with 3 mM spermidine


title: P007821.10102013.TTCgP.01

description:
Sample 5
P007821.10102013.TTCgP.01

tag: Sex

value: F

value: HL (Healthy control (Lab volunteer))

value: Never

value: WB

value: E


title: Endometrial samples from sub clinical endometritis cows (SE)rep 2

description:
Endometrial gene expression from cows classified as affected by sub clinical endometritis (SE)
s2


title: P009028.09122013.TTCgP.01

description:
Sample 6
P009028.09122013.TTCgP.01

value: M

tag: disease state (diagnosisfull)

value: HC (Healthy control)


title: P009021.02122013.TTC8.01

description:
Sample 7
P009021.02122013.TTC8.01

tag: smoking status

value: Current

value: G


title: Aged_Spermidine_75_rep2

description:
Aged_Spermidine_75
Gene expression data from heart, Aged mice, treated with 3 mM spermidine

value: heart


title: MM35-P

description: DNA copy number change of MM35-P

value: malignant mesothelioma primary culture

value: PBL


title: P008940-24082013-TB-01

description: sample

value: wh blood

value: CD


title: X9157.PAX.GC

description:
Sample 3
X9157.PAX.GC

value: Ex

tag: disease state (simplediagnosis)

value: HC

value: C


title: Aged_Spermidine_36_rep1

description:
Aged_Spermidine_36
Gene expression data from heart, Aged mice, treated with 3 mM spermidine

value: 30-32 months

value: treated with 3 mM spermidine


title: P008931-19082013-TDM-01

description: sample

value: F

tag: cell type

value: monocytes


title: Endometrial samples from clinical endometritis cows (CE) rep3

description:
Endometrial gene expression from cows classified as affected by clinical endometritis (CE)
cl3

source_name: Endometrial biopsy samples collected from Holstein Friesian cows at 42-60 days postpartum and the biopsies were classified as clinical endometritis (CE) based on clinical examination of the animal and histological evaluation of the biopsies

value: Holstein Friesian

value: Endometrial biopsy

value: clinical endometritis (CE)


title: MM29

description: DNA copy number change of

value: malignant mesothelioma tissue


title: NYU0047

description: DNA copy number change of


title: MM57-P

description: DNA copy number change of MM57-P


title: X9080.CD4

description:
Sample 4
X9080.CD4

value: M

value: CD (Crohn's disease)

value: Current

tag: scandate

value: D


title: P008874.13052013.TTC4.02

description:
Sample 2
P008874.13052013.TTC4.02

value: Never

tag: samplenumber

value: B


title: Young_52_rep4

description:
Young_52
Gene expression data from heart, Young mice, untreated

value: 6 months

value: untreated

value: heart


title: P009039-18122013-TB-01

description: sample

value: wh blood

value: CD


title: MM48-P

description: DNA copy number change of MM48-P

value: malignant mesothelioma primary culture

value: PBL


title: P008931-19082013-TD4-01

description: sample

value: F


title: Aged_66_rep4

description:
Aged_66
Gene expression data from heart, Aged mice, untreated

source_name: Heart, Aged mice, untreated

value: 30-32 months


title: Endometrial samples from clinical endometritis cows (CE) rep2

description:
Endometrial gene expression from cows classified as affected by clinical endometritis (CE)
cl2

value: Holstein Friesian

value: Endometrial biopsy

value: clinical endometritis (CE)


title: P009051.12012014.TTC8.01

description:
Sample 1
P009051.12012014.TTC8.01

value: UC (Ulcerative colitis)

value: UC

tag: sentrixbarcode

value: A


title: Aged_04_rep1

description:
Aged_04
Gene expression data from heart, Aged mice, untreated


title: Endometrial samples from clinical endometritis cows (CE) rep1

description:
Endometrial gene expression from cows classified as affected by clinical endometritis (CE)
cl1


title: Aged_05_rep2

description:
Aged_05
Gene expression data from heart, Aged mice, untreated


title: Endometrial samples from healthy cows (HE) rep1

description:
Endometrial gene expression from cows classified as healthy (HE)
hy2

source_name: Endometrial biopsy samples collected from Holstein Friesian cows at 42-60 days postpartum and the biopsies were classified as healthy (HE) based on clinical examination of the animal and histological evaluation of the biopsies

value: healthy (HE)


title: Aged_65_rep3

description:
Aged_65
Gene expression data from heart, Aged mice, untreated


title: MM14-T

description: DNA copy number change of MM14-T

value: malignant mesothelioma tissue


title: EpiCAM only positive cells (P2B)

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: EpiCAM only Positive cells

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GeneSpring GX v 12.0

source_name: EpiCAM only Positive cells

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

growth_protocol: Primary cells Post Sort 12 hour incubation in DMEM high Glucose with 15% Ascites supplement.

extract_protocol: RNA isolation by Trizol Method

treatment_protocol: Patients were treated with standards chemotherapy (carboplatin 675mg, Paclitaxel 230mg)

tag: disease state

value: serous ovarian cancer

value: standard chemotherapy (carboplatin 675mg, Paclitaxel 230mg)

value: Treated EpiCAM only Positive cells


title: MM21-P

description: DNA copy number change of MM21-P


title: EpiCAM only positive cells (P1B)

description: EpiCAM only Positive cells


title: Aged_Spermidine_77_rep4

description:
Aged_Spermidine_77
Gene expression data from heart, Aged mice, treated with 3 mM spermidine

value: treated with 3 mM spermidine

value: heart


title: EpiCAM/CD45 dual positive cells (P2A)

description: EpiCAM/CD45 dual positive cells

source_name: EpiCAM/CD45 dual positive cells

value: Treated EpiCAM/CD45 dual positive cells


title: P008994-16102013-TDM-01

description: sample

value: monocytes

value: CD

tag: age at sample


title: Endometrial samples from sub clinical endometritis cows (SE) rep1

description:
Endometrial gene expression from cows classified as affected by sub clinical endometritis (SE)
s1

tag: tissue

value: sub clinical endometritis (SE)


title: EpiCAM/CD45 dual positive cells (P1A)

description: EpiCAM/CD45 dual positive cells


title: irrigation with 600mM NaCl, harvest at 6h after irrigation, biological rep2

status: Public on Nov 12 2016

city: Haidian

first: Mengzhu

last: Lu

state: Beijing

address: 1# Dongxiaofu,Xiangshan Road

department: Research Institute of Forestry

country: China

institute: Chinese Academy of Forestry

description: Gene expression data from P.euphratica shoots sampled at 6h after irrigation with 600 mM NaCl solution

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 Fluidics Station 400.

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

data_processing: The data were analyzed with GC-RMA using Affymetrix default analysis settings and global scaling as normalization method.

organism: Populus euphratica

source_name: shoots (terminal buds with 3 to 4 expanding leaves) grown in 600mM NaCl-irrigated soil

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: Well-grown 1-meter-high P. euphratica seedlings were individually planted in 10 L pots containing local loam soil  at Yuli, Xinjiang Uygur Autonomous Region of China (Longitude 86°17'21, latitude 41°19'08). Pot-planted seedlings were placed in the field for simulating its natural growth environment to the maximum extent.Plants in pots were completely irrigated once a week with 2 L local groundwater.

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

treatment_protocol: For salt treatment, 2 L Sodium Chloride (NaCl) solution, concentration in 400 mM and 600 mM respectively, was irrigated to each potted plants and equal amount of solution without NaCl was set as control (CK).

value: shoots（terminal bud with 3 to 4 leaves）

value: Seedlings irrigated with 600 mM NaCl solution

tag: time

value: sample harvested at 6 hours after irrigation with NaCl solution


title: irrigation with 600mM NaCl, harvest at 24h after irrigation, biological rep2

description: Gene expression data from P.euphratica shoots sampled at 24h after irrigation with 600 mM NaCl solution

tag: treatment

value: sample harvested at 24 hours after irrigation with NaCl solution


title: irrigation with 600mM NaCl, harvest at 12h after irrigation, biological rep1

description: Gene expression data from P.euphratica shoots sampled at 12h after irrigation with 600 mM NaCl solution

value: sample harvested at 12 hours after irrigation with NaCl solution


title: irrigation with 600mM NaCl, harvest at 24h after irrigation, biological rep1


title: irrigation with 400mM NaCl, harvest at 24h after irrigation, biological rep1

description: Gene expression data from P.euphratica shoots sampled at 24h after irrigation with 400 mM NaCl solution

source_name: shoots (terminal buds with 3 to 4 expanding leaves) grown in 400mM NaCl-irrigated soil

value: Seedlings irrigated with 400 mM NaCl solution


title: irrigation with 600mM NaCl, harvest at 12h after irrigation, biological rep2


title: irrigation with 400mM NaCl, harvest at 12h after irrigation, biological rep1

description: Gene expression data from P.euphratica shoots sampled at 12h after irrigation with 400 mM NaCl solution


title: irrigation with 400mM NaCl, harvest at 12h after irrigation, biological rep2


title: MM45-P

description: DNA copy number change of MM45-P

value: malignant mesothelioma primary culture

value: PBL


title: irrigation with 400mM NaCl, harvest at 6h after irrigation, biological rep1

description: Gene expression data from P.euphratica shoots sampled at 6h after irrigation with 400 mM NaCl solution


title: irrigation with 400mM NaCl, harvest at 24h after irrigation, biological rep2


title: irrigation with 600mM NaCl, harvest at 6h after irrigation, biological rep1


title: control, biological rep1

description: Gene expression data from P.euphratica shoots grown in natural condition

source_name: shoots (terminal buds with 3 to 4 expanding leaves) grown in natural condition

value: Control irrigated with natural water

value: sample harvested from control


title: P009050-10012014-TB-01_R1

description: replicate

value: M

value: wh blood

value: HL

value: HC


title: MM19-P

description: DNA copy number change of MM19-P


title: control, biological rep2


title: CD4T_infected_rep1

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

country: USA

institute: University of California, San Francisco

hyb_protocol: Aminoallyl-incorporated aRNA was conjugated to Cy3 dye (Life Technologies) for 1 h in sodium bicarbonate buffer and cleaned up on a spin column.

scan_protocol: 1.5 ug of Cy3-labeled aRNA was fragmented and hybridized to Agilent 8x60k mouse gene expression microarrays as per manufacturer instructions.

data_processing: Features were extracted using Agilent Feature Extraction software (v.10.7.3.1). Non-background subtracted raw Cy3 intensities were taken as gene expression values and quantile normalized.

label_protocol: RNA was amplified using the Amino Allyl Message Amp II aRNA Amplification kit (Ambion), which incorporates an amino-allyl modified UTP, allowing subsequent conjugation to Cy3.

growth_protocol: C57BL/6 mice were maintained in a specific pathogen free barrier facility.

extract_protocol: RNA was isolated from sorted cells using the RNAqueous Micro kit (Ambion) according to the manufacturer's protocol, with minor modifications.

treatment_protocol: Blood was obtained by cardiac puncture from naïve C57BL/6 mice or C57BL/6 mice infected 6 d with Plasmodium chabaudi AS. Blood leukocytes were labeled with antibodies and sorted twice on a FACS Aria II to obtain pure CD4+ T cell populations. 10,000 cells were sorted directly into RNA lysis buffer (RNAqeous Micro Kit, Ambion) and snap-frozen on dry ice.

tag: strain

tag: gender

value: female

tag: infected with

value: Plasmodium chabaudi

tag: time point

value: 6 d post-infection

value: Peripheral blood leukocytes

tag: cell subtype

value: TCRb+ CD4+ CD44 hi CD62L T cells


title: CD4T_naive_rep3

value: none (naïve)

value: TCRb+ CD4+ T cells


title: Endometrial samples from healthy cows (HE) rep2

description:
Endometrial gene expression from cows classified as healthy (HE)
hy3

tag: breed

value: Holstein Friesian

value: Endometrial biopsy

tag: biopsy classification

value: healthy (HE)


title: CD4T_infected_rep2


title: CD4T_naive_rep2


title: CD4T_naive_rep4


title: CD4T_naive_rep1


title: CD4T_infected_rep3


title: Sperm_Supplement-10-90d

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

description:
Supp-10-90d
raw data file: Human_Folate_Raw_data.txt

hyb_protocol: The hybridization protocol for Infinium® HumanMethylation450 BeadChip assays is provided by Illumina

scan_protocol: The scanning protocol for Infinium® HumanMethylation450 BeadChip assays is provided by Illumina using the Illumin HiScan fluorescent scanner

data_processing:
Beat values obtained from scanning were normalized with funNorm (Fortin et al. 2014)
Normalized beta values are provided for the 46 samples for 392,881 probes used in the analaysis (exclusion of several probes due to >90% similarity to multiple genomic location, to common SNPs within the entire probe sequences (minor allele frequency >2/120), as well as exclusion of X and Y chromosomes)

label: Cy3, Cy5

label_protocol: The labeling protocol for Infinium® HumanMethylation450 BeadChip assays is provided by Illumina

extract_protocol: Genomic DNA was extracted from the sperm pellets using 1,4-dithiothreitol, Proteinase K and phenol:chloroform extraction methods

treatment_protocol: Men were randomized in a double-blind fashion into either placebo or supplement group. Supplements contained 272 mg ascorbic acid, 31 mg all-rac-α-tocopherol acetate, and 400 μg folic acid. Post fortification group sperm was collected with no treatment

tag: subject status

value: men with no history of infertility

tag: treatment group

value: supplement containing 400 μg folic acid/day

value: sperm


title: Sperm_Post-08

description:
Post-08
raw data file: Human_Folate_Raw_data.txt

value: Post-fortification

value: baseline


title: Sperm_Post-06

description:
Post-06
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-10-baselineline

description:
Supp-10-baseline
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Post-02

description:
Post-02
raw data file: Post01-05_Raw_data.txt


title: Sperm_Post-05

description:
Post-05
raw data file: Post01-05_Raw_data.txt


title: Sperm_Supplement-07-90d

description:
Supp-07-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Post-03

description:
Post-03
raw data file: Post01-05_Raw_data.txt


title: Sperm_Supplement-08-90d

description:
Supp-08-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Post-07

description:
Post-07
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-06-baselineline

description:
Supp-06-baseline
raw data file: Human_Folate_Raw_data.txt


title: (shARID1B + 4OHT) Rep3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450

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

data_processing: Microarrays were normalized using RMA method available in oligo Bioconductor package and significant differentially expressed probesets were identified using Limma with Benjamini-Hochberg corrected p-value < 0.05

source_name: IRM90 ER:RAS

label_protocol: Biotinylated cRNA were prepared from 500 ng total RNA according to theThe Ambion iii ® WT Expression Kit Protocol For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays protocol in conjunction with the Affymetrix® GeneChip® WT Terminal Labeling Kit.

growth_protocol: IRM90 ER:RAS were grown in DMEM 10% FBS for 7 days

extract_protocol: Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

treatment_protocol: To induce RAS expression, cells were treated with 4OHT [100nM]

tag: cell line

tag: vector

tag: 4oht treatment

value: yes

tag: days after 4oht


title: Sperm_Supplement-07-baselineline

description:
Supp-07-baseline
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-09-90d

description:
Supp-09-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Post-04

description:
Post-04
raw data file: Post01-05_Raw_data.txt


title: (shARID1B + 4OHT) Rep2


title: Sperm_Supplement-06-90d

description:
Supp-06-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-03-90d

description:
Supp-03-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-05-90d

description:
Supp-05-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-01-90d

description:
Supp-01-90d
raw data file: Human_Folate_Raw_data.txt


title: (shARID1B + 4OHT) Rep1


title: Sperm_Supplement-02-90d

description:
Supp-02-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-03-baselineline

description:
Supp-03-baseline
raw data file: Human_Folate_Raw_data.txt


title: (vector + 4OHT) Rep3

value: empty


title: Sperm_Supplement-04-baselineline

description:
Supp-04-baseline
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-09-baselineline

description:
Supp-09-baseline
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Placebo-09-90d

description:
Placebo-09-90d
raw data file: Human_Folate_Raw_data.txt

value: Placebo


title: Sperm_Supplement-02-baselineline

description:
Supp-02-baseline
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-08-baselineline

description:
Supp-08-baseline
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Placebo-08-90d

description:
Placebo-08-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-04-90d

description:
Supp-04-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Supplement-05-baselineline

description:
Supp-05-baseline
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Post-01

description:
Post-01
raw data file: Post01-05_Raw_data.txt


title: (vector - 4OHT) Rep3

value: no


title: Sperm_Placebo-08-baseline

description:
Placebo-08-base
raw data file: Human_Folate_Raw_data.txt


title: (vector - 4OHT) Rep2


title: (vector + 4OHT) Rep2


title: (vector - 4OHT) Rep1


title: (vector + 4OHT) Rep1


title: Sperm_Placebo-09-baseline

description:
Placebo-09-base
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Placebo-07-90d

description:
Placebo-07-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Placebo-06-90d

description:
Placebo-06-90d
raw data file: Human_Folate_Raw_data.txt


title: WT-aa-30-min-4tU-b-2 vs. 4tU-refpool-pooled-Mot1-WT2

status: Public on Nov 11 2016

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)  * Priming: 5xSSC, 0.1%SDS  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ  * Wash: 5xSSC, 0.1%SDS  * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)  * Hybridization: 16 hours at 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC at 23C  * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using ImaGene software from Biodiscovery.

data_processing: Genes, no bg corr, dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

label_protocol: Robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).    mRNA amplification protocol description:  * All RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot scriptP  * Mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * Plate is incubated @ 70C for 10 mins, cooled to 48C.  * Mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * Plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 10^6 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNaseH (Promega) is added and mixed in each well.  * Plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturer's protocol, to an end volume of 25 ul .  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturer's protocol.   * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.    Labeling protocol description:   * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).    All subsequent steps are performed by the robot script:  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines Cy3 and Cy5 labeled material).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul Cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturer's protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

growth_protocol: growth_aa_labelling: Cells were grown for two doublings in synthetic complete (SC) medium containing 2% glucose. Rapamycin was added for the indicated amount of time at a final concentration of 7.5 uM (standard). 4-thiouracil (4tU) was added to a final concentration of 5 mM six minutes before harvesting by spinning at 3952 x g for 1 minute. The supernatant was decanted and the cells were snap-frozen in liquid nitrogen.

extract_protocol: Labelled 4thiouracil fraction: Separation of labeled RNA : 1) Labeling reaction; (use 100 µg total RNA); Heat RNA samples for 10 min at 60 degC, put on ice for 2 min; RNase free 10 x biotinylation buffer (10 mL: 100 mM Tris, pH 7.5, 10 mM EDTA, RNase_free H2O, Store in aliquots of 1 mL at 4 degC). Biotin-HPDP: Stock concentration: 1 mg/ml dissolved in dimethylformamide ( Stock can be aliquoted and stored frozen). For 100 µg RNA: 200 µl biotin-HDPD, 100 µl 10 x biotinylation buffer, 600 µl RNase-free H2O . Incubate at RT for 1.5hr 800 rpm in Eppendorf mixer at 24oC. Spin empty phase lock tubes 1 min at 16,000 rpm before use . Add RNA, Add app. equal volume chloroform to tubes (fill tubes), Mix vigorously; Spin at 20,000 rpm for 5 min at 4 degC. Transfer upper phase into new 2 ml tubes. 2) RNA precipitation: Add 1/10 vol 5M NaCl, mix; Add equal vol of isopropanol (app. 1 ml), mix and spin at 20,000 rpm for 30 min at 4oC. Remove supernatant; Add 1 ml of 75 % ethanol; Spin at 20,000 rpm for 10 min at 4oC; Remove supernatant, quickspin and remove rest of supernatant (don’t let RNA dry). Resuspend RNA in 100 µL RNase-free H20; Measure RNA concentration. 3) Separation of labeled and unlabeled RNA: Washing buffer (100 mM Tris, pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1 % Tween 20, RNase-free H2O).Heat washing buffer to 65oC. Elution Buffer (from - 20 oC aliquots or prepare fresh: 100 mM dithiothreitol (MW 154.25) in RNase-free H2O, need 200 µl / rxn). Heat biotinylated RNA to 65 degC for 10 min and immediately place on ice for 5 min; Add 100 µL of streptavidin beads to biotinylated RNA (max. 100 µl), final app 200 µl; Incubate with slight shaking for 15 min at RT/ 24 oC; Place µMacs columns into magnetic stand. Add 900 µl of RT washing buffer to columns (pre-run and equilibrate); (to initiate the flow through the column you can gently press on the top of the column with your finger); Apply beads/RNA mix (200 µl) to the columns. Labeled RNA fraction: Collect FT in 1.5 ml tubes and apply to column again; 1st wash (400 µL of 65oC washing buffer); Wash 5 x with 600, 700, 800, 900, 1000 µl washing buffer . Pipet 700 µl RLT buffer (RNeasy MinElute Cleanup Kit) into new tubes; Elute RNA directly into RLT buffer with 100 µl elution buffer; Perform a second round of elution (100 µl) into the same tubes after 5 min (final vol 900 µl). Continue with the RNeasy MinElute Cleanup protocol: Add 500 µL 96-100 % ethanol to the diluted RNA and mix thoroughly by pipetting; Do not centrifuge; Apply 700 µl of the sample to an RNeasy MinElute spin column in a 2 ml collection tube; Close the tube gently and spin for 15 s at > 8,000 g; Discard the FT; Apply remaining sample and repeat spin, discard FT; Transfer the spin column to new 2 ml collection tube; Pipet 500 µL RPE buffer onto the spin column, close the tube gently and spin 15 s at > 8,000 g; Discard the FT; Add 500 µL of 80 % ethanol to the spin column, close the tube gently and spin at > 8,000 g, discard the FT and collection tube; Transfer the spin column to a new 2 mL collection tube, open the cap of the spin column and spin at full speed for 5 min, discard FT and collection tube; To elute, transfer the spin column to a new 1.5 ml collection tube; Pipet 20 µl RNase-free H2O directly onto the center of the membrane; Close the tube gently and spin for 1 min at maximum speed; Measure RNA concentration.

tag: genotype/variation

value: WT-aa


title: WT-aa-10-min-4tU-b-2 vs. 4tU-refpool-pooled-Mot1-WT2


title: Sperm_Supplement-01-baselineline

description:
Supp-01-baseline
raw data file: Human_Folate_Raw_data.txt

tag: tissue


title: Mot1-aa-30-min-4tU-b2-2 vs. 4tU-refpool-pooled-Mot1-WT2


title: WT-aa-0-min-4tU-b-2 vs. 4tU-refpool-pooled-Mot1-WT2


title: Mot1-aa-20-min-4tU-b2-2 vs. 4tU-refpool-pooled-Mot1-WT2


title: WT-aa-20-min-4tU-b-2 vs. 4tU-refpool-pooled-Mot1-WT2


title: Mot1-aa-0-min-4tU-b2-2 vs. 4tU-refpool-pooled-Mot1-WT2


title: Sperm_Placebo-05-baseline

description:
Placebo-05-base
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Placebo-06-baseline

description:
Placebo-06-base
raw data file: Human_Folate_Raw_data.txt


title: 4tU-refpool-pooled-Mot1-WT2 vs. WT-aa-20-min-4tU-a-2


title: Sperm_Placebo-04-90d

description:
Placebo-04-90d
raw data file: Human_Folate_Raw_data.txt


title: 4tU-refpool-pooled-Mot1-WT2 vs. WT-aa-30-min-4tU-a-2


title: Sperm_Placebo-04-baseline

description:
Placebo-04-base
raw data file: Human_Folate_Raw_data.txt


title: 4tU-refpool-pooled-Mot1-WT2 vs. WT-aa-10-min-4tU-a-2


title: 4tU-refpool-pooled-Mot1-WT2 vs. Mot1-aa-30-min-4tU-a1-2


title: 4tU-refpool-pooled-Mot1-WT2 vs. Mot1-aa-20-min-4tU-a1-2


title: Sperm_Placebo-07-baseline

description:
Placebo-07-base
raw data file: Human_Folate_Raw_data.txt


title: Mot1-aa-10-min-4tU-b2-2 vs. 4tU-refpool-pooled-Mot1-WT2


title: 4tU-refpool-pooled-Mot1-WT2 vs. Mot1-aa-10-min-4tU-a1-2


title: 4tU-refpool-pooled-Mot1-WT2 vs. WT-aa-0-min-4tU-a-2


title: 4tU-refpool-pooled-Mot1-WT2 vs. Mot1-aa-0-min-4tU-a1-2


title: Sperm_Placebo-05-90d

description:
Placebo-05-90d
raw data file: Human_Folate_Raw_data.txt


title: wt-aa-90min-5-b vs. 4tU-refpool-pooled-hsf1-rapaT

growth_protocol: growth_aa_labelling: Cells were grown for two doublings in synthetic complete (SC) medium containing 2% glucose. Rapamycin was added for the indicated amount of time at a final concentration of 7.5 uM (standard) or 0.15 uM (slow depletion). 4-thiouracil (4tU) was added to a final concentration of 5 mM six minutes before harvesting by spinning at 3952 x g for 1 minute. The supernatant was decanted and the cells were snap-frozen in liquid nitrogen.


title: hsf1-aa-60min-2-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: wt-aa-60min-5-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: Sperm_Placebo-03-baseline

description:
Placebo-03-base
raw data file: Human_Folate_Raw_data.txt


title: wt-aa-30min-5-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: Sperm_Placebo-02-90d

description:
Placebo-02-90d
raw data file: Human_Folate_Raw_data.txt


title: wt-aa-15min-5-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: Sperm_Placebo-03-90d

description:
Placebo-03-90d
raw data file: Human_Folate_Raw_data.txt


title: Sperm_Placebo-02-baseline

description:
Placebo-02-base
raw data file: Human_Folate_Raw_data.txt


title: hsf1-aa-15min-2-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: hsf1-aa-90min-2-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: hsf1-aa-30min-2-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: 4tU-refpool-pooled-hsf1-rapaT vs. wt-aa-90min-5-a


title: BY42AA_001_labeled_30min-b vs. ref3

source_name: refpool

growth_protocol: yeast-deleteome [grow]: S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2% D-glucose) under agitation (230rpm), at 30C. The cells were collected at midlog.

extract_protocol: Yeast HTP RNA isolation for robot v2.0: Growth of deletion mutant is done using the 24-well Tecan Plate Reader and subsequent RNA extraction and cleanup for robotic amplification:  1. Take frozen cellpellets from 1.5 ml cultures (-80C) and resuspend in 500 ul Acid Phenol Chloroform (From Sigma, 5:1, pH 4.7). Immediately add the same volume TES-buffer (TES: 10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). Vortex very hard for 20 seconds to resuspend pellet.  2. Incubate in water bath for 10 minutes at 65C and vortex again.  3. Incubate tubes in the thermomixer (65C, 1400RPM) for 50 minutes.  4. Spin for 20 minutes at 14000 rpm at 4C.  5. Take new Eppendorf-tube, fill with 500 ul Phenol Chloroform (5:1, pH 4.7). Add water-phase from point 3. Vortex hard for 20 seconds. Spin down for 10 minutes at 14000 rpm at 4C.  6. Take new Eppendorf-tube, fill with 500 ul Chloroform:Isoamyl-alcohol (25:1). Add water-phase from point 4. Vortex hard for 20 seconds. Spin down for 10 minutes at 14000 rpm at 4C.  7. Take new Eppendorf-tube, fill with 50 ul Sodium Acetate (NaAc 3M, pH 5.2). Add water-phase from point 5. Fill tube with Ethanol (100%, -20C). Flip tubes three times. Incubate at -20C for longer than 30 minutes.  8. Spin tubes down for 5 minutes at room temperature, 14000 rpm. Remove fluid with pipette. Be careful not to touch RNA-pellet.  9. Wash pellet with Ethanol 500 ul (80%, -20C). Spin down shortly.  10. Remove Ethanol, do not air dry but directly proceed to 11.  11. Dissolve RNA-pellet in 93 ul sterile water (MQ, freshly tapped). Pipet untill the pellet is released from the side of the tube. Wait 5 minutes and pipet up and down 5 more times. Yield will be around 150ug. (Make sure all RNA is dissolved completely!)  12. RNA solution is transferred to a 96 wells plate (4titude, Bioke).      Subsequent protocols are processed automatically on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).      RNA cleanup protocol description:    * concentration of all RNAs is measured by diluting 5 ul RNA on the SpectraMax;  * 12.5 ul DNaseI dilution (RNase-free DNAse kit, Qiagen, nr 79254, diluted 1:5 in RDD)is mixed with remaining 87.5 ul RNA-solution and incubated @ 18C for 15 minutes;  * RNA is purified and concentrated with RNAClean (Agencourt, Beckman) according to manufacturers protocol, to an end volume of 25 ul;  * 4 ul cleaned RNA is diluted and measured on the SpectraMAX, concentrations are normalized to 0.2 ug/ul in each well;  * 5 ul of cleaned and normalized RNA is used to set up a startplate for RNA amplification.  * 1 ul of cleaned and normalized RNA is used to check integrety by running on a QiaXcel system.  * All plates are snapfrozen and stored at -80C until further use.

tag: strain/background


title: HSF1AA_001_labeled_30min-b vs. ref3

tag: treatment


title: wt-aa-0min-5-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: 4tU-refpool-pooled-hsf1-rapaT vs. wt-aa-60min-5-a


title: 4tU-refpool-pooled-hsf1-rapaT vs. wt-aa-30min-5-a


title: 4tU-refpool-pooled-hsf1-rapaT vs. hsf1-aa-30min-2-a


title: hsf1-aa-0min-2-b vs. 4tU-refpool-pooled-hsf1-rapaT


title: 4tU-refpool-pooled-hsf1-rapaT vs. hsf1-aa-60min-2-a


title: 4tU-refpool-pooled-hsf1-rapaT vs. wt-aa-0min-5-a


title: 4tU-refpool-pooled-hsf1-rapaT vs. hsf1-aa-15min-2-a


title: 4tU-refpool-pooled-hsf1-rapaT vs. hsf1-aa-90min-2-a


title: 4tU-refpool-pooled-hsf1-rapaT vs. wt-aa-15min-5-a


title: 4tU-refpool-pooled-hsf1-rapaT vs. hsf1-aa-0min-2-a


title: Sperm_Placebo-01-90d

description:
Placebo-01-90d
raw data file: Human_Folate_Raw_data.txt


title: 5198s4

city: Glasgow

first: Lisa

last: Hopcroft

address: Paul O'Gorman Leukaemia Research Centre

institute: University of Glasgow

description: Gene expression following 16h treatment

hyb_protocol: As per standard Affymetrix protocols.

scan_protocol: As per standard Affymetrix protocols.

data_processing: .CEL files were read using Bioconductor's ReadAffy() function.  Data were normalised by the rma() function using default settings.

source_name: Patient sample 5198

label_protocol: As per standard Affymetrix protocols.

growth_protocol: Cells were cultured in serum free media in the presence of drug for 16hrs.

extract_protocol: RNEasy minikit.

value: Peripheral blood

tag: cell type

value: CD34+ chronic Myeloid leukemia (CML)


title: Sperm_Placebo-01-baseline

description:
Placebo-01-base
raw data file: Human_Folate_Raw_data.txt


title: 5198s3

description: Gene expression following 16h treatment

value: 150nM Dasatinib


title: 5198s2

description: Gene expression following 16h treatment

value: 5uM Imatinib


title: 5198s5

description: Gene expression following 16h treatment


title: STEMI-d5-5

city: Hannover

first: Julia

last: Osipova

address: Carl-Neuberg Str. 1

department: IMTTS

institute: MHH

description:
Test
SAMPLE 18

data_processing:
Data was processed by Exiqon as standard data analysis:
For the normalization of the data it was used the geomean of all assays detected in all 18 samples.   The formula used is:  Normalized Cp = Geomean(n=18) – assay Cp.
The average normalized Cp of the samples in test groups and in a control group has been calculated.
ΔΔCp: The difference in normalized Cps has been calculated between the average normalized Cp of test and control sample groups.
Fold change = 2 ΔΔCp: Difference in normalized Cps (ΔΔCp) has been converted to fold change with  2 ΔΔCp.  A fold change > 1 indicate up-regulation and a fold change < 1 indicate down-regulation in test (sCAD- or STEMI d0- or STEMI d5-) sample group compared to contol (healthy control) sample group.

label: SYBR Green

source_name: peripheral blood derived CD34+ progenitor cells

label_protocol: RNA sample were sent to Exiqon (Vedbaek, Denmark) for labelling for miRCURYTM LNA Array microRNA profiling.

growth_protocol: CD34+   were isolated directly from the peripheral blood of the patients using CD34-MicroBead-Kit (Miltenyi Biotec) according to the manufacturer’s protocol

extract_protocol: Total RNA was extracted with miRNeasy Kit (Qiagen) following the manufacturer's recommendations

treatment_protocol: no treatment

value: CD34+ progenitor cells

tag: disease state (patient group)

value: STEMI d5

tag: time in culture

value: 0 days


title: 5198s6

description: Gene expression following 16h treatment

value: 250nM BMS214662 + 150nM Dasatinib


title: STEMI-d5-4

description:
Test
SAMPLE 17


title: STEMI-d5-3

description:
Test
SAMPLE 16


title: 174s3

description: Gene expression following 16h treatment

source_name: Patient sample 174


title: 174s5

description: Gene expression following 16h treatment


title: 174s6

description: Gene expression following 16h treatment


title: 5198s1

description: Gene expression following 16h treatment

value: PBS control


title: STEMI-d5-2

description:
Test
SAMPLE 15


title: 170s6

description: Gene expression following 16h treatment

source_name: Patient sample 170


title: STEMI-d5-1

description:
Test
SAMPLE 14


title: 170s5

description: Gene expression following 16h treatment


title: 174s1

description: Gene expression following 16h treatment


title: IGBP1-positive small invasive adenocarcinoma of lung (Noguchi type C) - test2

city: Tsukuba-shi

first: Taiki

last: Sato

state: Ibaraki

address: Tennodai

institute: University of Tsukuba

hyb_protocol: Hy3 labeling

scan_protocol: GenePix®4400A(Molecular Devices),  Array-Pro Analyzer ® Ver.4.5 (Media Cybernetics）

data_processing: miRBase Release 18, MicroArray Data Analysis Tool Ver3.2 (Filgen, Inc)

source_name: Noguchi type C

label_protocol: miRCURY LNATM microRNA Array 6th generation

extract_protocol: total RNA was extracted using a mirVana miRNA isolation kit (Thermo Fisher Scientific) in accordance with the manufacturer’s instructions from frozen materials of lung cancer

value: primary lung cancer

value: positive


title: IGBP1-negative minimally invasive adenocarcioma of lung (MIA) - control

value: negative


title: 174s4

description: Gene expression following 16h treatment


title: 166s6

description: Gene expression following 16h treatment

source_name: Patient sample 166


title: 170s4

description: Gene expression following 16h treatment


title: STEMI-d0-3

description:
Test
SAMPLE 12

value: STEMI d0


title: 170s3

description: Gene expression following 16h treatment


title: 170s1

description: Gene expression following 16h treatment


title: STEMI-d0-2

description:
Test
SAMPLE 11


title: IGBP1-positive small invasive adenocarcinoma of lung (Noguchi type C) - test1


title: 174s2

description: Gene expression following 16h treatment


title: STEMI-d0-4

description:
Test
SAMPLE 13


title: STEMI-d0-1

description:
Test
SAMPLE 10


title: 166s5

description: Gene expression following 16h treatment