title: TK620a

status: Public on Jun 02 2009

city: minneapolis

first: qingsheng

last: li

address: Box 196, 420 Delaware ST SE

department: Microbiology

institute: University of Minnesota

hyb_protocol: Fifteen micrograms of fragmented cRNA was hybridized to an Affymetrix Human Genome U133 Plus 2.0. After hybridization, chips were washed, stained with streptavidin-phycoerythrin, and scanned with GeneChip Operating Software at the Biomedical Genomics Center at the University of Minnesota. The experiments from each RNA sample were duplicated in the preparation of each cRNA probe and microarray hybridization.   Microarray data analysis

scan_protocol: Affymetrix protocol

data_processing: Cel. files were uploaded into the Expressionist program (Genedata, Pro version 4.5) and the expression level for each of the 47,000 transcripts in the arrays were analyzed by using the RMA algorithm. The expression levels from duplicated chips of the same individual’s RNA were correlated and averaged. The expression data from all individuals were exported as Excel files for statistical analysis.   Tests for differences between the stages were conducted using the 2-sample t-test assuming the variance of the measurements are the same in the two groups. Fold differences in the level of gene expression between any 2 stages were estimated with the ratio of the means in the 2 stages. All computations were conducted using the software S-plus version 3.4 from MathSoft.  After statistical analysis, data was sorted based on these transcript cutoffs: p-value of ≤ 0.05 and fold change ≥ 1.7. Significantly changed genes and transcripts were uploaded into NetAffix Analysis Center (http://www.affymetrix.com/analysis/index.affx) to query gene ontology information and into Ingenuity Pathways Analysis (Ingenuity® Systems, www.ingenuity.com) for gene annotation and pathway analysis.

source_name: lymph node

label_protocol: Double stranded cDNA and biotin-labeled cRNA probes were synthesized from 5 micrograms of total RNA with a MessageAmp II aRNA kit (Ambion, Cat# AM1757). The cRNA probes were column purified and fragmented with a Fragmentation kit (Ambion, cat# 8740).

extract_protocol: Inguinal lymph node biopsies from 24 HIV-1-infected subjects at different clinical stages and 6 uninfected subjects were obtained for this University of Minnesota institutional review board–approved microarray study. Each lymph node biopsy was placed into a Falcon tube and snap-frozen by dropping it into liquid nitrogen. Frozen lymph nodes were homogenized with a power homogenizer (Heat Systems Ultrasonic) in TRIzol (In vitrogen, Cat# 15596-018) without thawing. Total RNA was isolated following the manufacturer’s protocol and further purified with an RNeasy Mini Kit (Qiagen, Cat# 74104).

tag: patient id

tag: disease state

value: AIDS

value: Male

tag: race

value: Caucasian

tag: blood cd4+ t  cell count (cells/ml)

tag: plasma hiv-1     rna level   (copies/ml)


title: VM270b

type: RNA

state: MN

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: gender

value: Female

tag: age

value: African American

tag: tissue

value: lymph node


title: WB910a

value: Acute


title: WU590b

value: Asympt


title: WU590a


title: RR670a

value: Uninfected

value: Undetectable


title: WB550b


title: SU360b


title: TK07Nb


title: WB550a


title: TS350a


title: VM270a


title: RR670b


title: SU360a


title: RM08Nb


title: RJ560b


title: TH490b


title: TK620b


title: PR890a


title: PR890b


title: OB06Na


title: OB06Nb


title: PH290a


title: RJ560a


title: RM08Na


title: PH290b


title: TH490a


title: TK07Na


title: MS520b

value: Hispanic


title: MS520a


title: GL380a


title: JS42Nb


title: MH580a


title: GL380b


title: JS300a


title: KS640c


title: JR310a


title: DS350a


title: MH580b


title: JS300b


title: KS640d


title: JR310b


title: DB720a


title: JS42Na


title: DB720b


title: AP760b


title: DS350b


title: DP240a


title: CF630b


title: CF630a


title: DP240b


title: AP760a


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 250 pg, rep2

city: Paris

first: charles

last: decraene

address: 26 rue d'ULM

country: France

institute: Institut Curie

description: no additional information

hyb_protocol: Hybridization mixture was prepared according to Nugen and Affymetrix procedures

scan_protocol: GeneChips were scanned using a 7G scanner (Affymetrix)

source_name: Universal Human Reference RNA

label_protocol: FL-Ovation™ cDNA Biotin Module V2 (Nugen)

extract_protocol: not applicable

tag: protocol

value: WT-Amplification™ Pico kit (Nugen)


title: SkBr3 amplified using WT-Amplification™ Pico kit (Nugen)

description: no additional information

source_name: SkBr3, human breast cancer cell line

extract_protocol: RNeasy Mini Kit (Qiagen)


title: HCC38 amplified using WT-Amplification™ Pico kit (Nugen)

description: no additional information

source_name: HCC38, human breast cancer cell line


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 500 pg, rep1

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 1000 pg, rep2

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 250 pg, rep1

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 100 pg, rep2

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 50 pg, rep2

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 500 pg, rep2

description: no additional information


title: HCC38 amplified using the one cycle amplification kit from Affymetrix

description: no additional information

hyb_protocol: Hybridization mixture was prepared according to Affymetrix procedures

label_protocol: Biotinylated targets were prepared according to manufacturer's instructions (Affymetrix)


title: Universal Human Reference RNA_TargetAmp 2-Round Aminoallyl-aRNA Amplification_Epicentre, 500 pg

description: no additional information

label_protocol: Biotinylated targets were prepared according to manufacturer's instructions (Epicentre)


title: SkBr3 amplified using the one cycle amplification kit from Affymetrix

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 100 pg, rep1

description: no additional information


title: Universal Human Reference RNA amplified using RiboAmp™ HS RNA Amplification Kit  (Arcturus), 500 pg, rep1

description: no additional information

label_protocol: Biotinylated targets were prepared according to manufacturer's instructions (Arcturus)


title: Universal Human Reference RNA amplified using RiboAmp™ HS RNA Amplification Kit  (Arcturus), 500 pg, rep2

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 1000 pg, rep1

description: no additional information


title: Universal Human Reference RNA amplified using RiboAmp™ HS RNA Amplification Kit  (Arcturus), 250 pg, rep2

description: no additional information


title: Universal Human Reference RNA amplified using WT-Amplification™ Pico kit (Nugen), 50 pg, rep1

description: no additional information


title: A155_7423_early_rep1

city: London

first: Lucy

middle: R

last: Wedderburn

address: 30 Guilford Street

department: Rheumatology

country: United Kingdom

institute: Institute of Child Health, UCL

description: Female C57Bl/6 HT transgenic,doxycyline stopped age 21 days , muscle tissue, age at sacrifice 35 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Mouse Genome 430 2.0 Array. GeneChips were washed and stained on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Data was normalised using GC-RMA

organism: Mus musculus

source_name: Quadriceps femoris

label_protocol: RNA was coverted to cDNA (Roche) using an oligod(T) primer and converted to cRNA using In Vitro Triscription labelling kit (Affymetrix

extract_protocol: Total RNA was extracted from 100mg of quadriceps muscle using RNAB (Campro Scientific, Berlin germany).

treatment_protocol: early mice were removed from doxycycline at 21 days, and sacrificed at 35 days of age, after 2 weeks of transgene expression. late mice were maintained on doxycycline until 35 days and sacrificed at 49-50 days of age. Single transgenic littermate controls were age, sex-matched,maintained on doxycycline and sacrificed as the early group

value: muscle

tag: strain

value: C57Bl/6 HT transgenic

tag: age at sacrifice (days)

tag: treatment

value: doxycycline stopped age 21 days


title: A155_7444_late_rep3

description: Female C57Bl/6 HT transgenic,doxycyline stopped age 35 days , muscle tissue, age at sacrifice 50 days

value: doxycycline stopped age 35 days


title: A155_7425_early_rep2


title: Universal Human Reference RNA amplified using the one cycle amplification kit from Affymetrix, 2 µg, rep1

description: no additional information


title: A155_8423_late_rep1


title: A155_7459_control_rep1

description: Female C57Bl/6 HT transgenic, maintained on doxycyline throughout , muscle tissue, age at sacrifice 35 days

value: doxycycline throughout


title: A155_7458_control_rep2


title: A155_8424_late_rep2


title: Universal Human Reference RNA amplified using MessageAmp™ II aRNA Amplification (Ambion), 500 pg, rep1

description: no additional information

label_protocol: Biotinylated targets were prepared according to manufacturer's instructions (Ambion)


title: A155_7443_early_rep3


title: A155_7460_control_rep3


title: Universal Human Reference RNA amplified using the one cycle amplification kit from Affymetrix, 100 ng, rep1

description: no additional information

value: two cycle amplification kit from Affymetrix


title: Universal Human Reference RNA amplified using the one cycle amplification kit from Affymetrix, 100 ng, rep2

description: no additional information


title: Universal Human Reference RNA amplified using the one cycle amplification kit from Affymetrix, 2 µg, rep2

description: no additional information


title: Universal Human Reference RNA amplified using MessageAmp™ II aRNA Amplification (Ambion), 250 pg, rep1

description: no additional information


title: Universal Human Reference RNA amplified using RiboAmp™ HS RNA Amplification Kit  (Arcturus), 250 pg, rep1

description: no additional information


title: late cycle 14 wild-type embryos, biological rep3

city: Princeton

first: Xuemin

last: Lu

state: NJ

address: Washington Rd

department: Molecular biology

institute: Princeton University

description:
Expression data from precisely staged wild-type (diploid) Drosophila embryos.
Biological replicate 3 of 3.

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 GeneChip Fluidics Station 400.

scan_protocol: Gene chips were scaned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite using Affymetrix default analysis settings and global scaling as normalization method.

organism: Drosophila melanogaster

source_name: wild-type embryos, 40min after the nuclear division of cycle 13

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

growth_protocol: Both diploid and haploid flies were raised at 25C to lay embryos on apple juice agar plate for 2-3hours.

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

treatment_protocol: Embryos were identified under Epi fluorescent microscope, timed from telophase of the previous cycle to 15min and 40min later respectively, hand-selected and frozen by dry-ice cold heptane. Triplicates of about 50 embryos each with right age were collected for each time point.

tag: Age

value: late cycle 14

tag: Genotype

value: w;histone H2-GFP parents


title: Universal Human Reference RNA amplified using MessageAmp™ II aRNA Amplification (Ambion), 500 pg, rep2

description: no additional information


title: Universal Human Reference RNA amplified using MessageAmp™ II aRNA Amplification (Ambion), 250 pg, rep2

description: no additional information


title: late cycle 14 wild-type embryos, biological rep1

description:
Expression data from precisely staged wild-type (diploid) Drosophila embryos.
Biological replicate 1 of 3.


title: early cycle 14 wild-type embryos, biological rep1

source_name: wild-type embryos, 15min after the nuclear division of cycle 13

value: early cycle 14


title: late cycle 14 wild-type embryos, biological rep2

description:
Expression data from precisely staged wild-type (diploid) Drosophila embryos.
Biological replicate 2 of 3.


title: LSK_OP9-DL1+CompoundE_Rep1

city: Boston

first: Thomas

last: Mercher

state: MA

address: 1 blackfan circle

department: Hematology

institute: Harvard Medical School

description: Gene expression data from LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The ‘.CEL’ files from the MAS5 software  were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool  (Affymetrix).

label: Biotin

source_name: Hematopoietic LSK cells plated on OP9-DL1 stroma in presence of 1µM CompoundE (g-secretase inhibitor) for 3 days

label_protocol: For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.

growth_protocol: Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.

extract_protocol: RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation

treatment_protocol: After 3 days of co-cultures, non-adherent cells were collected


title: early cycle 14 wild-type embryos, biological rep3


title: late cycle 15 haploid embryos, biological rep3

description:
Expression data from precisely staged blastula haploid Drosophila embryos.
Biological replicate 3 of 3.

source_name: haploid embryos, 40min after the nuclear division of cycle 14

value: late cycle 15

value: maternal haploid;histone H2-GFP parents


title: LSK_OP9-DL1+CompoundE_Rep2


title: LSK_OP9-DL1_Rep3

description: Gene expression data from LSK cells plated on OP9-DL1 stroma for 3 days

source_name: Hematopoietic LSK cells plated on OP9-DL1 stroma for 3 days


title: early cycle 15 haploid embryos, biological rep1

description:
Expression data from precisely staged blastula haploid Drosophila embryos.
Biological replicate 1 of 3.

source_name: haploid embryos, 15min after the nuclear division of cycle 14

value: early cycle 15


title: early cycle 15 haploid embryos, biological rep3


title: late cycle 15 haploid embryos, biological rep1


title: cycle 13 wild-type embryos, biological rep3

source_name: wild-type embryos, 15min after the nuclear division of cycle 12

value: cycle 13


title: cycle 13 wild-type embryos, biological rep2


title: LSK_OP9-DL1+CompoundE_Rep3


title: early cycle 14 wild-type embryos, biological rep2


title: early cycle 15 haploid embryos, biological rep2

description:
Expression data from precisely staged blastula haploid Drosophila embryos.
Biological replicate 2 of 3.


title: LSK_OP9-GFP_Rep3

description: Gene expression data from LSK cells plated on OP9-GFP stroma for 3 days

source_name: Hematopoietic LSK cells plated on OP9-GFP stroma for 3 days


title: LSK_OP9-DL1_Rep1


title: late cycle 15 haploid embryos, biological rep2


title: cycle 13 wild-type embryos, biological rep1


title: LSK_OP9-DL1_Rep2


title: cycle 14 haploid embryos, biological rep1

source_name: haploid embryos, 15min after the nuclear division of cycle 13

value: cycle 14


title: cycle 14 haploid embryos, biological rep2


title: cycle 14 haploid embryos, biological rep3


title: LSK_OP9-GFP_Rep1


title: LSK_OP9-GFP_Rep2


title: Dros Roo line 6 Untreated

status: Public on Jun 01 2009

city: Birmingham

first: Grier

last: Page

state: AL

institute: University of Alabama at Birmingham

description: gene expression data from Dros Roo line 6 Untreated for an eQTL study

hyb_protocol: standard Affymetrix procedures

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

data_processing: The data were analyzed with R/Affy and data extracted using justRMA fucnation using default analysis settings.

label: Total RNA

label_protocol: standard Affymetrix procedures

growth_protocol: Flies from each of the 75 roo lines (20 males and 20 females) were placed in a vial with 10 ml of food (control or PbAc) for 3 days at 25oC and then the adults were discarded. The male progeny (5-10 days old) were pooled from each vial (65 males per vial) and frozen at -80oC.

extract_protocol: Total RNA was isolated following Trizol Manual (Invitrogen Life Technologies) with modifications made by Kevin Bogart and Justen Andrews at Indiana University. Frozen flies (50 mg) were homogenized with Poly Tron (Kinematica AG) in a 5 ml tube with 2 ml of Trizol. The homogenate was incubated at room temperature for 5 minutes followed by centrifuge at 12,000 rcf for 10 minutes at 4oC to pellet insoluble debris. 1 ml supernatant was transferred to a new centrifuge tube and 0.2 ml chloroform was added. After shaking the tube vigorously by hand for 15 seconds, sample was incubated for 3 minutes at room temperature and then was centrifuged at 10,000 rcf for 15 minutes at 4oC. 0.54 ml aqueous phase was carefully transferred to a fresh RNAse-free tube and 0.45 ml isopropanol was added to each tube followed by vortexing. After 10 minutes incubation at room temperature, sample was centrifuged at 12,000 rcf for 10 minutes at 4oC. Supernatant was then removed and the pellet was washed with 1 ml 75% ethanol followed by centrifuge at 7,500 rcf for 5 minutes at 4oC. After the supernatant was removed and the pellet was air dried for 10 minutes at room temperature, the pellet was resuspended in 40 ul Rnase free water at the end. All RNA samples were lead-treated with DNase I in order to get rid of potential DNA contamination.

treatment_protocol: Control food consisted of standard cornmeal, agar, sugar, yeast, and 250 uM NaAc (Ashburner 1989). Lead-contaminated food consisted of standard food plus 250 uM PbAc (lead exposure at this concentration has been shown to affect locomotion in adults (Hirsch et al. 2003))

tag: Whole Adult Drosophilia

tag: Dros Roo line 6


title: Dros Roo line 205 Lead Acetate treated

description: gene expression data from Dros Roo line 205 Lead Acetate added to diet for an eQTL study

source_name: Diet:Lead Acetate added to diet

tag: Dros Roo line 205


title: Dros Roo line 99 Untreated

description: gene expression data from Dros Roo line 99 Untreated for an eQTL study

tag: Dros Roo line 99


title: Dros Roo line 15 Untreated

description: gene expression data from Dros Roo line 15 Untreated for an eQTL study

tag: Dros Roo line 15


title: Dros Roo line 70 Lead Acetate treated

description: gene expression data from Dros Roo line 70 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 70


title: Dros Roo line 215 Untreated

description: gene expression data from Dros Roo line 215 Untreated for an eQTL study

tag: Dros Roo line 215


title: Dros Roo line 11 Lead Acetate treated

description: gene expression data from Dros Roo line 11 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 11


title: Dros Roo line 99 Lead Acetate treated

description: gene expression data from Dros Roo line 99 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 56 Lead Acetate treated

description: gene expression data from Dros Roo line 56 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 56


title: Dros Roo line 210 Lead Acetate treated

description: gene expression data from Dros Roo line 210 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 210


title: Dros Roo line 80 Untreated

description: gene expression data from Dros Roo line 80 Untreated for an eQTL study

tag: Dros Roo line 80


title: Dros Roo line 43 Untreated

description: gene expression data from Dros Roo line 43 Untreated for an eQTL study

tag: Dros Roo line 43


title: Dros Roo line 205 Untreated

description: gene expression data from Dros Roo line 205 Untreated for an eQTL study


title: Dros Roo line 223 Untreated

description: gene expression data from Dros Roo line 223 Untreated for an eQTL study

tag: Dros Roo line 223


title: Dros Roo line 76 Untreated

description: gene expression data from Dros Roo line 76 Untreated for an eQTL study

tag: Dros Roo line 76


title: Dros Roo line 213 Untreated

description: gene expression data from Dros Roo line 213 Untreated for an eQTL study

tag: Dros Roo line 213


title: Dros Roo line 58 Untreated

description: gene expression data from Dros Roo line 58 Untreated for an eQTL study

tag: Dros Roo line 58


title: Dros Roo line 79 Lead Acetate treated

description: gene expression data from Dros Roo line 79 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 79


title: Dros Roo line 48 Untreated

description: gene expression data from Dros Roo line 48 Untreated for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 48


title: Dros Roo line 46 Lead Acetate treated

description: gene expression data from Dros Roo line 46 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 46


title: Dros Roo line 12 Lead Acetate treated

description: gene expression data from Dros Roo line 12 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 12


title: Dros Roo line 67 Untreated

description: gene expression data from Dros Roo line 67 Untreated for an eQTL study

tag: Dros Roo line 67


title: Dros Roo line 85 Untreated

description: gene expression data from Dros Roo line 85 Untreated for an eQTL study

tag: Dros Roo line 85


title: Dros Roo line 75 Untreated

description: gene expression data from Dros Roo line 75 Untreated for an eQTL study

tag: Dros Roo line 75


title: Dros Roo line 224 Lead Acetate treated

description: gene expression data from Dros Roo line 224 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 224


title: Dros Roo line 27 Untreated

description: gene expression data from Dros Roo line 27 Untreated for an eQTL study

tag: Dros Roo line 27


title: Dros Roo line 29 Untreated

description: gene expression data from Dros Roo line 29 Untreated for an eQTL study

tag: Dros Roo line 29


title: Dros Roo line 81 Untreated

description: gene expression data from Dros Roo line 81 Untreated for an eQTL study

tag: Dros Roo line 81


title: Dros Roo line 15 Lead Acetate treated

description: gene expression data from Dros Roo line 15 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 15


title: Dros Roo line 11 Untreated

description: gene expression data from Dros Roo line 11 Untreated for an eQTL study

tag: Dros Roo line 11


title: Dros Roo line 17 Lead Acetate treated

description: gene expression data from Dros Roo line 17 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 17


title: Dros Roo line 212 Untreated

description: gene expression data from Dros Roo line 212 Untreated for an eQTL study

tag: Dros Roo line 212


title: Dros Roo line 85 Lead Acetate treated

description: gene expression data from Dros Roo line 85 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 97 Lead Acetate treated

description: gene expression data from Dros Roo line 97 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 97


title: Dros Roo line 207 Untreated

description: gene expression data from Dros Roo line 207 Untreated for an eQTL study

tag: Dros Roo line 207


title: Dros Roo line 77 Untreated

description: gene expression data from Dros Roo line 77 Untreated for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 77


title: Dros Roo line 44 Lead Acetate treated

description: gene expression data from Dros Roo line 44 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 44


title: Dros Roo line 50 Untreated

description: gene expression data from Dros Roo line 50 Untreated for an eQTL study

tag: Dros Roo line 50


title: Dros Roo line 43 Lead Acetate treated

description: gene expression data from Dros Roo line 43 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 43


title: Dros Roo line 38 Lead Acetate treated

description: gene expression data from Dros Roo line 38 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 38


title: Dros Roo line 52 Lead Acetate treated

description: gene expression data from Dros Roo line 52 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 52


title: Dros Roo line 13 Lead Acetate treated

description: gene expression data from Dros Roo line 13 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 13


title: Dros Roo line 36 Lead Acetate treated

description: gene expression data from Dros Roo line 36 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 36


title: Dros Roo line 86 Untreated

description: gene expression data from Dros Roo line 86 Untreated for an eQTL study

tag: Dros Roo line 86


title: Dros Roo line 87 Lead Acetate treated

description: gene expression data from Dros Roo line 87 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 87


title: Dros Roo line 52 Untreated

description: gene expression data from Dros Roo line 52 Untreated for an eQTL study


title: Dros Roo line 6 Lead Acetate treated

description: gene expression data from Dros Roo line 6 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 6


title: Dros Roo line 51 Lead Acetate treated

description: gene expression data from Dros Roo line 51 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 51


title: Dros Roo line 27 Lead Acetate treated

description: gene expression data from Dros Roo line 27 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 27


title: Dros Roo line 202 Untreated

description: gene expression data from Dros Roo line 202 Untreated for an eQTL study

tag: Dros Roo line 202


title: Dros Roo line 37 Untreated

description: gene expression data from Dros Roo line 37 Untreated for an eQTL study

tag: Dros Roo line 37


title: Dros Roo line 35 Lead Acetate treated

description: gene expression data from Dros Roo line 35 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 35


title: Dros Roo line 84 Untreated

description: gene expression data from Dros Roo line 84 Untreated for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 84


title: Dros Roo line 216 Lead Acetate treated

description: gene expression data from Dros Roo line 216 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 216


title: Dros Roo line 89 Lead Acetate treated

description: gene expression data from Dros Roo line 89 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 89


title: Dros Roo line 35 Untreated

description: gene expression data from Dros Roo line 35 Untreated for an eQTL study


title: Dros Roo line 10 Lead Acetate treated

description: gene expression data from Dros Roo line 10 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 10


title: Dros Roo line 88 Untreated

description: gene expression data from Dros Roo line 88 Untreated for an eQTL study

tag: Dros Roo line 88


title: Dros Roo line 28 Lead Acetate treated

description: gene expression data from Dros Roo line 28 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 28


title: Dros Roo line 78 Untreated

description: gene expression data from Dros Roo line 78 Untreated for an eQTL study

tag: Dros Roo line 78


title: Dros Roo line 210 Untreated

description: gene expression data from Dros Roo line 210 Untreated for an eQTL study

tag: Dros Roo line 210


title: Dros Roo line 81 Lead Acetate treated

description: gene expression data from Dros Roo line 81 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 81


title: Dros Roo line 36 Untreated

description: gene expression data from Dros Roo line 36 Untreated for an eQTL study

tag: Dros Roo line 36


title: Dros Roo line 88 Lead Acetate treated

description: gene expression data from Dros Roo line 88 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 22 Untreated

description: gene expression data from Dros Roo line 22 Untreated for an eQTL study

tag: Dros Roo line 22


title: Dros Roo line 68 Lead Acetate treated

description: gene expression data from Dros Roo line 68 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 68


title: Dros Roo line 46 Untreated

description: gene expression data from Dros Roo line 46 Untreated for an eQTL study

tag: Dros Roo line 46


title: Dros Roo line 34 Untreated

description: gene expression data from Dros Roo line 34 Untreated for an eQTL study

tag: Dros Roo line 34


title: Dros Roo line 77 Lead Acetate treated

description: gene expression data from Dros Roo line 77 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 77


title: Dros Roo line 14 Lead Acetate treated

description: gene expression data from Dros Roo line 14 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 14


title: Dros Roo line 31 Untreated

description: gene expression data from Dros Roo line 31 Untreated for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 31


title: Dros Roo line 203 Lead Acetate treated

description: gene expression data from Dros Roo line 203 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 203


title: Dros Roo line 17 Untreated

description: gene expression data from Dros Roo line 17 Untreated for an eQTL study

tag: Dros Roo line 17


title: Dros Roo line 70 Untreated

description: gene expression data from Dros Roo line 70 Untreated for an eQTL study

tag: Dros Roo line 70


title: Dros Roo line 9 Lead Acetate treated

description: gene expression data from Dros Roo line 9 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 9


title: Dros Roo line 215 Lead Acetate treated

description: gene expression data from Dros Roo line 215 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 215


title: Dros Roo line 19 Lead Acetate treated

description: gene expression data from Dros Roo line 19 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 19


title: Dros Roo line 216 Untreated

description: gene expression data from Dros Roo line 216 Untreated for an eQTL study

tag: Dros Roo line 216


title: Dros Roo line 28 Untreated

description: gene expression data from Dros Roo line 28 Untreated for an eQTL study

tag: Dros Roo line 28


title: Dros Roo line 3 Lead Acetate treated

description: gene expression data from Dros Roo line 3 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 3


title: Dros Roo line 22 Lead Acetate treated

description: gene expression data from Dros Roo line 22 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 22


title: Dros Roo line 86 Lead Acetate treated

description: gene expression data from Dros Roo line 86 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 86


title: Dros Roo line 206 Lead Acetate treated

description: gene expression data from Dros Roo line 206 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 206


title: Dros Roo line 40 Untreated

description: gene expression data from Dros Roo line 40 Untreated for an eQTL study

tag: Dros Roo line 40


title: Dros Roo line 54 Untreated

description: gene expression data from Dros Roo line 54 Untreated for an eQTL study

tag: Dros Roo line 54


title: Dros Roo line 223 Lead Acetate treated

description: gene expression data from Dros Roo line 223 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 223


title: Dros Roo line 58 Lead Acetate treated

description: gene expression data from Dros Roo line 58 Lead Acetate added to diet for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 58


title: Dros Roo line 68 Untreated

description: gene expression data from Dros Roo line 68 Untreated for an eQTL study

tag: Dros Roo line 68


title: Dros Roo line 212 Lead Acetate treated

description: gene expression data from Dros Roo line 212 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 212


title: Dros Roo line 45 Untreated

description: gene expression data from Dros Roo line 45 Untreated for an eQTL study

tag: Dros Roo line 45


title: Dros Roo line 100 Lead Acetate treated

description: gene expression data from Dros Roo line 100 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 100


title: Dros Roo line 221 Lead Acetate treated

description: gene expression data from Dros Roo line 221 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 221


title: Dros Roo line 222 Lead Acetate treated

description: gene expression data from Dros Roo line 222 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 222


title: Dros Roo line 38 Untreated

description: gene expression data from Dros Roo line 38 Untreated for an eQTL study

tag: Dros Roo line 38


title: Dros Roo line 76 Lead Acetate treated

description: gene expression data from Dros Roo line 76 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 76


title: Dros Roo line 206 Untreated

description: gene expression data from Dros Roo line 206 Untreated for an eQTL study


title: Dros Roo line 203 Untreated

description: gene expression data from Dros Roo line 203 Untreated for an eQTL study

tag: Dros Roo line 203


title: Dros Roo line 84 Lead Acetate treated

description: gene expression data from Dros Roo line 84 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 84


title: Dros Roo line 37 Lead Acetate treated

description: gene expression data from Dros Roo line 37 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 37


title: Dros Roo line 54 Lead Acetate treated

description: gene expression data from Dros Roo line 54 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 221 Untreated

description: gene expression data from Dros Roo line 221 Untreated for an eQTL study


title: Dros Roo line 207 Lead Acetate treated

description: gene expression data from Dros Roo line 207 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 207


title: Dros Roo line 227 Untreated

description: gene expression data from Dros Roo line 227 Untreated for an eQTL study

tag: Dros Roo line 227


title: Dros Roo line 97 Untreated

description: gene expression data from Dros Roo line 97 Untreated for an eQTL study

tag: Dros Roo line 97


title: Dros Roo line 100 Untreated

description: gene expression data from Dros Roo line 100 Untreated for an eQTL study


title: Dros Roo line 13 Untreated

description: gene expression data from Dros Roo line 13 Untreated for an eQTL study

tag: Dros Roo line 13


title: Dros Roo line 14 Untreated

description: gene expression data from Dros Roo line 14 Untreated for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 14


title: Dros Roo line 9 Untreated

description: gene expression data from Dros Roo line 9 Untreated for an eQTL study

tag: Dros Roo line 9


title: Dros Roo line 48 Lead Acetate treated

description: gene expression data from Dros Roo line 48 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 48


title: Dros Roo line 47 Untreated

description: gene expression data from Dros Roo line 47 Untreated for an eQTL study

tag: Dros Roo line 47


title: Dros Roo line 218 Lead Acetate treated

description: gene expression data from Dros Roo line 218 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 218


title: Dros Roo line 42 Lead Acetate treated

description: gene expression data from Dros Roo line 42 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 42


title: Dros Roo line 227 Lead Acetate treated

description: gene expression data from Dros Roo line 227 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 224 Untreated

description: gene expression data from Dros Roo line 224 Untreated for an eQTL study

tag: Dros Roo line 224


title: Dros Roo line 89 Untreated

description: gene expression data from Dros Roo line 89 Untreated for an eQTL study

tag: Dros Roo line 89


title: Dros Roo line 10 Untreated

description: gene expression data from Dros Roo line 10 Untreated for an eQTL study

tag: Dros Roo line 10


title: Dros Roo line 51 Untreated

description: gene expression data from Dros Roo line 51 Untreated for an eQTL study

tag: Dros Roo line 51


title: Dros Roo line 45 Lead Acetate treated

description: gene expression data from Dros Roo line 45 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 45


title: Dros Roo line 73 Untreated

description: gene expression data from Dros Roo line 73 Untreated for an eQTL study

tag: Dros Roo line 73


title: Dros Roo line 222 Untreated

description: gene expression data from Dros Roo line 222 Untreated for an eQTL study

tag: Dros Roo line 222


title: Dros Roo line 29 Lead Acetate treated

description: gene expression data from Dros Roo line 29 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 29


title: Dros Roo line 44 Untreated

description: gene expression data from Dros Roo line 44 Untreated for an eQTL study

tag: Dros Roo line 44


title: Dros Roo line 226 Untreated

description: gene expression data from Dros Roo line 226 Untreated for an eQTL study

tag: Dros Roo line 226


title: Dros Roo line 93 Untreated

description: gene expression data from Dros Roo line 93 Untreated for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 93


title: Dros Roo line 42 Untreated

description: gene expression data from Dros Roo line 42 Untreated for an eQTL study


title: Dros Roo line 226 Lead Acetate treated

description: gene expression data from Dros Roo line 226 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 80 Lead Acetate treated

description: gene expression data from Dros Roo line 80 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 80


title: Dros Roo line 47 Lead Acetate treated

description: gene expression data from Dros Roo line 47 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 56 Untreated

description: gene expression data from Dros Roo line 56 Untreated for an eQTL study

tag: Dros Roo line 56


title: Dros Roo line 87 Untreated

description: gene expression data from Dros Roo line 87 Untreated for an eQTL study

tag: Dros Roo line 87


title: Dros Roo line 40 Lead Acetate treated

description: gene expression data from Dros Roo line 40 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 40


title: Dros Roo line 73 Lead Acetate treated

description: gene expression data from Dros Roo line 73 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 34 Lead Acetate treated

description: gene expression data from Dros Roo line 34 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 34


title: Dros Roo line 211 Untreated

description: gene expression data from Dros Roo line 211 Untreated for an eQTL study

tag: Dros Roo line 211


title: Dros Roo line 75 Lead Acetate treated

description: gene expression data from Dros Roo line 75 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 75


title: Dros Roo line 211 Lead Acetate treated

description: gene expression data from Dros Roo line 211 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 3 Untreated

description: gene expression data from Dros Roo line 3 Untreated for an eQTL study

tag: Dros Roo line 3


title: Dros Roo line 78 Lead Acetate treated

description: gene expression data from Dros Roo line 78 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 78


title: Dros Roo line 50 Lead Acetate treated

description: gene expression data from Dros Roo line 50 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 50


title: Dros Roo line 5 Lead Acetate treated

description: gene expression data from Dros Roo line 5 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 5


title: Dros Roo line 5 Untreated

description: gene expression data from Dros Roo line 5 Untreated for an eQTL study


title: Dros Roo line 19 Untreated

description: gene expression data from Dros Roo line 19 Untreated for an eQTL study

tag: Dros Roo line 19


title: Dros Roo line 218 Untreated

description: gene expression data from Dros Roo line 218 Untreated for an eQTL study

tag: Dros Roo line 218


title: Dros Roo line 12 Untreated

description: gene expression data from Dros Roo line 12 Untreated for an eQTL study

tag: Dros Roo line 12


title: Dros Roo line 93 Lead Acetate treated

description: gene expression data from Dros Roo line 93 Lead Acetate added to diet for an eQTL study


title: Dros Roo line 79 Untreated

description: gene expression data from Dros Roo line 79 Untreated for an eQTL study

tag: Dros Roo line 79


title: Dros Roo line 202 Lead Acetate treated

description: gene expression data from Dros Roo line 202 Lead Acetate added to diet for an eQTL study

tag: Whole Adult Drosophilia

tag: Dros Roo line 202


title: psad1-1 stn7-1 C

city: Planegg

first: Michael

last: Scharfenberg

state: Bayern

address: Großhaderner Str. 2-4

department: Botanik I

country: Germany

institute: LMU München

description: rosette leaves of 4-week-old

hyb_protocol: Hybridization procedure was performed as described in the Affymetrix technical manual

scan_protocol: Scanning procedure was performed as described in the Affymetrix technical manual

data_processing: Affymetrix GCOS/MAS5

organism: Arabidopsis thaliana

source_name: rosette leaves of 4-week-old

label_protocol: After second-strand synthesis, double-stranded cDNA was used in an in-vitro transcription reaction to generate biotinylated cRNA

growth_protocol: All plants were grown as reported previously (Bonardi et al., 2005)

tag: genotype

value: psad1-1 stn7-1

tag: tissue

value: rosette leaves

tag: age


title: AML sample #106

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

description: de novo AML, NPM1 mutated, other chromosomal aberrations

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.20.2) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

source_name: mononuclear cells after Ficoll purification

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: Samples are from untreated patients (de novo AML)

value: 3-positive (mutated)

tag: karyotype

value: other chromosomal aberrations


title: psad1-1 B

description: rosette leaves of 4-week-old


title: psae1-3 stn7-1 B

description: rosette leaves of 4-week-old

value: psae1-3 stn7-1


title: AML sample #107


title: AML sample #104


title: stn7-1 A

description: rosette leaves of 4-week-old


title: psad1-1 stn7-1 A

description: rosette leaves of 4-week-old


title: AML sample #105


title: stn7-1 C

description: rosette leaves of 4-week-old


title: Dros Roo line 31 Lead Acetate treated

description: gene expression data from Dros Roo line 31 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 31


title: psad1-1 A

description: rosette leaves of 4-week-old


title: psae1-3 stn7-1 A

description: rosette leaves of 4-week-old


title: Col-0 C

description: rosette leaves of 4-week-old


title: psae1-3 B

description: rosette leaves of 4-week-old


title: WS B

description: rosette leaves of 4-week-old

value: Wassilewskija


title: Col-0 A

description: rosette leaves of 4-week-old


title: Dros Roo line 213 Lead Acetate treated

description: gene expression data from Dros Roo line 213 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 213


title: psad1-1 stn7-1 B

description: rosette leaves of 4-week-old


title: Dros Roo line 67 Lead Acetate treated

description: gene expression data from Dros Roo line 67 Lead Acetate added to diet for an eQTL study

tag: Dros Roo line 67


title: Col-0 B

description: rosette leaves of 4-week-old


title: psae1-3 A

description: rosette leaves of 4-week-old


title: stn7-1 B

description: rosette leaves of 4-week-old


title: WS A

description: rosette leaves of 4-week-old


title: Single cell profile of P5 retinal amacrine cell E4; electroporated with pSynapsin

first: jeffrey

last: trimarchi

address: 77 Avenue Louis Pasteur

department: Genetics

description: Retinas were dissociated to individual cells using papain and single cells were harvested using a capillary pipette drawn into a fine needle. The isolated single cells were lysed, the RNA reverse transcribed, and the resulting cDNAs subjected to a 35 cycle RT-PCR based protocol that was previously shown to generate a sufficient amount of cDNA (10-20 ug) for hybridization on Affymetrix microarrays.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The MAS5.0 algorithm was used with the data normalized by scaling all probe sets to 500.

source_name: P5 single retinal amacrine cell E4

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

extract_protocol: Retinas were cultured for 5 days in vitro. Single GFP+ retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: Retinas from CD1 mice were electroporated at P0 with pSynapsin::GFP and single GFP+ cells were harvested after 5 days in vitro.


title: Single cell profile of P5 retinal amacrine cell E2; electroporated with pSynapsin

source_name: P5 single retinal amacrine cell E2


title: Single cell profile of P5 retinal amacrine cell D6; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell D6

tag: Retinas from CD1 mice were electroporated at P0 with pNdrg4::GFP and single GFP+ cells were harvested after 5 days in vitro.


title: Single cell profile of P5 retinal amacrine cell E3; electroporated with pSynapsin

source_name: P5 single retinal amacrine cell E3


title: Single cell profile of P5 retinal amacrine cell A8; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell A8

extract_protocol: Single GFP+ retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: Retinas from CD1 mice were electroporated at P0 with pNdrg4::GFP and single GFP+ cells were harvested after 5 days.


title: Single cell profile of P4 retinal amacrine cell B4; electroporated with pNdrg4

source_name: P4 single retinal amacrine cell B4

extract_protocol: Retinas were cultured for 4 days in vitro.  Single GFP+ retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: Retinas from CD1 mice were electroporated at P0 with pNdrg4::GFP and single GFP+ cells were harvested after 4 days in vitro.


title: Single cell profile of P5 retinal amacrine cell C1; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell C1


title: Single cell profile of P4 retinal amacrine cell A3; electroporated with pNdrg4

source_name: P4 single retinal amacrine cell A3


title: Single cell profile of P5 retinal amacrine cell D5; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell D5


title: Single cell profile of P5 retinal amacrine cell E1; electroporated with pSynapsin

source_name: P5 single retinal amacrine cell E1


title: Single cell profile of P5 retinal amacrine cell C6; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell C6


title: Single cell profile of P5 retinal amacrine cell A7; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell A7

tag: Retinas from CD1 mice were electroporated at P0 with pNdrg4::GFP and single GFP+ cells were harvested 5 days later.


title: Single cell profile of P5 retinal amacrine cell B4; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell B4


title: Single cell profile of P5 retinal amacrine cell D3; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell D3


title: Single cell profile of P5 retinal amacrine cell A5; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell A5


title: Single cell profile of P5 retinal amacrine cell B2; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell B2


title: Single cell profile of P5 retinal amacrine cell B3; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell B3


title: Single cell profile of P5 retinal amacrine cell A1; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell A1


title: Single cell profile of P5 retinal amacrine cell A6; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell A6


title: Single cell profile of P5 retinal amacrine cell A2; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell A2


title: Single cell profile of P8 retinal amacrine cell B3; electroporated with pSynapsin

source_name: P8 single retinal amacrine cell B3

extract_protocol: Retinas were cultured for 8 days in vitro. Single GFP+ retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: Retinas from CD1 mice were electroporated at P0 with pSynapsin::GFP and single GFP+ cells were harvested after 8 days in vitro.


title: Single cell profile of P5 retinal amacrine cell B1; electroporated with pNdrg4

source_name: P5 single retinal amacrine cell B1


title: hMSC control, biological rep1

city: Cold Spring Harbor

first: Weijun

last: Luo

address: 1 Bungtown Rd

institute: Cold Spring Harbor Lab

description: Gene expression data from mesenchymal stem cells cultured 8 hours without BMP6.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw data (.CEL file) were processed by using RMA.

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: Passage 5 human MSC (5x105) were plated in 24-well dishes and cultured for 3 days. The cells were subsequently placed in serum free media supplemented with ITS for 24 hours.

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

treatment_protocol: 20 nM BMP6 (R&D Systems) was then added for the pre-designed time periods and then removed. To remove BMP6, cells were rinsed 2 times and fresh media without BMP was added.

tag: 34 YO Male, vertebral bone marrow MSC


title: Single cell profile of P8 retinal amacrine cell A2; electroporated with pNdrg4

source_name: P8 single retinal amacrine cell A2

tag: Retinas from CD1 mice were electroporated at P0 with pNdrg4::GFP and single GFP+ cells were harvested after 8 days in vitro.


title: Single cell profile of P8 retinal amacrine cell A1; electroporated with pNdrg4

source_name: P8 single retinal amacrine cell A1


title: hMSC with 8h BMP6 treatment, biological rep1

description: Gene expression data from mesenchymal stem cells treated 8 hours with BMP6.


title: hMSC control, biological rep2

source_name: mesenchymal stem cells cultured 8 hours without BMP6


title: hMSC with 8h BMP6 treatment, biological rep2

source_name: mesenchymal stem cells treated 8 hours with BMP6


title: Single cell profile of P8 retinal amacrine cell B4; electroporated with pSynapsin

source_name: P8 single retinal amacrine cell B4


title: Low grade serous ovarian carcinoma LGOV8

status: Public on May 31 2009

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

hyb_protocol: Performed according to the manufacturer's instructions

scan_protocol: GeneChips were scanned using GeneArray Scanner

data_processing: normalized in dChip using PM only signal 5% as background

tag: Low-grade ovarian serous carcinoma


title: Low grade serous ovarian carcinoma LGOV6

label_protocol: Performed according to the manufacturer's instructions


title: High grade serous ovarian carcinoma HGOV7

extract_protocol: Performed according to the manufacturer's instructions

tag: High-grade ovarian serous carcinoma


title: High grade serous ovarian carcinoma HGOV2

tag: High-grade serous ovarian carcinoma


title: High grade serous ovarian carcinoma HGOV6


title: Single cell profile of E19 retinal amacrine cell B1; electroporated with pSynapsin

source_name: E19 single retinal amacrine cell B1

extract_protocol: Retinas were cultured for 4 days in vitro. Single GFP+ retinal cells were isolated, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified. Individual retinal cells were harvested using a mouth pipette and were expelled into cold lysis buffer (10 mM Tris-HCl [pH 8.3], 50 mM KCl, 1.5 mM MgCl2, 5 mM DTT, 0.5% NP-40). The total single cell RNA was reverse transcribed using Superscript II (Invitrogen) combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

tag: Retinas from CD1 mice were electroporated at E16 with pSynapsin::GFP and single GFP+ cells were harvested after 4 days in vitro.


title: Low grade serous ovarian carcinoma LGOV5


title: High grade serous ovarian carcinoma HGOV4

tag: High-grrade ovarian serous carcinoma


title: Low grade serous ovarian carcinoma LGOV9


title: High grade serous ovarian carcinoma HGOV10


title: High grade serous ovarian carcinoma HGOV9


title: High grade serous ovarian carcinoma HGOV3


title: Low grade serous ovarian carcinoma LGOV2

scan_protocol: GeneChips were scanned using GeneArray Scanner Model G2500


title: Low grade serous ovarian carcinoma LGOV7

tag: Low-grae ovarian serous carcinoma


title: Low grade serous ovarian carcinoma LGOV3

tag: low-grade ovarian serous carcinoma


title: Low grade serous ovarian carcinoma LGOV4


title: High grade serous ovarian carcinoma HGOV1

tag: Hig-grade ovarian serous carcinoma


title: High grade serous ovarian carcinoma HGOV5


title: Low grade serous ovarian carcinoma LGOV10


title: Ovarian surface epithelia HOSE1

hyb_protocol: Performed according to manufacturer's instructions

tag: Short term primary culture of human ovarian cells


title: High grade serous ovarian carcinoma HGOV8


title: Cultured OPCs Control Replicate 2

city: Stanford

first: Ben

last: Emery

state: CA

address: 299 Campus Dr. W.

department: Neurobiology

institute: Stanford University

description: Purified OPCs cultured in PDGF for 6 days

hyb_protocol: Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

scan_protocol: Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

data_processing: Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).

label_protocol: Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).

extract_protocol: Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)

tag: cell

value: Cultured oligodendrocyte progenitors


title: Cultured OPCs Control Replicate 4

source_name: Purified OPCs cultured in PDGF for 6 days


title: MRF control Oligodendrocyte Replicate 3

description: MRF control littermate cultured oligodendrocytes

value: Cultured oligodendrocytes

tag: genotype

value: Myelin-gene Regulatory Factor control littermate


title: MRF control Oligodendrocyte Replicate 2

source_name: MRF control littermate cultured oligodendrocytes


title: MRF control Oligodendrocyte Replicate 1


title: Ovarian surface epithelia HOSE2

scan_protocol: Performed according to the manufacturer's instructions

label_protocol: One-Cycle Affymetrix Kit

extract_protocol: RNAeasy

tag: short-term primary culture of human ovarian epithelial cells


title: MRF control Oligodendrocyte Replicate 4


title: GBS6 cells transfected with POU5F1 siRNA-2 (1st)

city: Koto ward

first: Takashi

last: Fujino

state: Tokyo

address: 3-10-6 Ariake

department: Carcinogenesis

country: Japan

institute: The Cancer Institute of Japanese Foundation of Cancer Research

description:
GBS6 cells were established from an undifferentiated bone sarcoma carrying a t(6;22)(p21;q12). The translocation resulted in a gene fusion between EWS and POU5F1.
Gene expression analysis of t(6;22) undifferentiated sarcoma cell line GBS6 transfected with POU5F1 specific siRNA-2.

hyb_protocol: According to Affymetrix's instructions.

scan_protocol: According to Affymetrix's instructions.

data_processing: Affymetrix MAS5.0

label: Biotin-labelled.

source_name: GBS6 cells established from a t(6;22) undifferentiated bone sarcoma

label_protocol: According to Affymetrix's instructions.

growth_protocol: Cells were grown in RPMI1640 medium.

extract_protocol: Total RNA was extracted using the RNA-Bee (Tel-Test) according to manufacturer’s protocol.

tag: cell line


title: Ovarian surface epithelia HOSE3

scan_protocol: Performed according to manufacturer's instructions


title: MRF CKO Oligodendrocyte Replicate 2

description: MRF conditional knockout cultured oligodendrocytes

value: Myelin-gene Regulatory Factor conditional knockout


title: MRF CKO Oligodendrocyte Replicate 3

source_name: MRF conditional knockout cultured oligodendrocytes


title: Cultured OPCs Control Replicate 1


title: GBS6 cells transfected with negative control siRNA (1st)

description:
GBS6 cells were established from an undifferentiated bone sarcoma carrying a t(6;22)(p21;q12). The translocation resulted in a gene fusion between EWS and POU5F1.
Gene expression analysis of t(6;22) undifferentiated sarcoma cell line GBS6 transfected with negative control siRNA.


title: Low grade serous ovarian carcinoma LGOV1

label_protocol: RNeasy was performed according to the manufacturer's instructions


title: Cultured OPCs Control Replicate 3


title: MRF CKO Oligodendrocyte Replicate 1


title: GBS6 cells transfected with POU5F1 siRNA-1 (1st)

description:
GBS6 cells were established from an undifferentiated bone sarcoma carrying a t(6;22)(p21;q12). The translocation resulted in a gene fusion between EWS and POU5F1.
Gene expression analysis of t(6;22) undifferentiated sarcoma cell line GBS6 transfected with POU5F1 specific siRNA-1.

data_processing: Affymetrix MAS5


title: Anoxia-treated replicate No. 1

status: Public on May 30 2009

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

description: no additional description required

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: GC-RMA algorithm

source_name: Arabidopsis seedlings, Anoxia-treated

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Seeds were sterilized with diluted bleach (10-min incubation in 1.7% sodium hypochlorite, rinsed and washed seven times in sterile water) and incubated in 2.5 mL of liquid growing media (Murashige and Skoog half-strength solution in six-well plates) containing 30 mM sucrose. The plates were incubated in the dark at 4°C for two days (vernalization, to promote homogeneous germination) and then transferred to 23°C for four days in the dark before the treatments.

extract_protocol: Total RNA was extracted from the seedling samples using the Ambion RNAqueous kit (Ambion). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix Arabidopsis ATH1 GeneChip arrays.

treatment_protocol: Arabidopsis seedlings. Ecotype: Columbia 0; Age: 4 days; Germination: aerobic; Medium: Murashige-Skoog medium, half-strenght, sucrose 30 mM, 23°C, darkness; Treated under anoxia for 6h at 23°C in the dark. Anoxic treatments were carried out in the dark. An enclosed anaerobic work station (Anaerobic System model 1025; Forma Scientific, Marietta, OH) was used to provide an oxygen-free environment for seedling incubation. This chamber uses palladium catalyst wafers and desiccant wafers to maintain strict anaerobiosis to less than 10 µg mL–1 O2 (according to the manufacturer’s specifications). High-purity N2 was used to purge the chamber initially, and the working anaerobic gas mixture was N2:H2 with a ratio of 90:10.

tag: growth stage

value: seedling

tag: ecotype

value: Columbia 0

tag: age

value: 4 days

tag: germination

value: aerobic

tag: growth conditions

value: Murashige-Skoog growth conditions, half-strength, sucrose 30 mM, 23°C, darkness

tag: treatment

value: anoxia for 6h at 23°C in the dark.


title: Anoxia-treated replicate No. 2

description: no additional description required


title: Heat-treated replicate No. 2

description: no additional description required

source_name: Arabidopsis seedlings, Heat-treated

treatment_protocol: Dark grown Arabidopsis seedlings, 4d-old, were treated at 38°C for 90 minutes in the dark.

value: 90 minutes at 38°C.


title: Heat-treated replicate No. 1

description: no additional description required


title: Control replicate No. 1

description: no additional description required

source_name: Arabidopsis seedlings, control

growth_protocol: Seeds were sterilized with diluted bleach (10-min incubation in 1.7% sodium hypochlorite, rinsed and washed seven times in sterile water) and incubated in 2.5 mL of liquid growing media (Murashige and Skoog half-strength solution in six-well plates) containing 30 mM sucrose. The plates were incubated in the dark at 4°C for two days (vernalization, to promote homogeneous germination) and then transferred to 23°C for four days in the dark before the treatments. This sample represents the control.

treatment_protocol: This sample represents the control. Dark grown Arabidopsis seedlings, 4d-old.

value: untreated control


title: Control replicate No. 2

description: no additional description required

source_name: Control Arabidopsis seedlings


title: Heat and anoxia-treated replicate No. 1

description: no additional description required

treatment_protocol: Arabidopsis seedlings. Ecotype: Columbia 0; Age: 4 days; Germination: aerobic; Medium: Murashige-Skoog medium, half-strenght, sucrose 30 mM, 23°C, darkness; Treated at 38°c for 90 minutes and thereafter under anoxia for 6h at 23°C in the dark.  An enclosed anaerobic work station (Anaerobic System model 1025; Forma Scientific, Marietta, OH) was used to provide an oxygen-free environment for seedling incubation. This chamber uses palladium catalyst wafers and desiccant wafers to maintain strict anaerobiosis to less than 10 µg mL–1 O2 (according to the manufacturer’s specifications). High-purity N2 was used to purge the chamber initially, and the working anaerobic gas mixture was N2:H2 with a ratio of 90:10.


title: Human Induced Pluripotent Stem Cells by Direct Delivery of Reprogramming Proteins (Line 2)

status: Public on May 29 2009

city: Belmont

first: Kwang-Soo

last: Kim

address: 115 Mill st

department: Molecular neurobiology lab

institute: McLean Hospital

description: Total RNAs were prepared from human fibroblasts, H9, and hiPS lines using TRIzol reagent (Invitrogen, Carlsbad, CA) and hybridized to Affymetrix Human Expression Array U133 Plus 2.0 analyzing over 47,000 human transcripts at the Harvard Partners Center for Genomics and Genetics. Detailed procedure is described in the website at http://www.hpcgg.org/Microarrays/overview.jsp.

hyb_protocol: Affymetrix expression projects are hybridized and scanned according to Affymetrix protocols by the Harvard Partners Center for Genomics and Genetics.

data_processing: Affymetrix MAS5.0 algorithm was used for data processing

label: Samples are labeled according to the Affymetrix GeneChip Expression Labeling protocol by the Harvard Partners Center for Genomics and Genetics.

source_name: Human newborn fibroblasts

value: hiPS induced pluripotent embryonic stem cell line (Line 2)

tag: protocol

value: direct delivery of reprogramming proteins


title: Heat and anoxia-treated replicate No. 2

description: no additional description required

value: 38°c for 90 minutes and thereafter under anoxia for 6h at 23°C in the dark.


title: GBM_TuBa2320_malePatient

city: Lausanne

first: Monika

middle: E.

last: Hegi

state: Vaud

address: Bugnon 46

department: Neurosurgery

country: Switzerland

institute: CHUV

hyb_protocol: Probes were hybridized to Affymetrix HG-133Plus2.0 GeneChips (Affymetrix, Santa Clara, CA) using the standard protocol.

scan_protocol: GeneChip Operating Software instructions using GeneChip Scanner 3000 High-Resolution Scanning Patch.

data_processing: The expression intensities for all probe-sets from Affymetrix CEL-files were estimated using robust multi-array average (RMA) with probe-level quantile normalization followed by median polish summarization as implemented in the BioConductor open source software (available at http://www.bioconductor.org/).

source_name: glioblastoma

label_protocol: Probes were prepared with the WT-Ovation Pico Kit (NuGEN; San Carlos, CA) for amplification.

extract_protocol: Total RNA was extracted from frozen tumor sections (10mg)  (Qiagen AllPrep Mini Kit). The first section served as reference for diagnosis and tumor content.

tag: tissue

value: glioblastoma, fresh frozen

tag: gender

value: male


title: Donor 2 Quiescent T cells

city: Los Angeles

first: Jerome

middle: A

last: Zack

address: 615 Charles Young Dr South

department: Medicine - Hem/Onc

institute: David Geffen School Of Medicine at UCLA

data_processing: standard Affymetrix protocol

source_name: Primary T cells

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

treatment_protocol: Activated cells were stimulated using plate bound CD3 (1ug/ml) and soluble CD28 (50ng/ml).

tag: Quiescent


title: H9 Human Embryonic Stem Cell

scan_protocol: Affymetrix expression projects are hybridized and scanned according to Affymetrix protocols by the Harvard Partners Center for Genomics and Genetics.

source_name: H9 Human Embryonic Stem Cell

label_protocol: Samples are labeled according to the Affymetrix GeneChip Expression Labeling protocol by the Harvard Partners Center for Genomics and Genetics.

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA)

value: H9 embryonic stem cell line


title: Donor 1 1-day activated T cells

tag: Stimulated


title: Human Induced Pluripotent Stem Cells by retroviral transfection of Reprogramming genes

source_name: human newborn fibroblasts

value: hiPS induced pluripotent embryonic stem cell line

value: retroviral transfection of reprogramming genes


title: mouse-MEF-PTIP +/+, replicate1

city: Bethesda

first: Young-Wook

last: Cho

state: MD

address: 9000 Rockville Pike

department: CEB

institute: NIDDK

description: Gene expression data from MEF PTIP +/+ cell

hyb_protocol: standard Affymetrix hyb protocol

scan_protocol: standard Affymetrix scan protocol

data_processing: data processing/normalization was performed using the RMA algorithm

source_name: immortalized mouse embryonic fibroblast

label_protocol: standard Affymetrix label protocol

growth_protocol: All cells were routinely cultured in DMEM plus 10% FBS (Hyclone). For selection, count cells and plate 5x105/10cm, add 2.5ug/ml puromycin for 2~3days. Repeat the selection one more time.

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNeasy mini kit purification was performed according to the manufacturer's instructions.

value: MEF

value: PTIP +/+


title: mouse-MEF-PTIP -/-, replicate2

description: Gene expression data from MEF PTIP -/- cell

value: PTIP -/-


title: Donor 2 2-day activated (stimulated) T cells


title: Human newborn fibroblast

description: Total RNAs were prepared from human fibroblasts using TRIzol reagent (Invitrogen, Carlsbad, CA) and hybridized to Affymetrix Human Expression Array U133 Plus 2.0 analyzing over 47,000 human transcripts at the Harvard Partners Center for Genomics and Genetics. Detailed procedure is described in the website at http://www.hpcgg.org/Microarrays/overview.jsp.

source_name: Human newborn fibroblast

tag: cell type

value: fibroblast


title: Human Induced Pluripotent Stem Cells by Direct Delivery of Reprogramming Proteins (Line 1)

value: hiPS induced pluripotent embryonic stem cell line (Line 1)


title: mouse-MEF-PTIP +/+, replicate2


title: Microglia-fraction_TuBa2321_of GBM

source_name: microglia derived from glioblastoma

extract_protocol: Total RNA was extracted from frozen tumor sections (10mg) (Qiagen AllPrep Mini Kit). The first section served as reference for diagnosis and tumor content.

treatment_protocol: Isolation of Microglia/Macrophages from Human Glioblastoma Tissue using a modified Percoll-gradient. Briefly, after resection, freshly isolated glioblastoma tissue was mechanically dissociated through a stainless steel sieve. The dissociated material was centrifuged, washed, and layered onto a Percoll gradient. After centrifugation, the cell layer was removed, washed, layered on top of a second gradient and centrifuged. Microglia/macrophages were collected from the interphase between the 1.065-g/ml and 1.03-g/ml layers. (Hussain  et al. (2006)  Neuro-oncol 8: 261-279)

value: microglia derived from glioblastoma (TuBa2320) (GSM403272)


title: mouse-MEF-PTIP -/-, replicate1

description: Gene expression data from Cre-expressing PTIP flox/flox MEF


title: Donor 2 1-day activated T cells


title: Lesional myeloid cells of MDS patient 10

status: Public on May 28 2009

first: Xianwen

last: Ren

address: 6565 Fannin Street

institute: The Methodist Hospital Research Institute

description: Expression profiling of normal lymphoid cells of a MDS patient

hyb_protocol: Human Genome U133 Plus 2.0 arrays

scan_protocol: GeneChip Scanner 3000

data_processing: Expression Console, RMA

source_name: lesional myeloid cells of MDS Patient 10

label_protocol: 2-cycle target labeling kit (Affymetrix)

extract_protocol: Allprep kit, Qiagen

value: Lesional myeloid cells


title: Lesional myeloid cells of MDS patient 9

source_name: lesional myeloid cells of MDS Patient 9


title: Normal lymophoid cells of MDS patient 6

source_name: normal lymophoid cells of MDS Patient 6

value: Normal lymophoid cells


title: Normal lymphoid cells of MDS patient 8

source_name: normal lymphoid cells of MDS Patient 8

value: Normal lymphoid cells


title: Lesional blastic cells of MDS patient 8

source_name: lesional blastic cells of MDS Patient 8

value: Lesional blastic cells


title: Lesional blastic cells of MDS patient 9

source_name: lesional blastic cells of MDS Patient 9


title: Normal lymophoid cells of MDS patient 5

source_name: normal lymophoid cells of MDS Patient 5


title: Normal lymophoid cells of normal person

description: Expression profiling of normal lymphoid cells from a normal person

source_name: normal lymophoid cells of normal person


title: Donor 1 2-day activated (stimulated) T cells


title: Donor 1 Quiescent T cells


title: Lesional erythroid cells of MDS patient 7

source_name: lesional erythroid cells of MDS Patient 7

value: Lesional erythroid cells


title: Lesional myeloid cells of MDS patient 3

source_name: lesional myeloid cells of MDS Patient 3


title: Lesional blastic cells of MDS patient 4

source_name: lesional blastic cells of MDS Patient 4


title: Normal lymophoid cells of MDS patient 4

source_name: normal lymophoid cells of MDS Patient 4


title: MCF-7 cells_NMNAT1 knockdown_E2_replicate 2

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: Standard hybridization to Affymetrix U133 Plus 2.0 microarray

scan_protocol: Standard scanning protocol using GeneChip Scanner

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling.  Signals were subsequently normalized through the following steps: common probe sets on both U133 A2.0 and U133 Plus2.0 platforms were selected; within each sample group hybridized to the same microarray platform, the signal values were log2 transformed, median centered for the array, and median centered for each gene; the data sets were further adjusted using the parametric empirical Bayes method (Combat R).

source_name: MCF-7 cells, NMNAT1 knockdown, E2 treatment 3 hours

label_protocol: Seven µg of total RNA were subjected to One-cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133 Plus 2.0 microarray

growth_protocol: MCF-7 cells were maintained in Eagle's minimum essential medium supplemented with 5% calf serum and antibiotics.

extract_protocol: Total RNA was prepared using Trizol reagent according to the manufacturer's instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen)

treatment_protocol: MCF-7 cells were cultured in estrogen-free media for 72 hours prior to hormone treatment. E2 samples were treated with 10-7M estradiol for 3 hours.


title: MCF-7 cells_luciferase knockdown_E2_replicate 2

source_name: MCF-7 cells, luciferase knockdown, E2 treatment 3 hours


title: MCF-7 cells_luciferase knockdown_control_replicate 2

source_name: MCF-7 cells, luciferase knockdown, no E2 treatment

treatment_protocol: MCF-7 cells were cultured in estrogen-free media for 72 hours prior to hormone treatment. Control cells were treated with vehicle (ethanol) for 3 hours.


title: MCF-7 cells_NMNAT1 knockdown_control_replicate 2

source_name: MCF-7 cells, NMNAT1 knockdown, no E2 treatment


title: CdLS patient PT5

city: Philadelphia

first: IAN

middle: D.

last: KRANTZ

state: PA

address: 34th and Civic Blvd.

department: Division of Human and Molecular Genetics

institute: The Children's Hospital of Philadelphia

description:
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B  isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Caucasian

hyb_protocol: Following fragmentation, 30 µl fragmented cRNA at the concentration of 500 ng/µl were hybridized for 16 hr at 45C on HG-U133 plus 2.0 GeneChips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files extracted from Microarray Suite version 5.0 (MAS 5.0) were processed with dCHIP using PM only background subtraction and the invariant set normalization

source_name: Lymphoblastoid cell line

label_protocol: Synthesis of double-stranded cDNA was performed using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogene), and cleaned up with GeneChip Sample Cleanup Module (Affymetrix), the resulting products were then be used to synthesize biotin-labeled cRNA with Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) and further fragmented to 35-200 bp oligos. All procedures were done according to manufacturer’s instruction.

growth_protocol: Lymphoblastoid cell lines (LCLs) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine.

extract_protocol: Total RNA from each sample was extracted with the RNeasy Mini-Kit (Qiagen) according to manufacturer's instruction

treatment_protocol: Five millions of exponentially growing cells were seeded in 15 ml media in 75 ml Falcon flask, and fed exactly after 24 hours, after another 24 hours in day 3, 8 ml of the media was removed and cells were pelleted by centrifuge and proceeded directly to RNA extraction

tag: Gender

value: Female

tag: Age, year

tag: Genotype

value: c.3048_3051delATTA / Frameshift

tag: disease_severity = Severe

tag: Picture_availability = Yes


title: Alagille syndrome patient ASG-Val-1 (test sample)

value: Male

value: JAG1 mutation

tag: disease_severity = N/A

value: ASG- J.S.


title: Normal lymphoid cells of MDS patient 1

source_name: normal lymphoid cells of MDS Patient 1


title: RBS patient RS-Val-2 (test sample)

description:
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B  isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
race unknown

value: ESCO2 mutation


title: CdLS patient PT13

value: c.2494C>T / nonsense


title: CdLS patient PT6

value: c.5167C>T / Nonsense

tag: Picture_availability = No


title: Alagille syndrome patient ASG-Val-2 (test sample)


title: CdLS patient (test sample)

description:
Gene expression data from EBV tranformed human lymphoblastoid cells
Nucleotide numbering refers to the NIPBL B  isoform cDNA sequence with GeneBank accession number NM_015384 and starting at the +1 position of the translation initiation codon
Egyptian


title: CdLS patient PT16

value: c.4606C>T / Nonsense


title: CdLS patient PT14

value: c.1546_1547insG / Frameshift


title: Normal lymphoid cells of MDS patient 2

source_name: normal lymphoid cells of MDS Patient 2


title: CdLS patient PT9

value: c.742_743delCT / Frameshift


title: RBS patient RS-Val-1 (test sample)


title: CdLS patient PT11

value: c.1902_1903insA / Frameshift


title: Healthy control (test sample)

value: WT


title: CdLS patient PT10

value: c.2969delG / Frameshift


title: CdLS patient PT15

value: c.1934delA / Nonsense


title: CdLS patient PT3

value: c.1444_1447delAGAG / Frameshift


title: CdLS patient PT8

value: c.961delA / Frameshift


title: CdLS patient PT12

value: c.150delG / Nonsense


title: Healthy control N18


title: CdLS patient PT2

value: c.2449_2450insG / Frameshift


title: Healthy control N14

value: Male


title: CdLS patient PT7

value: Female

value: c.4193C>G / Nonsense


title: CdLS patient PT4


title: CdLS patient PT1

value: c.6407insA / Frameshift


title: Healthy control N15


title: Healthy control N11


title: Healthy control N16


title: Healthy control N2


title: Healthy control N4


title: Healthy control N12


title: Healthy control N8


title: Healthy control N1


title: Healthy control N7


title: Healthy control N13


title: Healthy control N17


title: Healthy control N5


title: Healthy control N9


title: Healthy control N6


title: Healthy control N10


title: CD8-IGF1R 3T3 A-928605 1

status: Public on May 27 2009

city: Abbott Park

first: Paul

middle: M

last: Jung

state: IL

address: 100 Abbott Park Road

department: Gene Expression Analysis

institute: Abbott Laboratories

description: CD8-IGF1R 3T3 A-928605 1

hyb_protocol: standard Affymetrix protocol; EukGE-WS2v5

scan_protocol: standard Affymetrix protocol

data_processing: RMA algorithm; Rosetta Resolver 7.0

source_name: CD8-IGF1R Transfected 3T3 cells treated with A-928605 for 24 h

label_protocol: Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit with T7-Oligo(dT) primer followed by Ambion MessageAmp II-Biotin Enhanced In Vitro Transcription.

extract_protocol: Total RNA was isolated from Qiagen QIAzol lysed cells using Qiagen RNeasy 96 Universal Tissue 8000 Kit.

tag: 3T3 cells


title: CD8-IGF1R 3T3 A-928605 3

description: CD8-IGF1R 3T3 A-928605 3


title: 3T3 Vector Control A-928605 2

description: 3T3 Vector Control A-928605 2

source_name: Vector Control Transfected 3T3 cells treated with A-928605 for 24 h


title: 3T3 Vector Control Vehicle 2

description: 3T3 Vector Control Vehicle 2

source_name: Vector Control Transfected 3T3 cells treated with DMSO for 24 h


title: CD8-IGF1R 3T3 A-928605 2

description: CD8-IGF1R 3T3 A-928605 2


title: CD8-IGF1R 3T3 Vehicle 2

description: CD8-IGF1R 3T3 Vehicle 2

source_name: CD8-IGF1R Transfected 3T3 cells treated with DMSO for 24 h


title: 3T3 Vector Control A-928605 1

description: 3T3 Vector Control A-928605 1


title: CD8-IGF1R 3T3 Vehicle 3

description: CD8-IGF1R 3T3 Vehicle 3


title: CD8-IGF1R 3T3 Vehicle 1

description: CD8-IGF1R 3T3 Vehicle 1


title: 3T3 Vector Control A-928605 3

description: 3T3 Vector Control A-928605 3


title: 3T3 Vector Control Vehicle 3

description: 3T3 Vector Control Vehicle 3


title: 17-DMAG treated MT4 cells MT4_17DMAG_150nM1

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

description: Effect of 17-DMAG in MT-4 cells

hyb_protocol: GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Hybridization Oven 640 110V (Affymetrix 800138) Wash and staining: Fluidics Station 450 (Affymetrix 00-0079)

scan_protocol: GeneChip Scanner 3000 (Affymetrix 00-0074) GeneChip Operating Software ver.1.4 (Affymetrix 690036)

data_processing: Data Processing GeneChip Operating Software ver.1.4 (Affymetrix 690036)

source_name: 17-DMAG treated MT4 cells

label_protocol: One-cycle Target Labeling GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Section 2 Eukaryotic Sample and Array processing Chapter 1 Eukaryotic Target Prepartion

extract_protocol: RNeasy kit

treatment_protocol: Mock

tag: ATL sell line


title: Mock MT-2_Mock1

description: Mock

source_name: Mock

tag: ATL cell line


title: Mock MT-4_Mock2

description: Mock


title: 17-AAG treated MT-4 cells MT-4_17AAG_500nM2

description: Effect of 17-AAG in MT-4 cells

source_name: 17-AAG treated MT-4 cells


title: Mock MT-2_Mock2

description: Mock


title: 17-AAG treated E10 cells E10_17AAG_100nM_1

description: Effect of 17-AAG in E10 cells

source_name: 17-AAG treated E10 cells


title: 17-AAG treated E10 cells E10_17AAG_300nM1

description: Effect 17-AAG in E10 cells


title: 17-AAG treated MT-2 cells MT-2_17AAG_700nM1

description: Effect of 17-AAG in MT-2 cells

source_name: 17-AAG treated MT-2 cells


title: 17-DMAG treated MT2 cells MT2_17DMAG_150nM1

description: Effect of 17-DMAG in MT-2 cells

source_name: 17-DMAG treated MT2 cells


title: 17-DMAG treated MT4 cells MT4_17DMAG_150nM2

description: Effect of 17-DMAG in MT-4 cells


title: 17AAG treated MT-4 cells MT-4_17AAG_500nM1

description: Effect of 17-AAG in MT-4 cells

source_name: 17AAG treated MT-4 cells


title: 17AAG treated MT-2 cells MT-2_17AAG_700nM2

description: Effect of 17-AAG in MT-2 cells

source_name: 17AAG treated MT-2 cells


title: 3T3 Vector Control Vehicle 1

description: 3T3 Vector Control Vehicle 1


title: Mock E10_Mock2

description: Mock


title: Mock E10_Mock1

description: Mock


title: 17-AAG treated E10 cells E10_17AAG_300nM2

description: Effect of 17-AAG in E10 cells


title: Mock MT-4_Mock

description: Mock


title: 17-DMAG treated E10 cells E10_17DMAG_150nM2

description: Effect of 17-DMAG in E10 cells

source_name: 17-DMAG treated E10 cells


title: 17-AAG treated E10 cells E10_17AAG100nM2

description: Effect of 17-AAG in E10 cells


title: 17-DMAG treated MT2 cells MT2_17DMAG_150nM2

description: Effect of 17-DMAG in MT-2 cells


title: 17-DMAG treated E10 cells E10_17DMAG150nM1

description: Effect of 17-DMAG in E10 cells


title: Small Cell Lung Cancer cell line H187 (CL-H187_N_A)

status: Public on May 26 2009

city: Baltimore

first: Luigi

last: Marchionni

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: No additional description available for sample: CL-H187_N_A

hyb_protocol: Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin (Molecular Probes) using the GeneChip Fluidics Workstation 450 (Affymetrix).

scan_protocol: The gene chip was then scanned using a confocal laser scanner (Affymetrix GeneArray Scanner 3000)

data_processing: The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.

source_name: Small Cell Lung Cancer cell line: H187

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 to 5 microg total RNA. In brief, double-stranded cDNA synthesis was prepared from 2.5 to 5 µg of total RNA (SuperScript double-stranded cDNA synthesis kit; Invitrogen). After purification (QIAquick, Qiagen AG), the cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High yield T7 DNA transcription kit, ENZO Life Sciences). The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG).

extract_protocol: Total RNA was purified using RNAzol (Invitrogen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 7.5 were profiled.

tag: cell line

tag: type

value: Cell culture

tag: disease state

value: Small Cell Lung Cancer


title: Small Cell Lung Cancer cell line H128 (CL-H128_N_A)

description: No additional description available for sample: CL-H128_N_A

source_name: Small Cell Lung Cancer cell line: H128


title: Small Cell Lung Cancer cell line H345 (CL-H345_N_A)

description: No additional description available for sample: CL-H345_N_A

source_name: Small Cell Lung Cancer cell line: H345


title: Small Cell Lung Cancer cell line H82 (H82)

description: No additional description available for sample: H82

source_name: Small Cell Lung Cancer cell line: H82


title: Small Cell Lung Cancer cell line H187 (H187)

description: No additional description available for sample: H187


title: Small Cell Lung Cancer cell line H1618 (H1618)

description: No additional description available for sample: H1618

source_name: Small Cell Lung Cancer cell line: H1618


title: Small Cell Lung Cancer cell line H146 (CL-H146_N_A)

description: No additional description available for sample: CL-H146_N_A

source_name: Small Cell Lung Cancer cell line: H146


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H146 (CLX-H146_N_A)

description: No additional description available for sample: CLX-H146_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H146

value: Tissue


title: Small Cell Lung Cancer cell line H526 (H526)

description: No additional description available for sample: H526

source_name: Small Cell Lung Cancer cell line: H526


title: Universal human reference RNA (Stratagene) (Ref_N_B)

description: No additional description available for sample: Ref_N_B

tag: sample

value: Reference RNA


title: Small Cell Lung Cancer cell line H209 (CL-H209_N_A)

description: No additional description available for sample: CL-H209_N_A

source_name: Small Cell Lung Cancer cell line: H209


title: Small Cell Lung Cancer cell line H82 (CL-H82_N_A)

description: No additional description available for sample: CL-H82_N_A


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H128 (CLX-H128_N_B)

description: No additional description available for sample: CLX-H128_N_B

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H128


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H187 (CLX-H187_N_A)

description: No additional description available for sample: CLX-H187_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H187


title: Small Cell Lung Cancer Primary xenograft, sample LX36 (X-LX36_Y_A)

description: No additional description available for sample: X-LX36_Y_A

source_name: Small Cell Lung Cancer Primary xenograft, sample: LX36


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line LX36 (CLX-LX36_Y_B)

description: No additional description available for sample: CLX-LX36_Y_B

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: LX36


title: Small Cell Lung Cancer Primary xenograft, sample LX22 (X-LX22_Y_B)

description: No additional description available for sample: X-LX22_Y_B

source_name: Small Cell Lung Cancer Primary xenograft, sample: LX22


title: Normal Lung (Stratagene) (Norm_N_A)

description: No additional description available for sample: Norm_N_A

source_name: Normal Lung (Stratagene)

value: Normal Lung


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H345 (CLX-H345_N_A)

description: No additional description available for sample: CLX-H345_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H345


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H1930 (CLX-H1930_N_A)

description: No additional description available for sample: CLX-H1930_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H1930


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H526 (CLX-H526_N_A)

description: No additional description available for sample: CLX-H526_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H526


title: Small Cell Lung Cancer cell line H69 (CL-H69_N_A)

description: No additional description available for sample: CL-H69_N_A

source_name: Small Cell Lung Cancer cell line: H69


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H446 (CLX-H446_N_A)

description: No additional description available for sample: CLX-H446_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H446


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line LX33 (CLX-LX33_Y_A)

description: No additional description available for sample: CLX-LX33_Y_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: LX33


title: Small Cell Lung Cancer Primary xenograft, sample LX22 (X-LX22_Y_C)

description: No additional description available for sample: X-LX22_Y_C


title: Universal human reference RNA (Stratagene) (Ref_N_A)

description: No additional description available for sample: Ref_N_A


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line LX36 (CLX-LX36_Y_A)

description: No additional description available for sample: CLX-LX36_Y_A


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H1618 (CLX-H1618_N_A)

description: No additional description available for sample: CLX-H1618_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H1618


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H209 (CLX-H209_N_A)

description: No additional description available for sample: CLX-H209_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H209


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line LX22 (CLX-LX22_Y_A)

description: No additional description available for sample: CLX-LX22_Y_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: LX22


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H128 (CLX-H128_N_A)

description: No additional description available for sample: CLX-H128_N_A


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H69 (CLX-H69_N_A)

description: No additional description available for sample: CLX-H69_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H69


title: Small Cell Lung Cancer cell line LX36 (CL-LX36_Y_A)

description: No additional description available for sample: CL-LX36_Y_A

source_name: Small Cell Lung Cancer cell line: LX36


title: Small Cell Lung Cancer Secondary xenograft obtained from cell line H82 (CLX-H82_N_A)

description: No additional description available for sample: CLX-H82_N_A

source_name: Small Cell Lung Cancer Secondary xenograft obtained from the corresponding cell line: H82


title: Small Cell Lung Cancer cell line LX33 (CL-LX33_Y_A)

description: No additional description available for sample: CL-LX33_Y_A

source_name: Small Cell Lung Cancer cell line: LX33