title: S1_ebv05_picoplex

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S1. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl PBS by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were further whole genome amplified using PicoPLEX (Rubicon Genomics, USA), according to the protocol of the manufacturer. The WGA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies). Single-cell amplifications yielding less than 2 µg DNA were not further used. The sample was processed according to the manual of Infinium II assay (Illumina, USA).


title: S1_ebv02_mda_24h

status: Public on May 15 2015

type: genomic

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S1. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2.

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA), with the exception that the fragmentation step was shortened from 20-24h to 7h and the hybridization step was shortened from 16-20h to 6h for the rapid protocol.

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing: The genotypes, B allele frequencies and LogR values were extracted by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75 in GenCall.

molecule: genomic DNA

organism: Homo sapiens

source_name: EBV-transformed lymphoblast

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The embryos were in vitro cultured in Life Global medium (Life Global, Canada) or Quinns Advantage Protein Plus Medium (Cooper Surgical, USA). On day 2 and 3 after fertilization, embryo development was evaluated for the number of blastomeres, the percentage of fragmentation and the symmetry of the blastomeres. All ≥ 6 cell stage embryos that had less than 25% fragmentation on day 3 after fertilization were biopsied using a non-contact, 1.48 µm diode laser system (Fertilase®; MTG, Germany) coupled to an inverted microscope, after first being incubated in Ca2+/Mg2+ free medium. One or two blastomeres were gently aspirated from each embryo for the conventional FISH- or PCR-based PGD.  The embryos were immediately transferred to fresh medium; while the aspirated blastomeres were separately washed twice with Ca2+/Mg2+ free medium to remove possible oil remnants.

extract_protocol: Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with GenomiPhiV2 (GE Healthcare, USA). The MDA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer). Single-cell amplifications yielding less than 2 µg DNA were not further used.

treatment_protocol: The embryos that were not suitable for transfer on day 4 were dissociated and single blastomeres were collected for further analysis. The zona pellucida was removed by incubation in a droplet of Tyrode's solution (Sigma-Aldrich, USA). The acid was and consequently washed away and the embryos were dissociated in a droplet of Ca2+/Mg2+ free medium (Life Global, Canada).

tag: cell type

value: EBV-transformed lymphoblast

tag: dna sample

value: Single cell

tag: wga

value: MDA

tag: hybridization protocol

value: Rapid


title: S1_ebv03_mda

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S1. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. The sample was processed according to the manual of Infinium II assay (Illumina, USA).

value: Conventional


title: geral-00143: SL_U133A_B13-T

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

source_name: estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer subclass B

tag: er(-)subclass

value: B

tag: progesteronereceptorstatus

value: negative

tag: estrogenreceptorstatus

tag: treatment

tag: organismpart

value: breast

tag: strainorline

tag: disease state

value: breast carcinomas


title: geral-00143: MD_U133A_B97T

scan_protocol: See mage-tab files linked to series entry for additional details


title: geral-00143: MD_U133A_B95T

data_processing: See mage-tab files linked to series entry for additional details

value: positive


title: S1_ebv04_picoplex

value: PicoPlex


title: S1_ebv06_picoplex


title: S2_ebv12_picoplex

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S2. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl PBS by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were further whole genome amplified using PicoPLEX (Rubicon Genomics, USA), according to the protocol of the manufacturer. The WGA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies). Single-cell amplifications yielding less than 2 µg DNA were not further used. The sample was processed according to the manual of Infinium II assay (Illumina, USA).


title: geral-00143: MD_U133A_B96T

source_name: estrogen receptor-positive ER(+) breast cancer

label_protocol: See mage-tab files linked to series entry for additional details


title: geral-00143: MD_U133A_B94T

extract_protocol: See mage-tab files linked to series entry for additional details


title: S1_ebv02_mda


title: geral-00143: MD_U133A_B93T

source_name: estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer subclass A

value: A


title: geral-00143: MD_U133A_B91T


title: geral-00143: MD_U133A_B92T


title: geral-00143: MD_U133A_B90T


title: S1_ebv06_picoplex_24h

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S1. EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2. Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl PBS by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were further whole genome amplified using PicoPLEX (Rubicon Genomics, USA), according to the protocol of the manufacturer. The WGA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies). Single-cell amplifications yielding less than 2 µg DNA were not further used.


title: S1_ebv01_mda_24h


title: S1_ebv01_mda


title: geral-00143: SL_U133A_B11-Trep


title: geral-00143: MD_U133A_B89T


title: geral-00143: MD_U133A_B88T


title: S1_MC_24h

description: Multi-cell control DNA from sibling S1.

source_name: Blood

tag: tissue

value: Blood

value: Multi cell


title: geral-00143: MD_U133A_B87T


title: VOCs_Upper_10_12

city: Ansan

first: jiyoung

last: hong

address: Hanyang Univ.,55, Hanyangdaehak-ro, Sangrok-Gu

country: South Korea

institute: hanyang university

description: Gene expression in VOCs exposure_24

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 10x Gene Expression blocking agent and 25x Agilent fragmentation buffer following the manufacturers’ instructions. On completion of the fragmentation reaction, 25 ul of 2x Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Human GE 8x 60K (ver.2) oligo arrays (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent C scanner (Agilent Technologies) using one color scan setting Human GE 8x 60K (ver.2) oligo arrays slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMI and the gain of PMI is set to 100%).

data_processing: The scanned images were analyzed Feature Extraction software 10.7.3.1 (Agilent Technologies) and the extracted raw data were analyzed by GeneSpring GX v13.0 (Agilent Technologies). Gene expression data were flaged and normalized for 23070 probes of 50599 probes by quantile normalization. We used unpaired t-tests for selection of commonly expressed and differentially expressed genes. Genes were judged if P-values were 0.05 or less and fold changes were at least 1.5 compared with gene expression in the control group.

source_name: Human blood, VOCs Exposure_upper_10:12

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA(200ng) using the One-Color Low RNA Input Linear Amplification  kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop (Thermo Fisher Scientific, USA).

extract_protocol: Total mRNA was prepared using the PAXgene miRNA Kit (Qiagen, Valencia, CA, USA) following the manufacturer's recommendations. RNA yields were assessed using a NanoDrop (Thermo Fisher Scientific, USA), and the qualities of RNA were confirmed using a 2100 Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: The mRNA profiling in human blood samples (IRB #AS 14039) divided into three groups: control (unexposed workers; n = 12), short-term exposure (workers exposed to VOCs for less than 10 years; n = 12), and long-term exposure (workers exposed to VOCs for more than 10 years; n = 12) were used after exposure to VOCs

value: whole blood

tag: gender

value: male

tag: age


title: S1_MC

description: Multi-cell control DNA from sibling S1. The samples were processed according to the manual of Infinium II assay (Illumina, USA).


title: E14_Bl708_PGD021

description: Blastomere from cleavage stage day 4 embryo 'E14'.

source_name: Blastomere

tag: family

value: Blastomere


title: E06_Bl711_PGD022

description: Blastomere from cleavage stage day 4 embryo 'E06'.


title: geral-00143: MD_U133A_B86T


title: E06_Bl710_PGD022


title: Mother_PGD022

description: Maternal genomic DNA, carrier of monogenic X-linked disorder (Fragile X syndrome Xq27.3), family PGD022.


title: Grandmother_PGD022

description: Genomic DNA of family member: maternal grandmother, carrier of monogenic X-linked disorder (Fragile X syndrome Xq27.3), family PGD022.


title: Grandfather_PGD022

description: Genomic DNA of family member: maternal grandfather, family PGD022.


title: E10_Bl704_PGD021

description: Blastomere from cleavage stage day 4 embryo 'E10'.


title: E10_Bl705_PGD021


title: Father_PGD021

description: Genomic DNA of family member: father, carrier of an autosomal recessive disorder (OMIM 219700), affected with an autosomal dominant disorder (OMIM 105650), family PGD021.


title: Mother_PGD021

description: Genomic DNA of family member: mother, carrier of an autosomal recessive disorder (OMIM 219700), family PGD021.


title: geral-00143: MD_U133A_B85T


title: Sib_PGD020

description: Genomic DNA of family member: affected son, affected with an autosomal recessive disorder (OMIM 219700), family PGD020.


title: VOCs_Upper_10_9

description: Gene expression in VOCs exposure_21

source_name: Human blood, VOCs Exposure_upper_10:9


title: E02_Bl700_PGD020

description: Blastomere from cleavage stage day 4 embryo 'E04'.


title: E05_Bl701_PGD021

description: Blastomere from cleavage stage day 4 embryo 'E05'.


title: E05_Bl702_PGD021


title: Father_PGD022

description: Paternal genomic DNA, family PGD022.


title: geral-00143: MD_U133A_B84T


title: E02_Bl653_PGD018

description: Blastomere from cleavage stage day 4 embryo 'E02'.


title: geral-00143: MD_U133A_B83T


title: geral-00143: MD_U133A_B82T


title: VOCs_Upper_10_10

description: Gene expression in VOCs exposure_22

source_name: Human blood, VOCs Exposure_upper_10:10


title: Sib_PGD021

description: Genomic DNA of family member: daughter, affected with an autosomal recessive disorder (OMIM 219700), family PGD021.


title: Father_PGD020

description: Genomic DNA of family member: father, carrier of an autosomal recessive disorder (OMIM 219700), family PGD020.


title: Mother_PGD020

description: Genomic DNA of family member: mother, carrier of an autosomal recessive disorder (OMIM 219700), family PGD020.


title: Grandmother_PGD021

description: Genomic DNA of family member: paternal grandmother, affected with an autosomal dominant disorder (OMIM 105650), family PGD021.


title: geral-00143: MD_U133A_B81T


title: E02_Bl651_PGD018


title: E05_Bl635_PGD018


title: VOCs_Upper_10_7

description: Gene expression in VOCs exposure_19

source_name: Human blood, VOCs Exposure_upper_10:7


title: Father_PGD018

description: Genomic DNA of family member: father, affected with an autosomal recessive disorder (OMIM 603903), PGD018.


title: geral-00143: MD_U133A_B80T


title: VOCs_Upper_10_6

description: Gene expression in VOCs exposure_18

source_name: Human blood, VOCs Exposure_upper_10:6


title: E05_Bl632_PGD018


title: Sib1_PGD018

description: Genomic DNA of family member: son, affected with an autosomal recessive disorder (OMIM 603903), family PGD018.


title: VOCs_Upper_10_11

description: Gene expression in VOCs exposure_23

source_name: Human blood, VOCs Exposure_upper_10:11


title: geral-00143: MD_U133A_B79T


title: Sib2_PGD018

description: Genomic DNA of family member: daughter, carrier of an autosomal recessive disorder (OMIM 603903), family PGD018.


title: Grandfather_PGD021

description: Genomic DNA of family member: paternal grandfather, family PGD021.


title: geral-00143: MD_U133A_B78T


title: VOCs_Upper_10_4

description: Gene expression in VOCs exposure_16

source_name: Human blood, VOCs Exposure_upper_10:4


title: E14_Bl709_PGD021

description: Blastomere from cleavage stage day 4 embryo 'E14'.


title: geral-00143: MD_U133A_B77T


title: geral-00143: MD_U133A_B76T


title: VOCs_Upper_10_5

description: Gene expression in VOCs exposure_17

source_name: Human blood, VOCs Exposure_upper_10:5


title: geral-00143: MD_U133A_B75T


title: VOCs_Upper_10_2

description: Gene expression in VOCs exposure_14

source_name: Human blood, VOCs Exposure_upper_10:2


title: VOCs_Upper_10_8

description: Gene expression in VOCs exposure_20

source_name: Human blood, VOCs Exposure_upper_10:8


title: E05_Bl610_PGD016


title: VOCs_Upper_10_1

description: Gene expression in VOCs exposure_13

source_name: Human blood, VOCs Exposure_upper_10:1


title: VOCs_Upper_10_3

description: Gene expression in VOCs exposure_15

source_name: Human blood, VOCs Exposure_upper_10:3


title: VOCs_Under_10_12

description: Gene expression in VOCs exposure_12

source_name: Human blood, VOCs Exposure_under_10:12


title: geral-00143: MD_U133A_B74T

source_name: estrogen receptor-positive ER(+) breast cancer


title: E02_Bl601_PGD016


title: geral-00143: MD_U133A_B73T

source_name: estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer subclass B


title: E04_Bl604_PGD016


title: VOCs_Under_10_11

description: Gene expression in VOCs exposure_11

source_name: Human blood, VOCs Exposure_under_10:11


title: Mother_PGD018

description: Genomic DNA of family member: mother, carrier of an autosomal recessive disorder (OMIM 603903), family PGD018.

source_name: Blood


title: geral-00143: MD_U133A_B72T


title: E05_Bl611_PGD016

source_name: Blastomere


title: VOCs_Under_10_10

description: Gene expression in VOCs exposure_10

source_name: Human blood, VOCs Exposure_under_10:10


title: Maternalaunt_PGD016

description: Genomic DNA of family member: maternal aunt, carrier of monogenic X-linked recessive disorder (Duchenne Muscular Dystrophy), family PGD016.


title: E04_Bl605_PGD016


title: E03_Bl602_PGD016

description: Blastomere from cleavage stage day 4 embryo 'E03'.


title: Father_PGD016

description: Genomic DNA of family member: father, family PGD016.


title: VOCs_Under_10_9

description: Gene expression in VOCs exposure_9

source_name: Human blood, VOCs Exposure_under_10:9


title: geral-00143: MD_U133A_B71T


title: Maternaluncle_PGD016

description: Genomic DNA of family member: maternal uncle, affected with monogenic X-linked recessive disorder (Duchenne Muscular Dystrophy), family PGD016.


title: E02_Bl521_PGD014


title: VOCs_Under_10_8

description: Gene expression in VOCs exposure_8

source_name: Human blood, VOCs Exposure_under_10:8


title: Grandfather_PGD016

description: Genomic DNA of family member: maternal grandfather, family PGD016.


title: VOCs_Under_10_7

description: Gene expression in VOCs exposure_7

source_name: Human blood, VOCs Exposure_under_10:7


title: geral-00143: MD_U133A_B69T


title: Mother_PGD016

description: Genomic DNA of family member: mother, carrier of monogenic X-linked recessive disorder (Duchenne Muscular Dystrophy), family PGD016.


title: E02_Bl522_PGD014

description: Blastomere from cleavage stage day 4 embryo 'E02'.


title: VOCs_Under_10_6

description: Gene expression in VOCs exposure_6

source_name: Human blood, VOCs Exposure_under_10:6


title: geral-00143: MD_U133A_B68T


title: E03_Bl524_PGD014


title: geral-00143: MD_U133A_B67T


title: E03_Bl603_PGD016


title: geral-00143: MD_U133A_B70T


title: VOCs_Under_10_5

description: Gene expression in VOCs exposure_5

source_name: Human blood, VOCs Exposure_under_10:5


title: VOCs_Under_10_4

description: Gene expression in VOCs exposure_4

source_name: Human blood, VOCs Exposure_under_10:4


title: E03_Bl469_PGD012


title: Grandmother_PGD014

description: Genomic DNA of family member: paternal grandmother, family PGD014.


title: E01_Bl519_PGD014

description: Blastomere from cleavage stage day 4 embryo 'E01'.


title: E01_Bl520_PGD014


title: Grandfather_PGD014

description: Genomic DNA of family member: paternal grandfather affected with an autosomal disorder (OMIM 118220), family PGD014


title: Grandmother_PGD016

description: Genomic DNA of family member: maternal grandmother, carrier of monogenic X-linked recessive disorder (Duchenne Muscular Dystrophy), family PGD016.


title: geral-00143: MD_U133A_B63T


title: Mother_PGD014

description: Genomic DNA of family member: mother, PGD014.


title: Father_PGD014

description: Genomic DNA of family member: father, affected with an autosomal disorder (OMIM 118220), family PGD014.


title: E01_Bl466_PGD012


title: geral-00143: MD_U133A_B66T


title: geral-00143: MD_U133A_B62T


title: Father_PGD012

description: Genomic DNA of family member: father, family PGD012


title: VOCs_Under_10_2

description: Gene expression in VOCs exposure_2

source_name: Human blood, VOCs Exposure_under_10:2


title: Sib_PGD012

description: Genomic DNA of family member: affected son, monogenic X-linked disorder (hemophilia A Xq28), family PGD012.


title: E01_Bl465_PGD012


title: geral-00143: MD_U133A_B61T


title: E03_Bl677_PGD008C2

description: Blastomere from cleavage stage day 3 embryo 'E03' (PGD cycle 2). Day 3 biopsy using a non-contact, 1.48 µm diode laser system (Fertilase®; MTG, Aldorf, Germany) coupled to an inverted microscope, after first incubating the embryo in Ca2+/Mg2+ free medium.


title: E06_Bl679_PGD008C2

description: Blastomere from cleavage stage day 3 embryo 'E06' (PGD cycle 2). Day 3 biopsy using a non-contact, 1.48 µm diode laser system (Fertilase®; MTG, Aldorf, Germany) coupled to an inverted microscope, after first incubating the embryo in Ca2+/Mg2+ free medium.


title: Control_12

description: Gene expression of control_12

source_name: Human blood, Control

value: female


title: geral-00143: MD_U133A_B60T


title: geral-00143: MD_U133A_B59T


title: VOCs_Under_10_1

description: Gene expression in VOCs exposure_1

source_name: Human blood, VOCs Exposure_under_10:1


title: Control_10

description: Gene expression of control_10


title: E15_Bl363_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E15' (PGD cycle 1).

value: Single cell


title: geral-00143: MD_U133A_B58T


title: Control_9

description: Gene expression of control_9


title: geral-00143: MD_U133A_B57T


title: E02_Bl365_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E02' (PGD cycle 1).

value: MDA


title: E03_Bl523_PGD014

description: Blastomere from cleavage stage day 4 embryo 'E03'.

value: Rapid


title: E03_Bl468_PGD012


title: E04_Bl358_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E04' (PGD cycle 1).


title: E08_Bl681_PGD008C2

description: Blastomere from cleavage stage day 3 embryo 'E08' (PGD cycle 2). Day 3 biopsy using a non-contact, 1.48 µm diode laser system (Fertilase®; MTG, Aldorf, Germany) coupled to an inverted microscope, after first incubating the embryo in Ca2+/Mg2+ free medium.


title: geral-00143: MD_U133A_B56T


title: VOCs_Under_10_3

description: Gene expression in VOCs exposure_3

source_name: Human blood, VOCs Exposure_under_10:3


title: Control_11

description: Gene expression of control_11


title: Control_7

description: Gene expression of control_7


title: E10_Bl348_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E10' (PGD cycle 1).


title: E14_Bl350_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E14' (PGD cycle 1).


title: geral-00143: MD_U133A_B55T


title: geral-00143: MD_U133A_B54T


title: E11_Bl353_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E11' (PGD cycle 1).


title: E09_Bl361_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E09' (PGD cycle 1).


title: E09_Bl347_PGD008C1


title: Control_5

description: Gene expression of control_5


title: E08_Bl346_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E08' (PGD cycle 1).


title: E11_Bl349_PGD008C1


title: Control_4

description: Gene expression of control_4


title: E06_Bl344_PGD008C1

description: Blastomere from cleavage stage day 4 embryo 'E06' (PGD cycle 1).


title: Mother_PGD012

description: Genomic DNA of family member: mother, carrier of monogenic X-linked disorder (hemophilia A Xq28), family PGD012.


title: geral-00143: MD_U133A_B51T


title: Mother_PGD008

description: Genomic DNA of family member: mother, carrier of balanced complex chromosomal rearrangement t(6;13;16)(p25.1;q21.33;q24.2), family PGD008.


title: Control_3

description: Gene expression of control_3


title: E11_Bl507_PGD006

description: Blastomere from cleavage stage day 4 embryo 'E11'.


title: Control_2

description: Gene expression of control_2


title: Father_PGD008

description: Genomic DNA of family member: father, family PGD008


title: E11_Bl506_PGD006


title: geral-00143: MD_U133A_B50T


title: geral-00143: MD_U133A_B53T


title: Control_1

description: Gene expression of control_1


title: geral-00143: MD_U133A_B52T


title: geral-00143: MD_U133A_B49T


title: E10_Bl515_PGD006

description: Blastomere from cleavage stage day 4 embryo 'E10'.


title: E05_Bl678_PGD008C2

description: Blastomere from cleavage stage day 3 embryo 'E05' (PGD cycle 2). Day 3 biopsy using a non-contact, 1.48 µm diode laser system (Fertilase®; MTG, Aldorf, Germany) coupled to an inverted microscope, after first incubating the embryo in Ca2+/Mg2+ free medium.


title: E10_Bl514_PGD006


title: Sib_PGD008

description: Genomic DNA of family member: affected son, carrier of unbalanced complex chromosomal rearrangement, family PGD008


title: Control_8

description: Gene expression of control_8


title: E07_Bl680_PGD008C2

description: Blastomere from cleavage stage day 3 embryo 'E07' (PGD cycle 2). Day 3 biopsy using a non-contact, 1.48 µm diode laser system (Fertilase®; MTG, Aldorf, Germany) coupled to an inverted microscope, after first incubating the embryo in Ca2+/Mg2+ free medium.


title: geral-00143: MD_U133A_B48T


title: geral-00143: MD_U133A_B47T


title: E12_Bl508_PGD006

description: Blastomere from cleavage stage day 4 embryo 'E12'.


title: CLL 38

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

country: Spain

institute: IDIBAPS-HOSPITAL CLINIC

description: CD19+ tumoral cells from PBMCs of a CLL patient

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays

scan_protocol: Scanning was processed in the Gene Titan instrument

data_processing: Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software version 1.1 (AGCC) (Affymetrix)  Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm of the BioConductor Affy Package.

source_name: CD19+ purified cells from PBMCs of CLL patient

label_protocol: standard Affymetrix protocol

growth_protocol: CD19+ tumoral cells purified from PBMCs of CLL patients

extract_protocol: Total RNA was extracted, using the Trizol reagent

treatment_protocol: Untreated

value: CD19+ tumor cells

value: CLL


title: E12_Bl509_PGD006


title: CLL 37


title: geral-00143: MD_U133A_B46T

value: B

value: negative


title: CLL 35


title: Control_6

description: Gene expression of control_6


title: CLL 36


title: geral-00143: MD_U133A_B45T

source_name: estrogen receptor-positive ER(+) breast cancer

value: breast

value: breast carcinomas


title: E13_Bl497_PGD006

description: Blastomere from cleavage stage day 4 embryo 'E13'.


title: E07_Bl494_PGD006

description: Blastomere from cleavage stage day 4 embryo 'E07'.


title: geral-00143: MD_U133A_B44T

source_name: estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer subclass B


title: E13_Bl499_PGD006


title: Mother_PGD006

description: Genomic DNA of family member: mother, family PGD006.


title: CLL 34


title: geral-00143: MD_U133A_B43T

source_name: estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer subclass A


title: Father_PGD006

description: Genomic DNA of family member: father, carrier of 17q microdeletion, family PGD006.

source_name: Blood


title: CLL 33


title: geral-00143: MD_U133A_B42T

value: positive


title: E09_Bl164_PGD005

description: Blastomere from cleavage stage day 4 embryo 'E09'.

source_name: Blastomere


title: E04_Bl213_PGD006

description: Blastomere from cleavage stage day 4 embryo 'E04'.


title: CLL 32


title: CLL 31


title: Sib_PGD006

description: Genomic DNA of family member: affected son, carrier of 17q microdeletion, family PGD006.


title: E07_Bl495_PGD006


title: CLL 30


title: geral-00143: MD_U133A_B114T


title: E08_Bl147_PGD005

description: Blastomere from cleavage stage day 4 embryo 'E08'.


title: E06_Bl154_PGD005

description: Blastomere from cleavage stage day 4 embryo 'E06'.


title: CLL 29


title: geral-00143: MD_U133A_B115T


title: CLL 28


title: geral-00143: MD_U133A_B113T


title: E07_Bl159_PGD005


title: E07_Bl160_PGD005


title: E05_Bl131_PGD005

description: Blastomere from cleavage stage day 4 embryo 'E05'.


title: E08_Bl141_PGD005


title: geral-00143: MD_U133A_B112T

source_name: estrogen receptor-negative, progesterone receptor-positive (ER(-)/PR(+)) breast cancer


title: Foetus_PGD006

description: Genomic DNA of family member: aborted foetus, family PGD006.


title: E04_Bl126_PGD005


title: CLL 27


title: Mother_PGD005

description: Genomic DNA of family member: mother, carrier of X-linked microdeletion Xp22.31 syndrome, family PGD005.


title: CLL 26


title: E06_Bl152_PGD005


title: geral-00143: MD_U133A_B110T

value: A


title: Sib_PGD005

description: Genomic DNA of family member: affected son, carrier of X-linked microdeletion Xp22.31 syndrome, PGD005.

value: Blood


title: geral-00143: MD_U133A_B109T


title: geral-00143: MD_U133A_B111T


title: CLL 25


title: E10_Bl324_PGD004C2

description: Blastomere from cleavage stage day 4 embryo 'E10' (PGD cycle 2).


title: geral-00143: MD_U133A_B108T


title: E05_Bl132_PGD005


title: E07_Bl312_PGD004C2

description: Blastomere from cleavage stage day 4 embryo 'E07' (PGD cycle 2).


title: CLL 24


title: CLL 23


title: E02_Bl337_PGD004C2

description: Blastomere from cleavage stage day 4 embryo 'E02' (PGD cycle 2).


title: E11_Bl094_PGD004C1

description: Blastomere from cleavage stage day 4 embryo 'E11' (PGD cycle 1).


title: geral-00143: MD_U133A_B107T


title: Sib_PGD004

description: Genomic DNA of family member: affected daughter, carrier of unbalanced tranlocation, family PGD004.

value: Multi cell


title: CLL 22

description: CD19+ tumoral cells from PBMCs of a CLL patient


title: geral-00143: MD_U133A_B106T


title: E04_Bl341_PGD004C2

description: Blastomere from cleavage stage day 4 embryo 'E04' (PGD cycle 2).


title: geral-00143: MD_U133A_B105T


title: CLL 21


title: E11_Bl091_PGD004C1


title: E06_Bl288_PGD004C2

description: Blastomere from cleavage stage day 4 embryo 'E06' (PGD cycle 2).


title: E11_Bl092_PGD004C1


title: geral-00143: MD_U133A_B102T


title: geral-00143: MD_U133A_B103T


title: CLL 20


title: E04_Bl125_PGD005


title: CLL 19


title: CLL 18


title: E09_Bl108_PGD004C1

description: Blastomere from cleavage stage day 4 embryo 'E09' (PGD cycle 1).


title: E05_Bl095_PGD004C1

description: Blastomere from cleavage stage day 4 embryo 'E05' (PGD cycle 1).


title: Father_PGD005

description: Genomic DNA of family member: father, family PGD005.


title: geral-00143: MD_U133A_B101T


title: E06_Bl105_PGD004C1

description: Blastomere from cleavage stage day 4 embryo 'E06' (PGD cycle 1).


title: E06_Bl104_PGD004C1


title: E05_Bl098_PGD004C1


title: geral-00143: MD_U133A_B100T


title: E04_Bl118_PGD004C1

description: Blastomere from cleavage stage day 4 embryo 'E04' (PGD cycle 1).


title: Maternal-Grandfather_S1_S2

description: Genomic DNA of family member: maternal grandfather of siblings S1 and S2.

hyb_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

data_processing:
All the DNA samples were genotyped using the dynamic model (DM) algorithm embedded in the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1 (Affymetrix)’ using a homozygous and heterozygous calling threshold of 0.12, (2) the BRLMM algorithm within the ‘Genotyping console 3.0.1’ software (Affymetrix) using a scoring threshold of 0.1 and (3) the Birdseed algorithm using both 'birdseed-v1' and 'birdseed-dev' versions. The latter is the most recently incorporated development version of birdseed from The Broad Institute (http://www.broadinstitute.org/mpg/birdsuite/birdseed.html).
The CEL files are provided online, and DM-determined genotypes are provided in the 'NspMatrix' sheet.

growth_protocol: EBV-transformed lymphoblastoid cells were cultured in 75-cm2 plastic flasks (BD Falcon, USA) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium supplemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA) at 37oC, 5% CO2.

extract_protocol: Single-cell DNA was amplified following: (i) an MDA approach with Genomi Phi V2 (GE Healthcare, Piscataway, NJ). Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with GenomiPhiV2 (GE Healthcare, USA). The MDA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer). Single-cell amplifications yielding less than 2 µg DNA were not further used. (ii) A PCR-based approach with PicoPlex (Rubicon Genomics, MI, USA). Single cells were washed in 1xPBS and transferred into a 200 µl PCR tube containing 1.5 µl PBS by mouth controlled pipetting using 75 µm stripper tips (Origio, Denmark). The samples were further whole genome amplified using PicoPLEX (Rubicon Genomics, USA), according to the protocol of the manufacturer. The WGA products were purified using the High Pure PCR Product Purification Kit (Roche, Switzerland) and resuspended in 70 µl of elution buffer. All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies). Single-cell amplifications yielding less than 2 µg DNA were not further used.

treatment_protocol: Cultured cells were washed with phosphate buffered saline (PBS) solution to completely remove medium traces prior to the single cell isolation.

value: Conventional


title: CLL 17


title: CLL 16


title: E07_Bl314_PGD004C2


title: E09_Bl109_PGD004C1


title: geral-00143: MD_U133A_B104T


title: E02_Bl074_PGD002

description: Blastomere from cleavage stage day 4 embryo 'E02'.


title: RiceXoo_72hr_WT_rep3

city: Beijing

first: Tian

last: Caijuan

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute Of Microbiology Chinese Academy of Sciences

description: Gene expression in wild-type plant 72h after PXO99 inoculation.

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: Wild-type leaf,72hpi,replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Rice plants were maintained in the growth chamber with a setting on a 13 h daytime period, and 28/26°C temperature cycle.

extract_protocol: RNA was prepared using RiboPureTM kit (Ambion Inc) following the manufacturer's recommendations.

treatment_protocol: The fifth and sixth fully expanded leaves were inoculated with PXO99.

tag: genotype

value: wild type

tag: time

value: 72 hpi

value: leaf

tag: infection

value: Xoo infected


title: E04_Bl112_PGD004C1

value: Blastomere

tag: dna sample

value: Single cell

value: MDA


title: Maternal-Grandmother_S1_S2

description: Genomic DNA of family member: maternal grandmother of siblings S1 and S2.

scan_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

tag: wga


title: Father_S1_S2

description: Genomic DNA of family member: father of siblings S1 and S2.

label_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

tag: hybridization protocol


title: E03_Bl078_PGD002

description: Blastomere from cleavage stage day 4 embryo 'E03'.

value: Rapid


title: CLL 14

tag: cell type

value: CD19+ tumor cells

value: CLL


title: CLL 12


title: RiceXoo_72hr_WT_rep2

source_name: Wild-type leaf,72hpi,replicate 2


title: Father_PGD004

description: Genomic DNA of family member: father, carrier of balanced translocation t(1;16)(p36;p12), PGD004.


title: CLL 13


title: Mother_PGD004

description: Genomic DNA of family member: mother, family PGD004.


title: RiceXoo_72hr_WT_rep1

source_name: Wild-type leaf,72hpi,replicate 1


title: Father_PGD002

description: Genomic DNA of family member: father, family PGD002.


title: Mother_S1_S2

description: Genomic DNA of family member: mother of siblings S1 and S2.


title: CLL 11

description: CD19+ tumoral cells from PBMCs of a CLL patient


title: S2_ebv07_mda

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S2.

source_name: EBV-transformed lymphoblast

value: EBV-transformed lymphoblast


title: S2_ebv09_mda


title: RiceXoo_0hr_WT_rep3

description: Gene expression in wild-type plant 0h after PXO99 inoculation.

source_name: Wild-type leaf,0hpi,replicate 3

value: 0 hpi

value: Xoo not infected


title: S2_ebv12_picoplex

value: PicoPlex


title: S2_ebv08_mda


title: S2_ebv10_picoplex


title: Sib_PGD002

description: Genomic DNA of family member: affected daughter, carrier of unbalanced tranlocation, family PGD002.

value: Blood


title: RiceXoo_0hr_WT_rep2

source_name: Wild-type leaf,0hpi,replicate 2


title: CLL 10


title: RiceXoo_0hr_WT_rep1

source_name: Wild-type leaf,0hpi,replicate 1


title: IL-17RA-deficient_Infected

city: Galveston

first: Sara

middle: M

last: Dann

state: TX

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch

description: US22502657_251486825182_S01_GE1-v5_95_Feb07_1_4

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray Kit, 4x44K (G4122F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B). 5 µm scanning in green at 10% and 100% PMT

data_processing: Slide design ID was 26655 and the protocol used for extraction was GE1_107_Sep09. Version 10.7.3.1. of feature extraction. The data were normalized using the multi-loess method described in this paper: Microarray truths and consequences, R. Sasik, C. H. Woelk and J. Corbeil, J. Mol. Endocrinology, 33, 1 (2004)

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Quick Amplification Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA (isolated with TRIzol reagent) was prepared from whole small intestinal tissue of WT and IL-17RA-/- mice before or 2 weeks after infection with Giardia muris.

treatment_protocol: 8-wk-old mice were infected by oral gavage with 200 µl of Giardia muris  (1 x 10E4 cysts/mouse).

tag: strain background

tag: genotype/variation

value: female

value: 8 weeks

tag: infected with

tag: time point

value: 2 wks after infection

value: Whole small intestine


title: S2_ebv11_picoplex

value: Conventional


title: IL-17RA-deficient_Uninfected

description: US22502657_251486825182_S01_GE1-v5_95_Feb07_1_3

value: none (uninfected control)


title: E01_Bl122_PGD004C1

description: Blastomere from cleavage stage day 4 embryo 'E01' (PGD cycle 1).

value: Blastomere


title: C57BL/6_Infected

description: US22502657_251486825182_S01_GE1-v5_95_Feb07_1_2

source_name: WT_infected_whole small intestine

value: wild type

value: 200 µl of Giardia muris  (1 x 10E4 cysts/mouse)


title: E03_Bl077_PGD002

value: Single cell

value: MDA

value: Rapid


title: S2_MC

description: Multi-cell control DNA from sibling S2.

value: Multi cell


title: CLL 09

value: CD19+ tumor cells

value: CLL


title: S1_ebv04_picoplex

description: Single cell from an Epstein-Barr virus transformed lymphoblastoid cell line derived from sibling S1.

value: EBV-transformed lymphoblast

value: PicoPlex


title: S1_ebv02_mda


title: RiceXoo_72hr_Osaba1-1_rep2

description: Gene expression in Osaba1-1 mutant 72h after PXO99 inoculation.

source_name: Osaba1-1 mutant leaf,72hpi,replicate 2

value: 72 hpi

value: leaf

value: Xoo infected


title: S1_ebv03_mda


title: C57BL/6_Uninfected

description: US22502657_251486825182_S01_GE1-v5_95_Feb07_1_1

source_name: WT_uninfected_whole small intestine

value: female

value: 8 weeks

value: Whole small intestine


title: CLL 07

source_name: CD19+ purified cells from PBMCs of CLL patient


title: CLL 06


title: RiceXoo_72hr_Osaba1-1_rep3

source_name: Osaba1-1 mutant leaf,72hpi,replicate 3


title: S1_ebv05_picoplex

value: Conventional


title: CLL 08


title: S1_MC

description: Multi-cell control DNA from sibling S1.

value: Blood


title: S1_ebv06_picoplex


title: S1_ebv01_mda


title: RiceXoo_72hr_Osaba1-1_rep1

source_name: Osaba1-1 mutant leaf,72hpi,replicate 1


title: CLL 05


title: RiceXoo_0hr_Osaba1-1_rep3

description: Gene expression in Osaba1-1 mutant 0h after PXO99 inoculation.

source_name: Osaba1-1 mutant leaf,0hpi,replicate 3

value: 0 hpi

value: Xoo not infected


title: Mother_PGD002

description: Genomic DNA of family member: mother, carrier of balanced tranlocation t(10;16)(q23;p13.3), family PGD002.

source_name: Blood


title: golub-00142: T23_tumor

source_name: tumor

tag: tissue type

value: tumor


title: golub-00142: T18_tumor


title: golub-00142: T38_tumor


title: geral-00117: P7

source_name: primary prostate cancer

tag: organism

value: Homo Sapiens

tag: Sex

value: male

tag: disease state

value: prostate carcinoma

tag: disease location

value: prostate

tag: disease stage

tag: tumor grading

value: Gleason 7

tag: organism part


title: CLL 04

value: CD19+ tumor cells

value: CLL


title: geral-00117: P6

tag: age


title: geral-00117: P8

value: Gleason 6


title: geral-00117: P3


title: golub-00142: N59_normal

source_name: normal

value: normal


title: CLL 01


title: geral-00117: P23

value: Gleason 9


title: RiceXoo_0hr_Osaba1-1_rep2

source_name: Osaba1-1 mutant leaf,0hpi,replicate 2

tag: genotype

tag: time

tag: tissue

value: leaf

tag: infection


title: RiceXoo_0hr_Osaba1-1_rep1

source_name: Osaba1-1 mutant leaf,0hpi,replicate 1


title: CLL 02

tag: cell type


title: geral-00117: P2


title: geral-00117: P21


title: CLL 03


title: geral-00117: P4


title: geral-00117: P5


title: geral-00117: P19


title: geral-00117: P17


title: geral-00117: P22


title: geral-00117: P16

value: Gleason 8


title: geral-00117: P20


title: geral-00117: P18


title: LNCaP infected with shRNA library Replicate 2

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Biological replicate 2 of 2.

hyb_protocol: Microarray hybridization was performed using the Oligo cDGH/ChIP-on-ChIP Hybridization Kit (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 8.1).

data_processing: Agilent Feature Extraction Software (v 8.1) was used for background subtraction.

source_name: LNCaP cells, shRNA library, bicalutamide

label_protocol: The integrated shRNAs prepared from LNCaP genomic DNAs were amplified using primers (Decode RNAi-GIPZ, annotated genes screening library-negative selection kit from Thermo Scientific) specific for the barcodes for the library plasmid DNA. The PCR products were gel-purified using the QIAquick PCR purification Kit (QIAGEN). Purified DNA fragments (1.5 micro g) from LNCaP cells treated with vehicle or bicalutamide were labeled with cyanine-3 (Cy3) or cyanine-5 (Cy5) dye, respectively, using the Genome DNA Enzymatic Labeling Kit (Agilent; Santa Clara, CA, USA) and purified by the removal of unbound cyanine dyes with an Ultracell YM-30 Microcon centrifugal filter device (Millipore Japan; Tokyo, Japan).

growth_protocol: LNCaP cells were infected with lentiviral shRNA library (Decode RNAi Viral Screening Library, Thermo Scientific Open Biosystems) and then treated with bicalutamide (1 micro M) or vehicle for one month.

extract_protocol: Genomic DNA was isolated from the transduced cells using the DNeasy Purification Kit (QIAGEN; Tokyo, Japan) according to the manufacturer’s protocol.

tag: cell line

value: LNCaP

tag: ethnicity

value: Caucasian

source_name: LNCaP cells, shRNA library, vehicle

tag: strain


title: LNCaP infected with shRNA library Replicate 1

description: Biological replicate 1 of 2.


title: golub-00142: N23_normal

tag: tissue type


title: golub-00142: T17_tumor


title: golub-00142: T41_tumor


title: golub-00142: T53_tumor


title: geral-00117: P15

tag: organism


title: geral-00117: P13

tag: Sex


title: golub-00142: T47_tumor


title: golub-00142: N15_normal


title: geral-00117: P12

tag: disease state


title: geral-00117: P10

tag: disease location


title: golub-00142: T43_tumor


title: golub-00142: N16_normal


title: golub-00142: N50_normal


title: golub-00142: N38_normal


title: geral-00117: P11

tag: disease stage


title: golub-00142: T13_tumor


title: geral-00117: P14

tag: tumor grading


title: golub-00142: N46_normal


title: golub-00142: N55_normal


title: geral-00117: MET1

source_name: metastatic prostate cancer

value: lymph node

tag: organism part


title: geral-00117: MET7

tag: age


title: geral-00117: MET9

value: lung


title: geral-00117: MET2


title: geral-00117: nonneoplastic prostate stroma

value: normal prostate


title: geral-00117: MET4

value: Homo Sapiens

value: soft tissue


title: golub-00142: N44_normal


title: geral-00117: P1

value: male

value: prostate carcinoma


title: geral-00117: MET5

value: bone


title: geral-00117: MET8


title: geral-00117: bulk nonneoplastic prostate


title: golub-00142: T55_tumor

value: tumor


title: geral-00117: MET3

value: Gleason 7


title: geral-00117: MET6


title: geral-00117: nonneoplastic prostate epithelium


title: Oral 1

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr.

department: Surgery

institute: Stanford University

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Microarrays were normalized by robust multichip average (RMA) and quantile normalization in R. Cluster analysis was performed with AutoSOME (33), using the following settings for gene expression clustering: p-value threshold of 0.05, 100 ensemble iterations, unit variance normalization of arrays, median centering of genes, and sum of squares=1 normalization for both genes and arrays.

source_name: Oral

label_protocol: Not provided

growth_protocol: Dermal fibroblasts were harvested for FACS from the oral dermis and cranial dermis of Wnt1Cre; R26mTmG mice, and from ventral and dorsal dermis of En1Cre; R26mTmG mice as previously described. For all microarray analysis, EPFs and ENFs where harvested from backskin of mice at 30 days of age. Positivity for GFP or RFP allowed for the separation of EPFs from ENFs and WPFs from WNFs.

extract_protocol: RNA was precipitated via chloroform-phenol extraction. Samples were processed for cleanup and concentration using Rneasy MinElute cleanup kit (cat. 74204, QIAGEN). RNA yield was typically 0.5-1 µg RNA/sorted subpopulations. RNA samples from all sorted populations were converted to cDNA using SuperScript III first strand synthesis system for RT-PCR (cat. 18080-051, Invitrogen), and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

tag: genotype

value: Wnt1Cre; R26mTmG

tag: developmental stage

value: P30 (adult)

tag: treatment

value: No treatment or stimulus

value: Oral mucosa harvested

tag: cell population

value: FACS sorting for GFP pos RFP neg CD31 neg CD45 neg Tie2 neg Tie119 neg EpCAM neg DAPI neg


title: CLL 15

tag: cell type

value: CD19+ tumor cells

value: CLL


title: golub-00142: T25_tumor


title: golub-00142: N35_normal

value: normal


title: Dorsal 2

source_name: Dorsal

value: En1Cre; R26mTmG

tag: tissue

value: Dorsal dermis harvested


title: Ventral 2

source_name: Ventral

value: Ventral dermis harvested


title: Oral 2


title: Cranial 3

source_name: Cranial

value: Cranial dermis harvested


title: Cranial 2


title: golub-00142: N05_normal


title: Dorsal 3


title: Ventral 1


title: Oral 3


title: Ventral 3


title: golub-00142: T36_tumor


title: golub-00142: T49_tumor


title: golub-00142: T29_tumor


title: golub-00142: T26_tumor


title: golub-00142: N58_normal


title: golub-00142: N18_normal


title: ENF 3

source_name: ENF

value: P56 (adult)

value: FACS sorting for RFP pos GFP neg CD31 neg CD45 neg Tie2 neg Tie119 neg EpCAM neg DAPI neg


title: EPF 3

source_name: EPF


title: EPF 1


title: Cranial 1


title: ENF 1


title: Dorsal 1


title: golub-00142: T62_tumor


title: ENF 2


title: golub-00142: N14_normal


title: golub-00142: N61_normal


title: EPF 2


title: golub-00142: T45_tumor


title: golub-00142: T01_tumor


title: golub-00142: T06_tumor


title: golub-00142: T54_tumor


title: golub-00142: T40_tumor


title: golub-00142: T10_tumor


title: golub-00142: N24_normal


title: Planktonic_phase_2_15h

city: Nanjing

first: Dong

last: Liu

state: Jiangsu

address: No. 30, Puzhu South Road

department: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

description: Gene expression in 15h-grown C.acetobutylicum B3 planktonic cells

hyb_protocol: each Slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US). After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Clostridium acetobutylicum

source_name: Planktonic cells, 15h

label_protocol: Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Cultures of C. acetobutylicum B3 were grown in modified P2 medium containing 10 g/L glucose as the sole carbohydrate for seed culture. Fermentation experiments with planktonic cells were performed anaerobically in 500-mL Duran bottles with 300 mL of P2 medium (glucose 60 g/L; K2HPO4 0.5 g/L; KH2PO4 0.5 g/L; CH3COONH4 2.2 g/L; MgSO4•7H2O 0.2 g/L; MnSO4•H2O 0.01 g/L; NaCl 0.01 g/L; FeSO4•7H2O 0.01 g/L; p-aminobenzoic acid 1 mg/L; thiamine 1 mg/L; biotin 0.01 mg/L) at 37 °C with 10% inoculum (v/v). For fermentation with biofilm cells, 60 g/L of dried cotton towel was cut into pieces (approximately 2 cm × 3 cm) and sterilized by autoclaving at 121 °C for 15 min before being added to P2 medium with the bacterial inoculum.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: An 8-mL sample of planktonic culture was withdrawn and the cells were collected by centrifugation at 8,000 × g for 6 min at 4°C. To collect the biofilm cells, several pieces of cotton towel were harvested from the fermentation broth and rinsed twice with PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.40) to remove contaminating planktonic cells. Then the cotton towel was submerged in 8 mL PBS buffer and vortexed vigorously to disperse adsorbed cells, after which the cotton towel was removed and the resulting suspension was centrifuged to pallet the biofilm cells. All the cells were frozen immediately using liquid nitrogen and then stored at -80 °C prior to RNA extraction.

tag: growth phase

value: Transition


title: Planktonic_phase_4_34h

description: Gene expression in 34h-grown C.acetobutylicum B3 planktonic cells

source_name: Planktonic cells, 34h

tag: strain

value: Late solventogenesis


title: geral-00117: P9

value: Homo Sapiens

value: male

value: prostate carcinoma

value: prostate

value: Gleason 8


title: golub-00142: N20_normal

tag: tissue type


title: golub-00142: T56_tumor

value: tumor


title: golub-00142: N36_normal


title: Biofilm_phase_4_25h

description: Gene expression in 25h-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, 25h


title: Planktonic_phase_3_20h

description: Gene expression in 20h-grown C.acetobutylicum B3 planktonic cells

source_name: Planktonic cells, 20h

value: Early solventogenesis


title: golub-00142: N60_normal


title: 5CC7exvivo, 2ug MCC, experimental rep3

city: Bethesda

first: Rachel

middle: A

last: Gottschalk

address: 4 Memorial Dr

institute: NIAID

description:
Gene expression data from 5CC7 T cells stimlated in vivo
1million 5CC7 T cells were transferred into B10.A recipients by tail vein.
48 hours after peptide injection, lymph nodes were pooled and 5CC7 were purified by FACS.

hyb_protocol: Ten micrograms of labeled and fragmented cRNA were then hybridized to the mouse genome MOE430A2.0 array (Affymetrix)

scan_protocol: standard Affymetrix protocol

data_processing: Raw expression data were analyzed using GCOS 1.4 (Affymetrix) and normalized to a target intensity of 500 to account for differences in global chip intensity

source_name: 5CC7 T cells, stimulated in vivo with 2ug MCC peptide

label_protocol: 100 ng of total RNA was labeled using the GeneChip 3′ IVT express kit (Affymetrix) with the in vitro transcription step being carried out for 16 h

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

treatment_protocol: The indicated dose of peptide was diluted in PBS and injected by tail vein.

tag: cells

value: 5CC7 TCR tg T cells

tag: peptide

value: MCC

tag: dose


title: Planktonic_phase_1_10h

description: Gene expression in 10h-grown C.acetobutylicum B3 planktonic cells

source_name: Planktonic cells, 10h

value: Acidogenesis


title: 5CC7exvivo, 0.2ug MCC, experimental rep2

source_name: 5CC7 T cells, stimulated in vivo with 0.2ug MCC peptide


title: Biofilm_phase_3_20h

description: Gene expression in 20h-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, 20h


title: golub-00142: T39_tumor

source_name: tumor


title: 5CC7exvivo, 0.2ug MCC, experimental rep1


title: 5CC7exvivo, 0.2ug MCC, experimental rep3


title: Biofilm_phase_2_15h

description: Gene expression in 15h-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, 15h


title: golub-00142: T34_tumor


title: Biofilm_phase_1_10h

description: Gene expression in 10h-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, 10h


title: golub-00142: N30_normal

source_name: normal

value: normal


title: 5CC7exvivo, 2ug MCC, experimental rep2


title: 5CC7exvivo, 2ug MCC, experimental rep1


title: golub-00142: N42_normal


title: golub-00142: T15_tumor


title: 5CC7exvivo, 0.2ug 102S, experimental rep3

source_name: 5CC7 T cells, stimulated in vivo with 0.2ug 102S peptide


title: 5CC7exvivo, 0.2ug 102S, experimental rep1


title: Planktonic_phase_4_34h


title: 5CC7exvivo, 0.2ug 102S, experimental rep2


title: H1 shTerminator r2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: H1 cells with stable Terminator (scramble) shRNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina 450K Infinium Methylation Arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina GenomeStudio

label: Cy5 and Cy3

source_name: H1 ESCs

label_protocol: Standard Illumina Protocol

growth_protocol: Human ES cells, H1 (WA1, WiCell), (passage 25-40) were cultured in chemically defined hES/hiPS growth media, mTeSR on growth factor reduced matrigel (BD biosciences) coated plates. Briefly, 70-80% confluent hES/hiPS cells were treated with dispase (Invitrogen) for 7 minutes at 37¡C and the colonies were dispersed to small clusters and lifted carefully using a 5ml glass pipette, at a ratio of ~1:6. Human Umbilical Vein Endothelial Cells (HUVEC) were purchased from Promocell and cultivated in EBM medium supplemented with EGM singlequots (Lonza). iPS/ES-derived endothelial cells were cultivated in EGM-2 bullet kit (Lonza). All the endothelial cells were grown on collagen I coated plates (BD biosciences). All cell lines were maintained in an incubator (37¡C, 5% CO2) with media changes every day (hES/hiPS) or every second day (HUVEC).

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Pluripotent stem cells were differentiated as previously described (Kurian et al, 2012). Briefly, undifferentiated human ES/iPS cells were freshly split on to matrigel-coated plates, making sure the sub-colonies were of small size (~300-500 cells /colony). Cells were differentiated using the chemically defined mesodermal induction media (MIM) (DMEM:F12, 15mg/ml stem cell grade BSA (MP biomedicals), 17.5µg/ml Human Insulin, (SAFC bioscience),  275 µg/ml Human holo transferrin (Sigma Aldrich), 20ng/ml bFGF (Hymanzyme), 50ng/ml Human VEGF-165 aa (Humanzyme), 25ng/ml human BMP4 (Stemgent),  450µM monothioglycerol (Sigma Aldrich),  2.25mM  each L-Glutamine and Nonn-essential amino acids (Invitrogen).

tag: shRNA

value: stable Terminator (scramble) shRNA


title: HUVEC shPunisher

description: HUVEC cells with stable Punisher (scramble) shRNA

source_name: HUVEC

value: stable Punisher (scramble) shRNA


title: H1-Day8 shCtrl

description: late vascular progenitor cells with stable control (scramble) shRNA

source_name: Differentiated H1 ESCs

value: stable control (scramble) shRNA


title: golub-00142: T05_tumor


title: H1 shCtrl r2

description: H1 cells with stable control (scramble) shRNA


title: Planktonic_phase_2_15h


title: golub-00142: T11_tumor


title: HUVEC shCtrl

description: HUVEC cells with stable control (scramble) shRNA


title: Planktonic_phase_1_10h


title: golub-00142: T46_tumor


title: Biofilm_phase_4_25h


title: Biofilm_phase_3_20h


title: H1 shTerminator


title: 5CC7exvivo, 2ug 102S, experimental rep1

source_name: 5CC7 T cells, stimulated in vivo with 2ug 102S peptide


title: 5CC7exvivo, 2ug 102S, experimental rep3


title: golub-00095: FSCC19

source_name: Follicular Lymphoma

tag: disease state

value: Follicular Lymphoma

value: B-Lymphocyte

tag: disease stage

value: Lymphoid tissue

tag: individual


title: golub-00095: FSCC18

tag: organism part


title: H1-Day8 shAlien

description: late vascular progenitor cells with stable Alien (scramble) shRNA

value: stable Alien (scramble) shRNA


title: Biofilm_phase_2_15h

value: Transition


title: 5CC7exvivo, 2ug 102S, experimental rep2


title: golub-00095: FSCC16


title: golub-00142: T02_tumor


title: LSZ4 pLKO TRC2.0 shSiva2 -1

first: Stephano

last: Spano Mello

address: 269 Campus Drive

description: Gene expression after knockdown of Siva with shRNA in NSCLC cell line

hyb_protocol: 600 ng labeled cRNA were hybridized on the Whole Human Genome Expression Array G4851A (8x60K, Agilent) according to the manufacturer's instructions. Arrays were rotated overnight for 17 hours at 65°C at HI-RPM.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C. Feature Extraction Software 10.7.3.1 was used to process and analyse the images

data_processing: The raw data was processed using GeneSpring GX 12.6.1 (Normalization: Shift to 75.0 percentile; Baseline Transformation: Median of all samples).

source_name: LSZ4 NSCLC Cell line

label_protocol: 200 ng of RNA were amplified and Cy-3 labeled using the One Color Low Input Quick Amp Labeling Kit (Agilent), according to the manufacturer's instructions.

growth_protocol: Cells were grown in DMEM with 10% FBS at subconfluent densities.

extract_protocol: Trizol Extraction according to Life technology protocol (Cat #15596-026). RNA was quantified using a NanoDrop-1000 spectrophotometer

treatment_protocol: Cells were infected with virus produced by 293T cells following calcium phosphate transfection of viral vectors and shRNA plasmid (either control shGFP/shLacZ or shRNA targeted against Siva). Cells (except shLacZ transduced cells) were then selected with 2ug/ul Puromycin for three days prior to plating for RNA collection at subconfluent densities two days later.

value: Non-small cell cancer cell line


title: LSZ4 pLKO TRC2.0 shSiva2 -2


title: golub-00095: FSCC15


title: H1 shCtrl


title: Biofilm_phase_1_10h


title: golub-00095: FSCC14


title: LSZ2 pLKO TRC2.0 shSiva2 -2

source_name: LSZ2 NSCLC Cell line


title: golub-00142: N45_normal


title: golub-00142: T42_tumor


title: golub-00142: N39_normal


title: golub-00142: T24_tumor


title: golub-00142: T30_tumor


title: golub-00095: FSCC11


title: golub-00095: FSCC12


title: golub-00095: FSCC13


title: golub-00142: T32_tumor


title: golub-00142: T14_tumor


title: golub-00095: FSCC10


title: golub-00095: FSCC4


title: golub-00142: T19_tumor


title: LSZ2 pLKO TRC2.0 shSiva1 -2


title: Metastasis associated macrophage rep3 [140887_532]

city: Edinburgh

first: Bin-Zhi

last: Qian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

description: This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with FLT1 specific inhibitory  antibody (MF1). It is the third of three biological replicates used in this experiment, each from separate mouse.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Metastasis associated macrophage rep3

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Metastasis associated macrophage were FACS sorted from mice bearing pulmonary metastasis of breast tumor cells, lung and spleen resident macrophages were sorted from healthy non-tumour bearing mice

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA)  and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was amplified with Ambion MessageAmp II aRNA kit (Invitrogen, Grand Island, NY, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Einstein Genomic Core Facility

tag: genotype

value: Wild-type

tag: phenotype

value: lung metastasis associated

tag: accession

value: FVB


title: golub-00095: FSCC3


title: golub-00142: N43_normal


title: Metastasis associated macrophage rep2 [140885_532]

source_name: Metastasis associated macrophage rep2


title: Spleen resident macrophage rep3 [140887_635]

source_name: Spleen resident macrophage rep3

value: spleen resident


title: LSZ4 pLKO TRC2.0 shSiva1 -2


title: golub-00095: FSCC2


title: LSZ4 pLKO TRC2.0 shSiva1 -1


title: Spleen resident macrophage rep1 [140879_635]

source_name: Spleen resident macrophage rep1


title: LSZ2 pLKO TRC2.0 shSiva2 -1


title: LSZ2 pLKO TRC2.0 shSiva1 -1


title: LSZ4 LL37 shLacz2

description: Gene expression after control knockdown with shLacZ in NSCLC cell line


title: golub-00142: N27_normal


title: Spleen resident macrophage rep2 [140885_635]

source_name: Spleen resident macrophage rep2


title: Metastasis associated macrophage rep1 [140879_532]

source_name: Metastasis associated macrophage rep1


title: Metastasis associated macrophage rep3 [130203_635]


title: golub-00142: N04_normal


title: LSZ2 LL37 shLacz2


title: golub-00095: DLBC45

source_name: Diffuse large B-cell Lymphoma

value: Diffuse large B-cell Lymphoma

value: IPI high intermediate


title: golub-00095: FSCC1


title: Lung resident macrophage rep2 [128263_532]

description: This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with control antibody. It is the third of three biological replicates used in this experiment, each from separate mouse.

source_name: Lung resident macrophage rep2

value: lung resident


title: LSZ4 LL37 shLacz1


title: golub-00142: T16_tumor

source_name: tumor

value: tumor


title: Lung resident macrophage rep3 [130203_532]

description: This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with FLT1 specific inhibitory  antibody (MF1). It is the second of three biological replicates used in this experiment, each from separate mouse.

source_name: Lung resident macrophage rep3


title: LSZ4 pLKO.1 shGFP2

description: Gene expression after control knockdown with shGFP in NSCLC cell line


title: Metastasis associated macrophage rep2 [128263_635]

description: This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with FLT1 specific inhibitory  antibody (MF1). It is the first of three biological replicates used in this experiment, each from separate mouse.


title: golub-00142: N53_normal

source_name: normal

value: normal


title: Lung resident macrophage rep1 [128044_532]

description: This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with control antibody. It is the first of three biological replicates used in this experiment, each from separate mouse.

source_name: Lung resident macrophage rep1


title: golub-00142: T31_tumor


title: golub-00142: N41_normal


title: golub-00095: DLBC17


title: golub-00095: DLBC12


title: golub-00142: T33_tumor


title: golub-00142: T58_tumor


title: golub-00142: N21_normal


title: LSZ4 pLKO.1 shGFP1


title: golub-00142: N02_normal


title: golub-00142: T28_tumor


title: golub-00095: DLBC44

value: IPI low intermediate


title: bone marrow(BM)_mouse_leukemia_ALL3

first: Corina

last: Buechele

address: 1291 Welch Road

institute: Cleary lab

hyb_protocol: All steps were performed by Stanford Functional Genomic Facility and were according to the manufacturer's instructions of the standard Affymetrix Microarray GeneChip platform (HG-U133 Plus 2.0).

data_processing: Gene expression matrix from the arrays was normalized in the same way using RMA model from Bioconductor affy package. Gene expression values were then independently filtered to remove low variance probes using Bioconductor package, genefilter 1.50. Finally, 25,000 probes were then subjected to unsupervised hierarchical clustering analysis using R packages, ape and heatmap 2.0.

source_name: BM cells (sorted for hCD45) of leukemic mice (ALL)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Microarray GeneChip platform (HG-U133 Plus 2.0).

growth_protocol: Genome-engineered CD34+ cells were transplanted into NSG mice. NSG mice were sacrificed upon signs of illness. Median latency was 14.5 weeks.

treatment_protocol: CD34+ cells were nucleofected with TALENs (specifically cut in the MLL gene locus) and template (MLL-AF9 or MLL-ENL). After <3 days of culture, these cells were injected into NSG mice. After signs of illness, mice were sacrificed, bone marrow isolated and sorted for hCD45+ cells, which were then further used for RNA isolations.

value: bone marrow

tag: injected cells

value: CD34+ human umbilical cord blood cells


title: golub-00095: DLBC16

tag: cell type

value: B-Lymphocyte


title: bone marrow(BM)_mouse_leukemia_ALL1

scan_protocol: All steps were performed by Stanford Functional Genomic Facility and were according to the manufacturer's instructions of the standard Affymetrix Microarray GeneChip platform (HG-U133 Plus 2.0).

tag: tissue


title: golub-00095: DLBC54_lymphoma

value: IPI high

value: Lymphoid tissue


title: golub-00095: DLBC5

value: IPI low


title: golub-00142: N25_normal


title: golub-00095: DLBC6


title: golub-00142: T04_tumor


title: golub-00142: N47_normal


title: golub-00095: DLBC8


title: golub-00095: DLBC9


title: LSZ2 pLKO.1 shGFP1

value: Non-small cell cancer cell line


title: golub-00095: DLBC7


title: SD

city: Chapel Hill

first: Silva

last: Markovic-Plese

state: NC

address: 105 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

hyb_protocol: 15 ug of cRNA was used for gene array hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip® Hybridization Oven 640.The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip® Fluidics Station 400.

scan_protocol: The arrays were scanned with the Hewlett Packard GeneArray Scanner.

data_processing: Affymetrix GeneChip® Microarray Suite 5.0 software

label: Biotin

source_name: PBMCs from CIS patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA.

extract_protocol: Total RNA was extracted using a Rneasy kit according to the manufacturer's instructions.

treatment_protocol: PBMCs were separated from 15 CIS patients and 7 HCs

tag: condition

value: CIS patient

value: PBMCs


title: golub-00095: FSCC17

source_name: Follicular Lymphoma

value: Follicular Lymphoma


title: UP


title: WSD


title: Metastasis associated macrophage rep1 [128044_635]

description: This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with control antibody. It is the second of three biological replicates used in this experiment, each from separate mouse.

value: Wild-type

value: lung metastasis associated

value: FVB


title: PSa


title: MK


title: pDK


title: bone marrow(BM)_mouse_leukemia_ALL2


title: MC


title: PS


title: golub-00095: DLBC58_lymphoma

value: Diffuse large B-cell Lymphoma

value: IPI high intermediate


title: golub-00142: N34_normal

value: normal


title: golub-00142: N19_normal


title: golub-00142: T60_tumor

value: tumor


title: golub-00142: N13_normal


title: golub-00095: FSCC7


title: golub-00095: DLBC53_lymphoma


title: JW


title: golub-00142: T22_tumor


title: JD


title: golub-00095: DLBC55_lymphoma


title: golub-00095: DLBC48


title: golub-00142: N10_normal


title: golub-00142: T20_tumor


title: golub-00095: DLBC46_lymphoma


title: golub-00095: DLBC47


title: golub-00142: T03_tumor


title: golub-00095: DLBC43


title: CD


title: GMA


title: golub-00142: T59_tumor


title: golub-00095: DLBC42_lymphoma


title: golub-00142: N40_normal


title: golub-00142: N17_normal


title: golub-00095: DLBC41


title: GC


title: BH


title: golub-00095: Diffuse large B-cell Lymphoma 39


title: golub-00142: T57_tumor


title: golub-00095: DLBC4


title: golub-00142: T37_tumor


title: MJ

source_name: PBMCs from healthy control

value: healthy control


title: KC


title: JS


title: golub-00142: T21_tumor


title: EW


title: GL


title: TSN


title: golub-00142: N06_normal


title: golub-00095: DLBC35


title: golub-00095: DLBC20_lymphoma


title: golub-00142: N31_normal


title: golub-00095: DLBC34


title: golub-00095: DLBC37_lymphoma


title: golub-00142: N54_normal


title: golub-00142: N11_normal


title: golub-00142: N26_normal


title: golub-00095: DLBC49

value: IPI low intermediate


title: golub-00095: DLBC51_lymphoma

value: B-Lymphocyte


title: golub-00142: N03_normal


title: EWS-FLI1+_differentiated 6 weeks_3

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

hyb_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions

scan_protocol: scanning of HuEx1.0 microarrays was carried out following the manufacturer’s instructions

data_processing:
Signal intensities from core probesets were quantile normalized by robust multichip averaging and transcript expression levels median summarized using Partek Genomics Suite software (Partek, St. Louis, MO).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: differentiating neural crest cells-EWS-FLI1+

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara)

extract_protocol: Qiagen miRNA easy

tag: treatment

value: differentiating neural crest cells


title: EWS-FLI1+_undifferentiated_2

source_name: undifferentiated neural crest cells-EWS-FLI+

value: undifferentiated neural crest cells


title: golub-00142: N62_normal

tag: tissue type


title: golub-00095: DLBC40_lymphoma

value: Lymphoid tissue


title: golub-00095: DLBC21_lymphoma


title: EWS-FLI1+_differentiated 6 weeks_2


title: golub-00095: DLBC3_lymphoma


title: EWS-FLI1+_differentiated 6 weeks_1


title: golub-00095: DLBC28


title: Control vector_differentiated 6 weeks_3

source_name: differentiating neural crest cells-control

value: control


title: golub-00142: N33_normal


title: EWS-FLI1+_undifferentiated_3


title: EWS-FLI1+_undifferentiated_1


title: AK


title: EDE


title: golub-00095: DLBC14_lymphoma


title: golub-00142: N28_normal


title: Control vector_differentiated 6 weeks_1


title: LSZ2 LL37 shLacz1

source_name: LSZ2 NSCLC Cell line

value: Non-small cell cancer cell line


title: golub-00142: T27_tumor


title: golub-00142: N37_normal


title: golub-00095: DLBC19_lymphoma


title: golub-00142: N01_normal


title: golub-00095: DLBC13_lymphoma


title: Control vector_differentiated 6 weeks_2


title: golub-00095: DLBC10_lymphoma


title: Control vector undifferentiated_3

source_name: undifferentiated neural crest cells-control


title: golub-00142: T50_tumor


title: VOCs_Upper_10_12

description:
Methylation in VOCs exposure_24
input samples: Cy3; IP samples: Cy5

hyb_protocol: 2ug of Cy3-labeled reference gDNA and Cy5-labelled IP gDNA were mixed to Hybridization Master Mix containing 10x aCGH blocking agent, 2x HI-RPM Hybridization buffer, Deionized Formamide. On completion of creating mixture, the mixture was reactioned for 3 minutes at 95 and immediately transferred for 37 for 30 minutes following the manufacturers’ instructions, and then 25 ul of 2x Hi-RPM Hybridization Buffer was added to the mixture and hybridized to methylation ChIP/CH3 2x400K Custom array (Agilent Technologies) for 40 hours at 67°C in a rotating Agilent hybridization oven at 20rpm. After hybridization, microarrays were washed 5 minute at room temperature with Agilent Oligo aCGH/ChIP-on-chip Wash buffer1 (Agilent) and 1 minute with 37°C Agilent Oligo aCGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent C scanner (Agilent Technologies) using two color scan(red and green) setting  the protocol AgilentG3_CGH for G3 microarrays slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel are set to Green PMT and Red PMT, the gain of PMT is set to 100%, each).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Version 9.1 software using aCGH protocols and settings and enrichments were obtained by extracting the Cy5 (methylated DNA) signals over Cy3 (input DNA) signals. We performed lowness normalization and applied the “Pre-defined Peak Shape Detection 2.0” algorithm provided within the CH3 Analytics software package from Agilent Technologies. We optimized the peak-shape model and identified the significant methylation events among the DNA methylation array data using default algorithm parameters (with a score threshold of 2.0) and applying the option to repeat the peak-finding calculation through the analysis. Correlations of methylation events with genes through the results were determined by comparing predicted peak centers to transcription start sites as defined by the “refFlat” table of RefSeq genes for Hg19 provided at the UCSC Genome Browser Database.

source_name: Human blood, VOCs Exposure_upper_10:12

label_protocol: Cyanine-3-dUTP (Cy3) labeled reference gDNA  and Cyanine-5-dUTP (Cy5) labeled IP gDNA were parpared from total DNA(1ug;each) using  SureTag DNA Labeling Kit (Agilent Technologies). The labeled gDNA were purified with purification column and 1x TE buffer including SureTag DNA Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Dye incorporation and labeled DNA yield were checked with the NanoDrop (Thermo Fisher Scientific, USA).

extract_protocol: Total genomic DNA(gDNA) was prepared using the EDTA tubes for gDNA isolation (DNeasy Mini Kit; Qiagen) following the manufacturer's recommendations. gDNA yields were assessed using a NanoDrop (Thermo Fisher Scientific, USA), and the qualities of gDNA were confirmed using a agarose gel electrophoresis (2% agarose). gDNA samples were fragmented into 200–300-bp fragments using a sonicator (Sonics & Materials, Inc., USA). 1 μg of fragmented gDNA was immunoprecipitated using a MethylMiner Methylated gDNA Enrichment Kit (Invitrogen, Carlsbad, CA, USA). The fragmented gDNA(reference gDNA) and immunoprecipitated (IP) gDNA were confirmed using polymerase chain reaction (PCR). gDNA samples were amplified using a Whole Genome Amplification 2 Kit (Sigma, St. Louis, MO, USA).

treatment_protocol: Genomic DNA in human blood samples (IRB #AS 14039) divided into three groups: control (unexposed workers; n = 12), short-term exposure (workers exposed to VOCs for less than 10 years; n = 12), and long-term exposure (workers exposed to VOCs for more than 10 years; n = 12) were used after exposure to VOCs

value: whole blood

tag: gender

value: male

tag: age

tag: sample type

value: immunoprecipitated

value: input


title: VOCs_Upper_10_10

description:
Methylation in VOCs exposure_22
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:10


title: VOCs_Upper_10_11

description:
Methylation in VOCs exposure_23
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:11


title: golub-00095: Follicular Lymphoma 9

hyb_protocol: See mage-tab files linked to series entry for additional details

value: Follicular Lymphoma


title: golub-00142: N32_normal

scan_protocol: See mage-tab files linked to series entry for additional details


title: golub-00095: Follicular Lymphoma 8

data_processing: See mage-tab files linked to series entry for additional details


title: golub-00095: Follicular Lymphoma 6

label_protocol: See mage-tab files linked to series entry for additional details


title: VOCs_Upper_10_9

description:
Methylation in VOCs exposure_21
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:9


title: VOCs_Upper_10_8

description:
Methylation in VOCs exposure_20
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:8


title: Control vector undifferentiated_1


title: Control vector undifferentiated_2


title: VOCs_Upper_10_7

description:
Methylation in VOCs exposure_19
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:7


title: golub-00095: Follicular Lymphoma 5


title: golub-00095: Diffuse large B-cell Lymphoma 57

source_name: Diffuse large B-cell Lymphoma

value: Diffuse large B-cell Lymphoma

value: IPI low


title: SARC4

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: CD4+ T cells, SARC subject

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was isolated from frozen CD4+ T cells pellets from ICL and sarcoidosis patients and healthy donnors using miRNAeasy mini kit (Qiagen, Courtaboeuf, France) and quality control was performed using RNA 6000 Nano LabChip kit (Agilent Technologies, Massy, France) and a NanoDrop spectrophotometer (Thermo, Palaiseau, France).

treatment_protocol: Isolation of pure CD4+ T cells from ACD-treated peripheral whole blood from ICL, SARC and Healthy individuals was performed using Whole Blood MicroBeads (Miltenyi Biotec) and the autoMACS device (Miltenyi Biotec). Labeled CD4+ T cells were automatically isolated using the POSSELD2 program (Miltenyi Biotec). Results were regarded as reliable if purity exceeded 90%. After isolation CD4+ T cells pellets were rapidly frozen at   -80°C and then used for RNA extraction.

tag: clinical status

value: SARC subject

value: female


title: SARC8


title: SARC6


title: golub-00095: Diffuse large B-cell Lymphoma 56

extract_protocol: See mage-tab files linked to series entry for additional details

tag: disease state


title: ZIPK siRNA 3

city: Calgary

middle: Patrick

last: Walsh

state: Alberta

address: 3330 Hospital Drive NW

department: Biochemistry & Molecular Biology

country: Canada

institute: University of Calgary

description:
Gene expression data from ZIPK-knockdown cells
CASMC exposed to ZIPK siRNA

hyb_protocol: Labeled cRNA was hybridized to Human Gene 1.0 ST arrays (Affymetrix) at 45 oC for 16 h. The probe arrays were washed and stained on an Affymetrix GeneChip Fluidics-450 following the manufacturer's instructions.

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

data_processing: Array data files were generated with GeneChip® Command Console® Software (AGCC) and statistical significance was determined using GeneSpringTM (Agilent Technologies).  The Fold Change between treatments and control was based on p<0.05 from Student's unpaired t-test.

source_name: Human CASMCs, ZIPK siRNA, 48 h

label_protocol: 250 ng of RNA in each sample with RNA integrity number > 9 was reverse transcribed, amplified and labeled with the Ambion WT Express kit (Ambion).

growth_protocol: Human coronary artery smooth muscle cells (CC-2583, Lonza) were cultured in smooth muscle growth medium (Lonza SmGM-2: CC-3182) containing 5% fetal bovine serum, growth factors (hEGF, insulin and hFGF-β), gentamicin and amphotericin-B at 37 oC in a humidifed incubator with 5% CO2.

extract_protocol: Total RNA was isolated from the cells using the RNeasy Micro kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Human coronary artery smooth muscle cells were transfected with siRNA targeting ROCK1 or ZIPK or with negative control siRNA that does not target any gene product. 48 h later, total RNA was isolated.

value: muscle

value: coronary artery smooth muscle

tag: cell line


title: VOCs_Upper_10_6

description:
Methylation in VOCs exposure_18
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:6


title: SARC5


title: golub-00095: Diffuse large B-cell Lymphoma 23

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

value: B-Lymphocyte

tag: disease stage

tag: individual


title: SARC7


title: ZIPK siRNA 2


title: SARC2


title: SARC3


title: VOCs_Upper_10_5

last: hong

address: Hanyang Univ.,55, Hanyangdaehak-ro, Sangrok-Gu

description:
Methylation in VOCs exposure_17
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:5


title: golub-00095: Diffuse large B-cell lympnoma 50

tag: organism part


title: VOCs_Upper_10_3

description:
Methylation in VOCs exposure_15
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:3


title: ROCK1 siRNA 2

description:
Gene expression data from ROCK1-knockdown cells
CASMC exposed to ROCK1 siRNA

source_name: Human CASMCs, ROCK1 siRNA, 48 h


title: ZIPK siRNA 1


title: VOCs_Upper_10_4

description:
Methylation in VOCs exposure_16
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:4


title: ROCK1 siRNA 3


title: SARC1


title: VOCs_Under_10_12

description:
Methylation in VOCs exposure_12
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:12


title: VOCs_Upper_10_1

description:
Methylation in VOCs exposure_13
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:1


title: ROCK1 siRNA 1


title: golub-00095: Diffuse large B-cell lympnoma 38


title: golub-00095: Diffuse large B-cell lympnoma 36


title: HER

source_name: CD4+ T cells, ICL patients

value: ICL patients


title: Control siRNA 3

description:
Gene expression data from control cells
CASMC exposed to control siRNA

source_name: Human CASMCs, control siRNA, 48 h


title: AUB


title: VOCs_Under_10_11

description:
Methylation in VOCs exposure_11
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:11


title: TAR


title: VOCs_Under_10_9

description:
Methylation in VOCs exposure_9
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:9


title: golub-00095: Diffuse large B-cell lympnoma 33


title: Control siRNA 1


title: CIA


title: QUE


title: VOCs_Under_10_7

description:
Methylation in VOCs exposure_7
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:7


title: VOCs_Upper_10_2

description:
Methylation in VOCs exposure_14
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_upper_10:2


title: golub-00095: Diffuse large B-cell lympnoma 32


title: VOCs_Under_10_8

description:
Methylation in VOCs exposure_8
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:8


title: golub-00095: Diffuse large B-cell lympnoma 31

source_name: Diffuse large B-cell Lymphoma


title: HUVEC shCtrl

description: HUVEC cells with stable control (scramble) shRNA

hyb_protocol: Samples were hybridized to Human Gene 1.0 ST for 16 h at 45ºC and 60 rpm in a GeneChip® Hybridization Oven 640

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: CEL files were analyzed using the oligo package in R/Bioconductor and normalized using RMA

source_name: HUVEC

label_protocol: 200 ng of total RNA were amplified using the Ambion WT Expression Kit (Ambion/Applied Biosystems), labeled using the WT Terminal Labeling Kit (Affymetri

extract_protocol: Total RNA from roughly 10x106 cells was isolated using TRIzol reagent (Invitrogen). Intact total RNA samples were treated with DNase1. All the RNA samples met the following RNA quality- OD260/280 = 2-2.2; OD260/230 ³ 2.0; 28S:18S > 1.0, RIN>7.

tag: shRNA

value: stable control (scramble) shRNA


title: Control siRNA 2


title: SJA


title: VOCs_Under_10_5

description:
Methylation in VOCs exposure_5
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:5


title: VOCs_Under_10_4

description:
Methylation in VOCs exposure_4
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:4


title: golub-00095: Diffuse large B-cell lympnoma 29

value: Lymphoid tissue


title: PUG


title: OLI


title: golub-00095: Diffuse large B-cell lympnoma 26


title: golub-00095: Diffuse large B-cell lympnoma 27


title: VOCs_Under_10_2

description:
Methylation in VOCs exposure_2
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:2


title: VOCs_Under_10_3

description:
Methylation in VOCs exposure_3
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:3


title: golub-00095: Diffuse large B-cell lympnoma 25


title: golub-00095: Diffuse large B-cell lympnoma 24


title: H1-Day8 shAlien

description: late vascular progenitor cells with stable Alien (scramble) shRNA

source_name: Differentiated H1 ESCs

value: stable Alien (scramble) shRNA


title: H1-Day8 shCtrl

description: late vascular progenitor cells with stable control (scramble) shRNA


title: CHR

source_name: CD4+ T cells, Healthy individual

value: Healthy individual


title: MCI


title: golub-00095: Diffuse large B-cell lympnoma 22


title: FNG


title: H1 shTerminator

description: H1 cells with stable Terminator (scramble) shRNA

source_name: H1 ESCs

value: stable Terminator (scramble) shRNA


title: H1 shCtrl

description: H1 cells with stable control (scramble) shRNA


title: VOCs_Under_10_1

description:
Methylation in VOCs exposure_1
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:1

value: whole blood

value: male


title: VNB


title: Control_12

description:
Methylation of control_12
input samples: Cy3; IP samples: Cy5

source_name: Human blood, Control

value: immunoprecipitated

value: input


title: ABI


title: golub-00095: Diffuse large B-cell lympnoma 52

value: Diffuse large B-cell Lymphoma


title: golub-00095: Diffuse large B-cell lympnoma 11

value: IPI low


title: AMC


title: Control_9

description:
Methylation of control_9
input samples: Cy3; IP samples: Cy5


title: MAT


title: golub-00095: Diffuse large B-cell lympnoma 2


title: golub-00095: Diffuse large B-cell Lymphoma 15


title: golub-00095: Diffuse large B-cell lympnoma 18


title: rat_non-basal cells_rep 3

city: laval

first: Daniel

last: Cyr

state: Québec

address: 531 boulevard des Prairies

institute: INRS-IAF

hyb_protocol: Hybridization was done according to Affymetrix protocol using GeneChip WT Plus Reagent kit. 5,5uf of cDNA were hybridized at 45 during 16 hrs. Wash/stain step was performed with GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChipScanner 3000 7G autoloader with an excitation wavelength of 488nm.

data_processing:
Data were RMA-normalized with Expression console and further analyzed with GeneSpring 12.6 software.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

organism: Rattus norvegicus

source_name: epididymal non-basal cells

label_protocol: Biotinylated cRNA was prepared according to the standard affymetrix protocol from 100ng of total RNA.  After purification of cRNA, 15ug were used to generate cDNA.

extract_protocol: extraction of total RNA was performed using Qiagen's kit according to manufacturer's instructions

tag: strain

value: Sprague-Dawley

value: 48 days

value: epididymis

tag: type of cells

value: non-basal


title: HOP

value: female


title: rat_non-basal cells_rep 2


title: rat_basal cells_rep2

source_name: epididymal basal cells

value: basal


title: Control_10

description:
Methylation of control_10
input samples: Cy3; IP samples: Cy5


title: rat_non-basal cells_rep 1


title: Control_8

description:
Methylation of control_8
input samples: Cy3; IP samples: Cy5


title: VOCs_Under_10_10

description:
Methylation in VOCs exposure_10
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:10


title: Control_11

description:
Methylation of control_11
input samples: Cy3; IP samples: Cy5


title: rat_basal cells_rep3


title: golub-00095: Diffuse large B-cell Lymphoma 1

first: Mervi

institute: NCI

tag: cell type

value: B-Lymphocyte


title: golub-00095: Diffuse large B-cell lympnoma 30

value: Lymphoid tissue


title: FAB


title: Control_7

first: jiyoung

institute: hanyang university

description:
Methylation of control_7
input samples: Cy3; IP samples: Cy5

tag: tissue


title: rat_basal cells_rep1


title: Control_6

description:
Methylation of control_6
input samples: Cy3; IP samples: Cy5


title: fine-00037: HF0491_T

status: Public on May 14 2015

source_name: Brain

value: ASTROCYTOMA

value: Brain

tag: tumor grading

value: Grade 2

tag: sample


title: fine-00037: HF1220_T

value: GBM

value: Grade 4


title: fine-00037: HF0120_T


title: fine-00037: HF1185_T

value: Grade 3


title: fine-00037: 03448110_T


title: fine-00037: HF0990_T


title: fine-00037: HF1357_T

value: OLIGODENDROGLIOMA


title: fine-00037: E09801_T


title: VOCs_Under_10_6

description:
Methylation in VOCs exposure_6
input samples: Cy3; IP samples: Cy5

source_name: Human blood, VOCs Exposure_under_10:6

value: whole blood

value: male

value: immunoprecipitated

value: input


title: fine-00037: E09263_T

value: UNKNOWN


title: fine-00037: E09916_T


title: fine-00037: 03512529_T


title: fine-00037: E10433_T


title: fine-00037: E10253_T


title: fine-00037: 03486876_T


title: Control_4

description:
Methylation of control_4
input samples: Cy3; IP samples: Cy5


title: Control_3

description:
Methylation of control_3
input samples: Cy3; IP samples: Cy5


title: fine-00037: E09348_T


title: fine-00037: E09857_T


title: Control_2

description:
Methylation of control_2
input samples: Cy3; IP samples: Cy5


title: fine-00037: E09263B_T


title: Control_5

description:
Methylation of control_5
input samples: Cy3; IP samples: Cy5


title: fine-00037: HF0702_T


title: fine-00037: E09503_T


title: Control_1

description:
Methylation of control_1
input samples: Cy3; IP samples: Cy5


title: fine-00037: HF0975_T


title: fine-00037: E10077_T


title: HUVEC shPunisher

description: HUVEC cells with stable Punisher (scramble) shRNA

value: stable Punisher (scramble) shRNA


title: fine-00037: E09998_T


title: fine-00037: E09825_T


title: fine-00037: 03473067_T


title: fine-00037: E09759_T


title: fine-00037: HF0467_T


title: fine-00037: E10102_T


title: fine-00037: 00518392_T


title: fine-00037: E10596_T


title: fine-00037: HF0435_T


title: fine-00037: HF0332_T


title: fine-00037: 03437691_T


title: fine-00037: 03431774_T


title: fine-00037: E09192_T


title: fine-00037: E10235_T


title: fine-00037: 03484586_T


title: fine-00037: HF0962_T


title: fine-00037: HF0822_T


title: fine-00037: E10540_T


title: fine-00037: HF1057_T


title: fine-00037: HF0137_T


title: fine-00037: E10019_T


title: fine-00037: E09670_T


title: fine-00037: E09892_T


title: fine-00037: E09138_T


title: fine-00037: HF0131_T


title: fine-00037: HF1137_T


title: fine-00037: HF0920_T


title: fine-00037: HF1078_T


title: fine-00037: NT4_T


title: fine-00037: E09921_T


title: fine-00037: MD621233_T


title: fine-00037: HF0828_T


title: fine-00037: E09888_T


title: fine-00037: E10024_T


title: fine-00037: 00860772_T


title: fine-00037: HF1262_T


title: fine-00037: HF0445_T


title: fine-00037: 03425149_T