title: ChIP Input cell cycle CCTS, 80 min, array replicate 1 | array na_22_67

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 80 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: ChIP Input pool

source_name: 80 min


title: H3K4Me3 cell cycle CCTS, 150 min, array replicate 2 | array na_20_21

status: Public on Jan 28 2009

type: genomic

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

country: USA

institute: UMass Medical School

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

hyb_protocol: Amplified, labeled ChIP DNA were mixed, purified by microcon, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 55 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy5/Cy3) were calculated to produce the values given in the data table.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Mid-log H3K4Me3 (unsynchronized)

label_protocol: The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

extract_protocol: DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.

tag: Strain

source_name: 150 min


title: ChIP Input cell cycle CCTS, 10 min, array replicate 1 | array na_22_64

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 10 min


title: T Cells Replicate 1

type: RNA

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

description: Biological replicate 1 of 3. T cell, untreated, purified from reactive tonsils

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump. Hybridization solution consisted of 100 µL of 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. After hybridization, the miRNAs were detected by fluorescence labeling using tag-specific Cy3 and Cy5 dyes

scan_protocol: Scanned on a GenePix 4000B (Molecular Device) laser scanner Images were quantified using Array-Pro image analysis software (Media Cybernetics)

data_processing: Median normalized, background subtracted data was used to calculate the ratio of processed Green signal/processed Red signal, and ratios were then log2 transformed. Probes hsa-miR-377 and hsa-miR-542-5p were excluded due to systematic dye bias, following manufacturer instructions.

molecule: total RNA

organism: Homo sapiens

source_name: Tonsilar T cells

label_protocol: The assay started with 5 µg of total RNA sample. The RNA was size-fractionated using a YM-100 Microcon centrifugal filter (GE Millipore), and the 3′ ends of the small RNAs (<300 nt) were extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in the dual-sample experiments

extract_protocol: Total RNA extracted using mirVana™ miRNA Isolation Kit (Ambion) following manufacturer's instructions

tag: Extracted from reactive tonsils

source_name: FirstChoice® Human Skeletal Muscle Total RNA (Ambion)

tag: Total RNA from healthy human skeletal muscle

tag: Tissue

value: skeletal muscle


title: Naïve B Cells Replicate 4

description: Biological replicate 4 of 4. Naïve B cell, untreated, purified from reactive tonsils

source_name: Tonsilar naïve B cells


title: H3K4Me3 cell cycle CCTS, 120 min, array replicate 2 | array na_20_18

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 120 min


title: H3K4Me3 cell cycle CCTS, 100 min, array replicate 2 | array na_20_24

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 100 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 100 min


title: H3K4Me3 cell cycle CCTS, 70 min, array replicate 2 | array na_20_10

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 70 min


title: H3K4Me3 cell cycle CCTS, 110 min, array replicate 2 | array na_20_13

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 110 min


title: ChIP Input cell cycle CCTS, 70 min, array replicate 1 | array na_22_60

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: Naïve B Cells Replicate 2

description: Biological replicate 2 of 4. Naïve B cell, untreated, purified from reactive tonsils


title: H3K4Me3 cell cycle CCTS, 80 min, array replicate 2 | array na_20_20

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 80 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: H3K4Me3 cell cycle CCTS, 130 min, array replicate 2 | array na_20_09

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 130 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 130 min


title: H3K4Me3 cell cycle CCTS, 90 min, array replicate 2 | array na_21_70

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 90 min


title: ChIP Input cell cycle CCTS, 110 min, array replicate 1 | array na_22_69

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: H3K4Me3 cell cycle CCTS, 30 min, array replicate 2 | array na_21_69

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 30 min


title: H3K4Me3 cell cycle CCTS, 0 min, array replicate 2 | array na_20_19

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested immediately, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 0 min


title: Naïve B Cells Replicate 1

description: Biological replicate 1 of 4. Naïve B cell, untreated, purified from reactive tonsils


title: H3K4Me3 cell cycle CCTS, 20 min, array replicate 2 | array na_20_08

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 20 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 20 min


title: H3K4Me3 cell cycle CCTS, 170 min, array replicate 1 | array na_21_16

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 170 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 170 min


title: H3K4Me3 cell cycle CCTS, 40 min, array replicate 2 | array na_20_16

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 40 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 40 min


title: Memory B Cells Replicate 4

description: Biological replicate 4 of 4. Memory B cell, untreated, purified from reactive tonsils

source_name: Tonsilar memory B cells


title: H3K4Me3 cell cycle CCTS, 50 min, array replicate 2 | array na_20_22

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 50 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: Mid-log H3K4Me3 (unsynchronized)

source_name: 50 min


title: Memory B Cells Replicate 3

description: Biological replicate 3 of 4. Memory B cell, untreated, purified from reactive tonsils


title: Memory B Cells Replicate 2

description: Biological replicate 2 of 4. Memory B cell, untreated, purified from reactive tonsils


title: Memory B Cells Replicate 1

description: Biological replicate 1 of 4. Memory B cell, untreated, purified from reactive tonsils


title: H3K4Me3 cell cycle CCTS, 160 min, array replicate 1 | array na_21_26

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 160 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 160 min


title: T Cells Replicate 2

description: Biological replicate 2 of 3. T cell, untreated, purified from reactive tonsils

source_name: Tonsilar T cells

source_name: FirstChoice® Human Skeletal Muscle Total RNA (Ambion)


title: H3K4Me3 cell cycle CCTS, 10 min, array replicate 2 | array na_20_11

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 10 min


title: Centroblasts Replicate 4

description: Biological replicate 4 of 4. Centroblast, untreated, purified from reactive tonsils

source_name: Tonsilar centroblasts


title: H3K4Me3 cell cycle CCTS, 140 min, array replicate 2 | array na_20_23

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 140 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 140 min


title: H3K4Me3 cell cycle CCTS, 80 min, array replicate 1 | array na_21_23

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 80 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 80 min


title: H3K4Me3 cell cycle CCTS, 150 min, array replicate 1 | array na_21_20

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 150 min


title: H3K4Me3 cell cycle CCTS, 110 min, array replicate 1 | array na_21_18

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 110 min


title: H3K4Me3 cell cycle CCTS, 140 min, array replicate 1 | array na_21_12


title: H3K4Me3 cell cycle CCTS, 100 min, array replicate 1 | array na_21_27

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 100 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 100 min


title: Centroblasts Replicate 3

description: Biological replicate 3 of 4. Centroblast, untreated, purified from reactive tonsils


title: H3K4Me3 cell cycle CCTS, 120 min, array replicate 1 | array na_21_15

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 120 min


title: Naïve B Cells Replicate 3

description: Biological replicate 3 of 4. Naïve B cell, untreated, purified from reactive tonsils

source_name: Tonsilar naïve B cells


title: H3K4Me3 cell cycle CCTS, 90 min, array replicate 1 | array na_21_17

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 90 min


title: H3K4Me3 cell cycle CCTS, 130 min, array replicate 1 | array na_21_22

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 130 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 130 min


title: H3K4Me3 cell cycle CCTS, 70 min, array replicate 1 | array na_21_19

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 70 min


title: H3K4Me3 cell cycle CCTS, 60 min, array replicate 1 | array na_21_13

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 60 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: Mid-log H3K4Me3 (unsynchronized)

source_name: 60 min


title: H3K4Me3 cell cycle CCTS, 50 min, array replicate 1 | array na_21_24

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 50 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 50 min


title: Centroblasts Replicate 2

description: Biological replicate 2 of 4. Centroblast, untreated, purified from reactive tonsils


title: H3K4Me3 cell cycle CCTS, 60 min, array replicate 2 | array na_20_15


title: H3K4Me3 cell cycle CCTS, 30 min, array replicate 1 | array na_21_28

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 30 min


title: Centroblasts Replicate 1

description: Biological replicate 1 of 4. Centroblast, untreated, purified from reactive tonsils

source_name: FirstChoice® Human Skeletal Muscle Total RNA (Ambion)


title: Derriere depleted embryos stage 18

city: New York

first: Ali

middle: H

last: Brivanlou

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: Gene expression data from posterior poles of embryos containing mostly mesoderm

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 50.

label: biotin

organism: Xenopus laevis

source_name: Posterior poles dissected from stage 18 embryos

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

growth_protocol: Embryos were grown to stage 18.

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

treatment_protocol: For Derriere depletion, embryos were injected with 2 nanograms MO oligonucleotide in the lateral side of both dorsal blastomeres at 4-cell stage. Localization was verified by fluoresence for co-injected GFP. At stage 18, dorsal posterior fragments were di

tag: Genotype

tag: Age

value: Neurula Stage 18


title: Sox2 IP from partial iPS cells

city: Los Angeles

first: Kathrin

last: Plath

state: CA

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

hyb_protocol: Hybridization done according to manufacturer's protocol

scan_protocol: Scanning was performed with manufacturer's protocol

data_processing: Data analysis was performed using the Agilent Chip-Analytics software v1.3

organism: Mus musculus

source_name: partial iPS cells - Sox2 IP

label_protocol: Labeling done according to manufacturer's protocol

extract_protocol: Genomic DNA was isolated using standard procedures and an IP was performed for Sox2

tag: Cultured partial iPS cells

source_name: partial iPS cells - no IP

extract_protocol: Genomic DNA was isolated using standard procedures and no IP was performed


title: Sox2 IP from iPS cells

source_name: iPS cells - Sox2 IP

tag: Cultured iPS cells

source_name: iPS cells - no IP


title: wildtype embryos stage 18


title: CFS patient 6, chip A

status: Public on Jan 27 2009

city: Glasgow

first: Suzanne

last: Hagan

state: Lanarkshire

address: Cowcaddens Road

department: Biological Sciences

country: United Kingdom

institute: Glasgow Caledonian University

description: Gene expression data from PBMC.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C onto GeneChip HG-U133A and HG-U133B chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned using the GeneChip Scanner 2500.

data_processing: The raw data were generated with GeneChip Operating Software (GCOS). Data was normalised with Robust Multichip Average (RMA) method using Bioconductor module Affy implemented into the automated FunAlyse pipeline in the Sir Henry Wellcome Functional Genomics Facility. Differential expression was calculated using RankProducts method, separately for each A and B chip.

source_name: PBMC, CFS

extract_protocol: Total RNA was isolated from PBMC pellets following the detailed manufacturer’s protocols in the Promega RNAgents Total Isolation System.

treatment_protocol: Patients with CFS and normal healthy controls underwent venous blood sample collection (prior to 11am) in 2x5ml EDTA tubes. PBMC were isolated immediately and stored within 2 hours of sampling. EDTA-treated whole blood was diluted 1:1 with phosphate-buffered saline (PBS). Two volumes of blood were overlaid onto one volume Histopaque-1077 (Sigma) and centrifuged at 20oC, 500g for 30 min. The PBMC interfaces were washed twice with PBS and the pellets were re-suspended in PBS. Aliquots were counted and dry pellets (2x105 cells) were stored under liquid nitrogen.

tag: Male, post-infectious CFS patient


title: CFS patient 8, chip A

description: Gene expression data from PBMC.


title: CFS patient 9, chip A

description: Gene expression data from PBMC.


title: CFS patient 7, chip A

description: Gene expression data from PBMC.


title: Sox2 IP from ES cells

source_name: ES cells - Sox2 IP

tag: Cultured ES cells

source_name: ES cells - no IP


title: CFS patient 5, chip A

description: Gene expression data from PBMC.


title: CFS patient 4, chip A

description: Gene expression data from PBMC.


title: Oct4 IP from partial iPS cells

source_name: partial iPS cells - Oct4 IP

extract_protocol: Genomic DNA was isolated using standard procedures and an IP was performed for Oct4


title: H3K4Me3 cell cycle CCTS, 10 min, array replicate 1 | array na_21_21

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 10 min


title: H3K4Me3 cell cycle CCTS, 20 min, array replicate 1 | array na_21_25

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 20 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 20 min


title: CFS patient 3, chip A

description: Gene expression data from PBMC.


title: H3K4Me3 cell cycle CCTS, 0 min, array replicate 1 | array na_21_14

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested immediately, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 0 min


title: control patient 7, chip A

description: Gene expression data from PBMC.

source_name: PBMC, control

tag: Male, healthy normal control


title: CFS patient 2, chip A

description: Gene expression data from PBMC.


title: control patient 5, chip A

description: Gene expression data from PBMC.


title: control patient 6, chip A

description: Gene expression data from PBMC.


title: control patient 8, chip A

description: Gene expression data from PBMC.


title: control patient 2, chip A

description: Gene expression data from PBMC.


title: control patient 3, chip A

description: Gene expression data from PBMC.


title: miR-124 transfection AGO2-IP RNA, biological replicate 1, technical replicate 2

first: Markus

last: Landthaler

description: Gene expression data from total RNA AGO2-immunoprecipitate of miR-124-transfected cells

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

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

data_processing: CEL files were imported into R / BioConductor using the affy package. The raw intensities were corrected using gcRMA. The 18 arrays were finally quantile-normalized.

source_name: miR-124 transfection 1, AGO2-IP total RNA 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle Eukaryotic Target Labeling Assay protocol from total RNA.

growth_protocol: HEK293 cells were grown in DMEM suppl. with FBS and 2mM Glutamine

extract_protocol: After proteinase K treatment extraction of total RNA was performed using Trizol.

treatment_protocol: FLAG/HA-AGO2 was immunoprecipitated with anti-FLAG M2 agarose

tag: FLPin HEK 293 cells stably transfected with FLAG/HA-AGO2


title: miR-7 transfection AGO2-IP RNA, biological replicate 2, technical replicate 1

description: Gene expression data from total RNA AGO2-immunoprecipitate of miR-7-transfected cells

source_name: miR-7 transfection 2, AGO2-IP total RNA 1


title: miR-7 transfection AGO2-IP RNA, biological replicate 2, technical replicate 2

source_name: miR-7 transfection 2, AGO2-IP total RNA 2


title: miR-124 transfection AGO2-IP RNA, biological replicate 2, technical replicate 2

source_name: miR-124 transfection 2, AGO2-IP total RNA 2


title: miR-124 transfection AGO2-IP RNA, biological replicate 1, technical replicate 1

source_name: miR-124 transfection 1, AGO2-IP total RNA 1


title: miR-124 transfection lysate RNA, biological replicate 2

description: Gene expression data from total RNA of mock-transfected cells

source_name: miR-124 transfection 2, total RNA


title: miR-124 transfection AGO2-IP RNA, biological replicate 2, technical replicate 1

source_name: miR-124 transfection 2, AGO2-IP total RNA 1


title: miR-124 transfection lysate RNA, biological replicate 1

source_name: miR-124 transfection 1, total RNA


title: CFS patient 9, chip B

description: Gene expression data from PBMC.


title: Klf4 IP from partial iPS cells

source_name: partial iPS cells - Klf4 IP

extract_protocol: Genomic DNA was isolated using standard procedures and an IP was performed for Klf4

source_name: partial iPS cells - no IP


title: Klf4 IP from ES cells

source_name: ES cells - Klf4 IP


title: CFS patient 8, chip B

description: Gene expression data from PBMC.

source_name: PBMC, CFS


title: miR-7 transfection AGO2-IP RNA, biological replicate 1, technical replicate 2

source_name: miR-7 transfection 1, AGO2-IP total RNA 2


title: CFS patient 7, chip B

description: Gene expression data from PBMC.


title: miR-7 transfection lysate RNA, biological replicate 2

source_name: miR-7 transfection 2, total RNA


title: miR-7 transfection AGO2-IP RNA, biological replicate 1, technical replicate 1

source_name: miR-7 transfection 1, AGO2-IP total RNA 1


title: miR-7 transfection lysate RNA, biological replicate 1

source_name: miR-7 transfection 1, total RNA


title: MOCK transfection lysate RNA, biological replicate 2

source_name: Mock transfection 2, total RNA


title: caco_gamma4

city: Marseille cedex 05

first: Jean-Francois

last: Landrier

address: 27 Bd Jean Moulin

department: AlimH

country: France

institute: INRA

description:
mixed micelles (control) cyanin 3
gamma tocopherol cyanin 5

hyb_protocol: Agilent hybridization protocol

scan_protocol: Agilent scan protocol

data_processing: genespring GX 7.1

source_name: control

label_protocol: Agilent protocol

extract_protocol: trizol

treatment_protocol: cells were incubated with mixed micelles (control) for 24h

tag: caco-2 cells teated with mixed micelles (control) for 24h

source_name: gamma

treatment_protocol: cells were incubated with mixed micelles enriched in gamma tocopherol for 24h

tag: caco-2 cells treated with mixed micelles enriched in gamma tocopherol for 24h


title: MOCK transfection AGO2-IP RNA, biological replicate 1, technical replicate 2

description: Gene expression data from total RNA AGO2-immunoprecipitate of mock-transfected cells

source_name: Mock transfection 1, AGO2-IP total RNA 2


title: CFS patient 5, chip B

description: Gene expression data from PBMC.


title: CFS patient 4, chip B

description: Gene expression data from PBMC.


title: MOCK transfection AGO2-IP RNA, biological replicate 1, technical replicate 1

source_name: Mock transfection 1, AGO2-IP total RNA 1


title: MOCK transfection AGO2-IP RNA, biological replicate 2, technical replicate 1

source_name: Mock transfection 2, AGO2-IP total RNA 1


title: H3K27me3 IP from partial iPS cells

source_name: partial iPS cells - H3K27me3 IP

extract_protocol: Genomic DNA was isolated using standard procedures and an IP was performed for H3K27me3


title: CFS patient 2, chip B

description: Gene expression data from PBMC.


title: Oct4 IP from ES cells

source_name: ES cells - Oct4 IP

tag: Cultured ES Cells

source_name: ES cells - no IP


title: c-Myc IP from partial iPS cells

source_name: partial iPS cells - c-Myc IP

extract_protocol: Genomic DNA was isolated using standard procedures and an IP was performed for c-Myc


title: H3K4me3 IP from partial iPS cells

source_name: partial iPS cells - H3K4me3 IP

extract_protocol: Genomic DNA was isolated using standard procedures and an IP performed for H3K4me3

source_name: partial iPS cells - no IP


title: CFS patient 3, chip B

description: Gene expression data from PBMC.

source_name: PBMC, CFS


title: caco_alpha4

description:
mixed micelles (control) cyanin 3
alpha tocopherol cyanin 5

source_name: alpha

treatment_protocol: cells were incubated with mixed micelles enriched in alpha tocopherol for 24h

tag: caco-2 cells treated with mixed micelles enriched in alpha tocopherol for 24h


title: MOCK transfection lysate RNA, biological replicate 1

source_name: Mock transfection 1, total RNA


title: Sporulating mycelia, replicate 1

city: Riverside

first: Howard

middle: S

last: Judelson

address: Boyce Hall

department: Plant Pathology

institute: University of California

description: Culture was grown for 10 days on a polycarbonate membrane laid on rye-sucrose agar (1.5%) at 18C.   By this time the entire plate was sporulating.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

label: Biotin

organism: Phytophthora infestans

source_name: mycelia, 10 days old, sporulating

label_protocol: standard Affymetrix procedures

extract_protocol:
RNA was extracted by grinding in liquid nitrogen followed by use of the RNAEasy
Plant Mini kit (Qiagen, Valencia, CA USA) according the manufacturer's instructions.

tag: mycelia, 10 days old, sporulating, strain 88069.


title: control patient 8, chip B

description: Gene expression data from PBMC.

source_name: PBMC, control


title: Nanog IP from ES cells

source_name: ES cells - Nanog IP

extract_protocol: Genomic DNA was isolated using standard procedures and an IP was performed for Nanog


title: caco_alpha3

description:
mixed micelles (control) cyanin 5
alpha tocopherol cyanin 3

source_name: control

tag: caco-2 cells treated with mixed micelles (control) for 24h

tag: caco-2 cells treated with alpha tocopherol in mixed micelles for 24h


title: Sporulating mycelia, replicate 2

source_name: Sporulating mycelia, 10 day culture.

tag: Sporulating mycelia, 10 day culture.


title: control patient 7, chip B

description: Gene expression data from PBMC.


title: CFS patient 6, chip B

description: Gene expression data from PBMC.


title: caco_alpha2

source_name: alpha tocopherol

tag: caco-2 treated with alpha tocopherol in mixed micelles for 24h


title: c-Myc IP from iPS cells

source_name: iPS cells - c-Myc IP

source_name: iPS cells - no IP


title: Klf4 IP from iPS cells

source_name: iPS cells - Klf4 IP


title: Early sporulation sample, 20 hr, replicate 2

description: Mycelia from 4 day rye-sucrose broth culture (nonsporulating) was lifted out of the liquid, placed on a 1.5% agar rye-sucrose plate, and incubated at 18C in the dark for 18-24 hr.  This treatment stimulates sporulation, as sporulation is inhibited during submerged growth.

tag: Mycelia induced to sporulate for 18-24 hr.  Strain 88069.


title: Early sporulation sample, 20 hr, replicate 1

description: Mycelia from 4 day rye-sucrose broth culture (nonsporulating) was lifted out of the liquid, placed on a 1.5% agar rye-sucrose plate, and incubated at 18C for 18-24 hr.  This treatment stimulates sporulation.

source_name: mycelia induced to sporulate

tag: Induced to sporulate for 18 to 24 hr.  Strain 88069.


title: Oct4 IP from iPS cells

source_name: iPS cells - Oct4 IP


title: Nonsporulating mycelia from aerial culture, replicate 2

description: Mycelia from 4 day culture (nonsporulating) grown on rye-sucrose agar overlaid with polycarbonate membrane, inoculated on top of membrane, at 18C in the dark.

source_name: P. infestans, wild type, aerial, nonsporulating, 3-4 days

tag: Wild type mycelia, nonsporulating, aerial, strain 88069.


title: control patient 1, chip B

description: Gene expression data from PBMC.


title: control patient 2, chip B

description: Gene expression data from PBMC.


title: control patient 6, chip B

description: Gene expression data from PBMC.


title: control patient 3, chip B

description: Gene expression data from PBMC.


title: Cdc14-silenced transformant, replicate 2

description: Mycelia grown on rye-sucrose agar, 10 days

source_name: Cdc14-silenced transformant, strain B2, mycelia


title: Nonsporulating mycelia from aerial culture, replicate 1

description: Mycelia from 4 day culture (nonsporulating) was grown on rye-sucrose agar overlaid with polycarbonate membrane, inoculated on top of membrane, at 18C in the dark.

source_name: nonsporulating mycelia, wild type P. infestans

tag: 4 day mycelia, strain 88069


title: caco_gamma1

description:
mixed micelles (control) cyanin 5
gamma tocopherol cyanin 3

source_name: gamma tocopherol

tag: caco-2 cells treated with gamma tocopherol in mixed micelles for 24h


title: MOCK transfection AGO2-IP RNA, biological replicate 2, technical replicate 2

source_name: Mock transfection 2, AGO2-IP total RNA 2


title: control patient 5, chip B

description: Gene expression data from PBMC.


title: caco_alpha1

description:
mixed micelles cyanin 3
alpha tocopherol cyanin 5


title: Cdc14-silenced transformant, replicate 1

description: Mycelia grown on rye-sucrose agar, 10 days, in dark at 18C.  In wild type this would normally stimulate sporulation.  However, in this strain sporulation is arrested due to the Cdc14 defect.

source_name: Cdc14-silenced transformant A1

tag: Generated by sense-mediated suppression of Cdc14 gene using protoplast transformation method.


title: MIFS_case_8

status: Public on Jan 26 2009

city: Lund

first: Karolin

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

description: Genome-wide gene expression profiling of MIFS using the Affymetrix GeneChip® Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA, USA)

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA)

scan_protocol: Arrays were scanned in a GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA)

data_processing: Image analysis was performed using GeneChip® Operating Software (GCOS, Affymetrix). Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console™ version 1.0 software.

source_name: Case 8

label_protocol: GeneChip® WT Terminal Labelling Kit (Affymetrix Inc, Santa Clara, CA, USA)

extract_protocol:
Total RNA was extracted from frozen tumor biopsies using Trizol reagent  (Invitrogen, Carlsbad, CA, USA) and RNeasy (Qiagen, Valencia, CA, USA) according to the manufacturers' instructions.
RNA quality and concentration were measured using an Agilent 2100 bioanalyzer and Nanodrop ND-1000, respectively. cDNA was generated with the GeneChip® Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix) using 300 ng total RNA.  Amplified cDNA was fragmented and end labeled using the GeneChip® WT Terminal Labelling Kit (Affymetrix).  Subsequently, the fragmented and biotinylated cDNA was hybridized to the GeneChip® Human Gene 1.0 ST Arrays (Affymetrix). The arrays were washed and stained on a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommendations.

tag: RNA from fresh frozen tumor biopsy


title: caco_gamma3

tag: caco-2 cells were treated with mixed micelles (control) for 24h

source_name: gamma

tag: caco-2 cells were teated with mixed micelles enriched with gamma tocopherol for 24h


title: MIFS_case_5

source_name: Case 5


title: MIFS_case_control

source_name: Case control


title: MIFS_case_2

source_name: Case 2


title: MIFS_case_6

source_name: Case 6


title: MIFS_case_1

source_name: Case 1


title: MIFS_case_8

description: 32k BAC array CGH data on MIFS

hyb_protocol: Arrays were hybridized and washed as described in Heidenblad et al. (Oncogene 2006;25:7106-16)

scan_protocol: Arrays were scanned in Agilent Microarray scanner

data_processing: Primary data were collected using the GenePix Pro 4.0 software, and the quantified data matrix was deposited into the web-based database BioArray Software Environment (BASE), where filtering and pin-based lowess normalization were performed.

label_protocol: BioPrime array CGH labeling module (Invitrogen, Carlsbad, CA, USA)

extract_protocol: DNeasy Tissue Kit (Qiagen, Valencia, CA, USA)

tag: Genomic DNA from fresh frozen tumor biopsy

source_name: Promega reference male DNA (Promega, Madison, WI, USA)

tag: Pooled lymphoblastoid genomic DNA from ten male individuals


title: MIFS_case_6

description: 32k BAC array CGH data on MIFS


title: MIFS_case_7

description: 32k BAC array CGH data on MIFS

source_name: Case 7


title: caco_gamma2

source_name: control


title: MIFS_case_1

description: 32k BAC array CGH data on MIFS


title: c-Myc IP from ES cells

source_name: ES cells - c-Myc IP

tag: Cultured ES cells

source_name: ES cells - no IP


title: corpusluteum_A+LH+TRL+R5020_Rep4

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

description: Treated

hyb_protocol: Labeled target is fragmented at 95o C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Ten ug of target is hybridized with the GeneChip Rhesus Macaque Genome array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: The distribution of fluorescent material on the processed array is determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade. Image inspection is performed manually immediately following each scan. All array scanning and data processing on the Affymetrix system is performed with GeneChip Operating System (GCOS) software.

data_processing: The probe-level Cel file is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioB, BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged. Using MAS 5.0, array data is globally scaled to auniform, average target intensity for all assays prior to further analysis.

organism: Macaca mulatta

source_name: Day 12 corpus luteum, Anide + LH + TRL + R5020 treated

label_protocol: Messenger RNA is amplified and labeled from 2 ug of total RNA in two steps. In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix). In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix.). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

extract_protocol: Invitrogen TRIzol Plus RNA Purification Kit

treatment_protocol: See 'Young KA, Stouffer RL. Gonadotropin and steroid regulation of matrix metalloproteinases and their endogenous tissue inhibitors in the developed corpus luteum of the rhesus monkey during the menstrual cycle. Biol Reprod. 2004 Jan;70(1):244-52 (PMID: 13679308)'

tag: Female, Antide + LH + TRL + R5020 treated days 9-11 of luteal phase, CL collected day 12


title: corpusluteum_A+LH+TRL+R5020_Rep6

description: Treated


title: corpusluteum_A+LH+TRL+R5020_Rep2

description: Treated


title: corpusluteum_A+LH+TRL+R5020_Rep3

description: Treated


title: corpusluteum_A+LH+TRL_Rep3

description: Treated

source_name: Day 12 corpus luteum, Anide + LH + TRL treated

tag: Female, Antide + LH + TRL treated days 9-11 of luteal phase, CL collected day 12


title: corpusluetum_A+LH_Rep3

description: Treated

source_name: Day 12 corpus luteum, Anide + LH treated

tag: Female, Antide + LH treated days 9-11 of luteal phase, CL collected day 12


title: Rat_Kidney_Medullary_Thick_Ascending_Limb_2

city: Taipei

first: Ming-Jiun

last: Yu

address: Rm 816, No. 1 Ren-Ai Road Section 1

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University College of Medicine

description: Profiling of gene expression in mTAL cell of rat

hyb_protocol: Labeled cRNA were hybridized to Rat 230 2.0 Array in Affymetrix Hybridization Oven 640 and washed in GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols.

scan_protocol: Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recomended protocols

data_processing: Affymetrix default parameters, Algorithm: ExpressionStat 5.0

organism: Rattus norvegicus

source_name: Medullary thick ascending limb of Henle of rat

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

extract_protocol: Total RNA were extracted by using Trizol reagent according to manufacturer's protocols.

treatment_protocol: Rats were injected with 250 u of heparin and 1 mg of furosemide intraperitoneum 30 minutes before decapitation. Retrograde perfusion through abdominal aorta with 10 ml of ice cold PBS and 10 ml of pre-warmed collagenase solution (1 mg/ml collagenase, 0.5 mg/ml hyarulonidase). Outer medulla were excised and digested in collagenase solution for 60 minutes with 95% O2 and 5% CO2. mTAL were separate from other tissue by gradient centrifugation in 33.3% Percoll solution.

tag: Strain

value: Sprague-Dawley

tag: Sex

value: Male

tag: Age

value: 7-8 weeks old

tag: Tissue

value: Medullary thick ascending limb of Henle’s


title: corpusluteum_A+LH+TRL+R5020_Rep1

description: Treated


title: corpusluetum_Control_Rep1

description: Control

source_name: Day 12 corpus luteum, untreated

tag: Female, No treatment, CL collected day 12


title: Rat_Kidney_Medullary_Thick_Ascending_Limb_3


title: corpusluteum_A+LH+TRL_Rep2

description: Treated


title: corpusluetum_A+LH_Rep2

description: Treated


title: corpusluetum_Control_Rep5

description: Control


title: Rat_Kidney_Medullary_Thick_Ascending_Limb_1

source_name: Medullary thick ascending limb of Henle’s of rat


title: corpusluetum_Antide_Rep1

description: Treated

source_name: Day 12 corpus luteum, Anide treated

tag: Female, Antide treated days 9-11 of luteal phase, CL collected day 12


title: corpusluetum_Antide_Rep4

description: Treated


title: corpusluetum_Control_Rep2

description: Control


title: corpusluetum_Control_Rep4

description: Control


title: corpusluetum_A+LH_Rep4

description: Treated


title: Rat_Kidney_Proximal_Tubule_2

description: Profiling of gene expression in proximal tubule cell of rat

source_name: Proximal tubules of rat

treatment_protocol: Rats were injected with 250 u of heparin intraperitoneum 30 minutes before decapitation. Retrograde perfusion through abdominal aorta with 10 ml of ice cold PBS and 10 ml of pre-warmed collagenase solution (2 mg/ml collagenase). Renal cortexes were excised and digested in collagenase solution for 20 minutes. Proximal tubules were separate from other tissue by gradient centrifugation in 42.5% Percoll solution.

value: Proximal tubules


title: corpusluteum_A+LH+TRL_Rep1

description: Treated


title: Rat_Kidney_Proximal_Tubule_3


title: corpusluetum_Antide_Rep3

description: Treated


title: corpusluetum_Antide_Rep5

description: Treated


title: corpusluteum_A+LH+TRL_Rep4

description: Treated


title: corpusluetum_A+LH_Rep1

description: Treated


title: corpusluetum_Antide_Rep2

description: Treated


title: Pancreatic Islets_18h culture_30 mmol/l glucose_rep1

city: Brussels

first: Jean-Christophe

last: Jonas

address: Av. Hippocrate, 55

department: Physiology and Pharmacology

country: Belgium

institute: UCL, Faculty of Medicine

description: Before the experiment, the islets were precultured for 1 week in serum-free RPMI medium containing 5 g/l BSA and 10 mmol/l glucose

hyb_protocol: Fragmented cRNA was hybridized 16h at 45°C to a Rat Genome 230 2.0 array.

scan_protocol: After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Raw data were analyzed using the Affymetrix GCOS software. Signal intensities were scaled using the global scaling method of the statistical expression algorithm taking 150 as target intensity value. Scaling factors were less than 3 times different from each other in all used arrays.

source_name: Pancreatic islets, 18h culture, 30 mmol/l glucose

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

growth_protocol: After isolation, the islets were precultured for 1 week in serum-free RPMI medium containing 5 g/l BSA and 10 mmol/l glucose. The medium was renewed after 24h, then every 48h.

extract_protocol: Islet total RNA was extracted using the Absolutely microprep kit (Stratagene, city, CA, USA) following manufacturer’s instructions.

treatment_protocol: After preculture, the islets were cultured 18h in serum-free RPMI medium containing 5 g/l BSA and 2, 5, 10 or 30 mmol/l glucose (1000 islets per condition).

value: Wistar (male)

tag: Weight


title: Pancreatic Islets_18h culture_10 mmol/l glucose_rep1

source_name: Pancreatic islets, 18h culture, 10 mmol/l glucose


title: Pancreatic Islets_18h culture_5 mmol/l glucose_rep2

source_name: Pancreatic islets, 18h culture, 5 mmol/l glucose


title: Pancreatic Islets_18h culture_30 mmol/l glucose_rep2


title: Pancreatic Islets_18h culture_10 mmol/l glucose_rep4


title: Rat_Kidney_Proximal_Tubule_1


title: Pancreatic Islets_18h culture_5 mmol/l glucose_rep3


title: Pancreatic Islets_18h culture_10 mmol/l glucose_rep3


title: Pancreatic Islets_18h culture_2 mmol/l glucose_rep4

source_name: Pancreatic islets, 18h culture, 2 mmol/l glucose


title: Pancreatic Islets_18h culture_5 mmol/l glucose_rep1


title: Pancreatic Islets_18h culture_10 mmol/l glucose_rep2


title: Pancreatic Islets_18h culture_2 mmol/l glucose_rep3


title: Pancreatic Islets_18h culture_2 mmol/l glucose_rep2


title: Pancreatic Islets_18h culture_30 mmol/l glucose_rep3


title: Pancreatic Islets_18h culture_5 mmol/l glucose_rep4


title: Pancreatic Islets_18h culture_2 mmol/l glucose_rep1


title: H3K4Me3 cell cycle CCTS, 40 min, array replicate 1 | array na_21_11

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 40 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: Mid-log H3K4Me3 (unsynchronized)

extract_protocol: DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.

source_name: 40 min


title: K562_IP-PABP_4

status: Public on Jan 24 2009

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Standard Affymetrix WT protocol for Exon arrays

data_processing: CEL files for each sample were processed using the apt-probeset-summarize binary provided by Affymetrix. One qualitative (DABG) and two quantitative (RMA, PLIER) measures of expression were derived for each gene-level metaprobeset on the chips using command line parameters (see Workflow PDF linked to GSE14535 for full details).

source_name: PABP-associated RNA

extract_protocol: RNA from Immunoprecipitated samples was isolated using phenol-chloroform and cleaned up on Qiagen Rneasy columns before QC on a bioanlyzer and a nanodrop spectrophotometer


title: K562_IP-PABP_2

scan_protocol: Standard Affymetrix WT protocol for Exon arrays


title: K562_IP-PABP_1

description: ST_10_PABP4_K562_IP07222008_08252008.CEL

label_protocol: Standard Affymetrix WT protocol for Exon arrays


title: K562_IP-Imp_3

source_name: Imp-associated RNA


title: K562_Input_7

source_name: Input RNA


title: K562_IP-Imp_1


title: K562_IP-PABP_3


title: K562_IP-Imp_2


title: K562_Input_8


title: K562_IP-HuR_1

description: ST_8_HUR_K562_LuizIP08012008_08252008.CEL

source_name: HuR-associated RNA


title: K562_IP-HuR_2

description: ST_11_HUR_K562_TD_IP07222008_08252008.CEL


title: GM12878_IP-PABP_3


title: GM12878_IP-PABP_1


title: K562_Input_5


title: K562_Input_4


title: GM12878_Input_4


title: GM12878_Input_6


title: GM12878_IP-HuR_2


title: GM12878_IP-PABP_2


title: K562_Input_6


title: 2006-12-22 Metabolomics time course (a) Control 3D7 time point 48 (hr)

city: Princeton

first: Kellen

last: Olszewski

state: NJ

address: Carl Icahn Lab

department: Molecular Biology

institute: Princeton University

hyb_protocol: Hybridization date : 1/9/07 Temperature : 63 Hyb buffer : "3X SSC, 0.2% SDS,25mM HEPES, 5 ug poly A RNA" Hyb volume : 27.5 uL Cover slip type : 22 X 25 glass Duration : 16 hrs

scan_protocol: Scan Power : 100 PMT Volts : 376 Pixel Size : 5 Laser on time : 32066 Laser Power : 2.42 Scan Date : 2007-01-10 Scan Temperature : 25.00 Scan Time : 16:44:04 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01  [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.00
Datafile type : GenePix Results 3
Image Origin : 1240, 5080

organism: Plasmodium falciparum

source_name: 3D7 Reference pool

label_protocol:
Amount of extract labeled : 12 micrograms
Type of label : Cy3

extract_protocol: Extraction method : Trizol

treatment_protocol: Time : 48 hour mixed stage

tag: Species

value: Plasmodium falciparum (3D7)

source_name: 3D7 time point 48 (hr)

label_protocol:
Amount of extract labeled : 12 micrograms
Type of label : Cy5

treatment_protocol: Time : 48 Hour

tag: Strain Name


title: GM12878_IP-G10_1

source_name: G10-associated RNA


title: GM12878_IP-HuR_3


title: 2006-12-22 Metabolomics time course (a) Control 3D7 time point 40 (hr)

scan_protocol: Scan Power : 100 PMT Volts : 411 Pixel Size : 5 Laser on time : 32048 Laser Power : 2.47 Scan Date : 2007-01-10 Scan Temperature : 24.94 Scan Time : 16:26:18 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01  [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.00
Datafile type : GenePix Results 3
Image Origin : 1240, 5320

source_name: 3D7 time point 40 (hr)

treatment_protocol: Time : 40 Hour


title: GM12878_Input_3


title: 10 mM B(OH)3 treatment (10B) - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Eight day old aseptically grown seedlings were subjected to 10 mM (milimolar) boric acid (B(OH)3) treatment (10B) for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: leaf: 10 mM B(OH)3 treatment (10B)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Aseptical germination and growth on half strength Hoagland’s solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days and transfer to sterile hydroponic half strength Hoagland’s solution containing 10 milimolar boric acid (B(OH)3) (10B treatment)  Environmental Conditions:  23±2ºC, 16 h light (400 µmol m–2 s–1) and 8 h dark photo-cycle, 70% relative humidity

extract_protocol: TRIzol Reagent (Qiagen) and sodium acetate-ethanol precipitation

tag: cultivar Hamidiye (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007098 LP.02 two leaves visible (Development Stage); 13 days old (Age); hydroponic 1/2 strength hoagland's solution (Growth Media).


title: K562_IP-HuR_3


title: 2006-12-22 Metabolomics time course (a) Control 3D7 time point 32 (hr)

hyb_protocol: Hybridization date : 5/22/07 Temperature : 63 Hyb buffer : "3X SSC, 0.2% SDS,25mM HEPES, 5 ug poly A RNA" Hyb volume : 27.5 uL Cover slip type : 22 X 25 glass Duration : 16 hrs

scan_protocol: Scan Power : 100 PMT Volts : 378 Pixel Size : 5 Laser on time : 32032 Laser Power : 2.43 Scan Date : 2007-01-10 Scan Temperature : 25.00 Scan Time : 16:10:12 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01  [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: 3D7 time point 32 (hr)

treatment_protocol: Time : 32 Hour


title: 2006-12-22 Metabolomics time course (a) Control 3D7 time point 24 (hr)

scan_protocol: Scan Power : 100 PMT Volts : 392 Pixel Size : 5 Laser on time : 38421 Laser Power : 2.34 Scan Date : 2007-05-23 Scan Temperature : 24.06 Scan Time : 16:05:25 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01  [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.00
Datafile type : GenePix Results 3
Image Origin : 1640, 5280

source_name: 3D7 time point 24 (hr)

treatment_protocol: Time : 16 Hour


title: K562_Input_3


title: GM12878_IP-HuR_1


title: GM12878_Input_5


title: 5 mM B(OH)3 treatment (5B) - rep3

description: Eight day old aseptically grown seedlings were subjected to 5 mM (milimolar) boric acid (B(OH)3) treatment (5B) for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues

source_name: leaf: 5 mM B(OH)3 treatment (5B)

growth_protocol: Growth Description:  Aseptical germination and growth on half strength Hoagland’s solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days and transfer to sterile hydroponic half strength Hoagland’s solution containing 5 milimolar boric acid (B(OH)3) (5B treatment)  Environmental Conditions:  23±2ºC, 16 h light (400 µmol m–2 s–1) and 8 h dark photo-cycle, 70% relative humidity


title: 5 mM B(OH)3 treatment (5B) - rep2


title: 10 mM B(OH)3 treatment (10B) - rep1


title: K562_IP-G10_2


title: 10 mM B(OH)3 treatment (10B) - rep2


title: 5 mM B(OH)3 treatment (5B) - rep1


title: Control (C) - rep3

description: Eight day old aseptically grown seedlings were subjected to 10 uM (micromolar) boric acid (B(OH)3) treatment (control) for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues

source_name: leaf: Control (C)

growth_protocol: Growth Description:  Aseptical germination and growth on half strength Hoagland’s solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days and transfer to sterile hydroponic half strength Hoagland’s solution containing 10 micromolar boric acid (B(OH)3) (control)  Environmental Conditions:  23±2ºC, 16 h light (400 µmol m–2 s–1) and 8 h dark photo-cycle, 70% relative humidity


title: 2006-12-22 Metabolomics time course Control 3D7 time point 8 (hr)

scan_protocol: Scan Power : 100 PMT Volts : 541 Pixel Size : 5 Laser on time : 31976 Laser Power : 2.41 Scan Date : 2007-01-10 Scan Temperature : 24.38 Scan Time : 15:13:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01  [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.00
Datafile type : GenePix Results 3
Image Origin : 1240, 5440

source_name: 3D7 time point 8 (hr)

treatment_protocol: Time : 8 Hour


title: K562_IP-G10_1


title: 2006-12-22 Metabolomics time course Control 3D7 time point 16 (hr)

scan_protocol: Scan Power : 100 PMT Volts : 474 Pixel Size : 5 Laser on time : 31994 Laser Power : 2.39 Scan Date : 2007-01-10 Scan Temperature : 24.75 Scan Time : 15:32:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01  [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.00
Datafile type : GenePix Results 3
Image Origin : 1440, 5720

source_name: 3D7 time point 16 (hr)

treatment_protocol: Time : 24 Hour


title: 2006-12-22 Metabolomics time course Control 3D7 time point 0 (hr)

scan_protocol: Scan Power : 100 PMT Volts : 484 Pixel Size : 5 Laser on time : 31961 Laser Power : 2.39 Scan Date : 2007-01-10 Scan Temperature : 23.63 Scan Time : 14:58:48 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4200A 01  [111967] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.0.1.00
Datafile type : GenePix Results 3
Image Origin : 1400, 5480

source_name: 3D7 time point 0 (hr)

treatment_protocol: Time : 0 Hour


title: K562_Input_2


title: GM12878_Input_2


title: K562_Input_1


title: CHD7_6_ENCODE_regions_Agilent44K_HG18_2

status: Public on Jan 23 2009

city: Cleveland

first: Mike

middle: Paul

last: Schnetz

state: OH

address: 10900 Eulid Ave

department: Genetics

institute: Case Western Reserve University

hyb_protocol: Samples were hybridized according to Agilent established protocol

scan_protocol: Samples were scanned according to Agilent established protocol

data_processing: Ratios computed and normalized using Agilent feature extraction software package

source_name: CHD7 ChIP in DLD1

label_protocol: Sample was labeled using Enzo Life Sciences labeling kit according to manufacturer's instructions

extract_protocol: Refer to Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis Scacheri PC et al, PLoS Genet. 2006 Apr;2(4):e51. Epub 2006 Apr 7.

treatment_protocol: Immunoprecipitated chromatin

tag: ChIP from DLD1 extract

source_name: Genomic DNA in DLD1

treatment_protocol: No Immunoprecipitation

tag: Isolated DLD1 genomic DNA


title: CHD7_6_ENCODE_regions_Agilent44K_HG18_1


title: CHD7_6_ENCODE_regions_Agilent44K_HG18_3


title: H3K4me2_6_ENCODE_regions_Agilent44K_HG18_1

source_name: H3K4 dimethyl ChIP in DLD1


title: H3K4me1_6_ENCODE_regions_Agilent44K_HG18_1

source_name: H3K4 monomethyl ChIP in DLD1


title: H3K4me3_6_ENCODE_regions_Agilent44K_HG18_1

source_name: H3K4 trimethyl ChIP in DLD1


title: Flag-CHD7_6_ENCODE_regions_Agilent44K_HG18_2

source_name: Flag ChIP in DLD1


title: Flag-CHD7_6_ENCODE_regions_Agilent44K_HG18_3


title: Flag-CHD7_6_ENCODE_regions_Agilent44K_HG18_1


title: Fe(III), Experiment 3, Time point 2

city: Santa Cruz

first: Aaron

middle: E

last: Cozen

address: 1165 High St.

department: Ocean Sciences

institute: University of California, Santa Cruz

hyb_protocol: Spotted microarray slides were hydrated for three minutes in a humidified chamber, snap-dried at 100˚C, covalently linked with 250mJoules in a UV crosslinker (Stratagene), and incubated at 42˚C in a solution of 5X SSC, 1% BSA and 0.1%SDS for 45 minutes prior to hybridization. For each hybridization Cy3-labeled cDNA derived from 5ug of experimental RNA and Cy5-labeled cDNA derived from 5µg reference pool RNA were combined with 1mg/ml herring sperm DNA, 0.38mg/ml yeast tRNA, 4X SSC and 0.5%SDS in a total volume of 55µl, and hybridized for 14 to 18 hours at 60˚C in sealed hybridization chambers. After hybridization slides were washed for two minutes in 0.05%SDS and 0.1X SSC followed by two minutes in 0.05X SSC and dried by room temperature centrifugation at 100X G for eight minutes.

scan_protocol: Slides were scanned at 5µm resolution immediately after washing using a Genepix 4000B microaray scanner (Molecular Devices).

data_processing: Microarray features were analyzed using Genepix 6 software, using median pixel intensities at each of the two channel wavelengths for each spotted feature (Molecular Devices). These values were normalized using the loess function of the open-source Bioconductor package “marray” for the statistical program R (Gentleman, Carey et al. 2004), so that the normalized global and print-tip median log2(Ch1/Ch2) ratio of each array was zero. For each individual array feature the median intensity values of four replicate spots were used for subsequent analyses.

organism: Pyrobaculum aerophilum

source_name: total RNA from P. aerophilum cultures

label_protocol: Aminoallyl-labeled cDNAs were prepared from 5µg of sample RNA using 5µg of random hexamers (3µg/µl) and the Superscript III labeling kit (Invitrogen). These were subsequently labeled with cy3-NHS ester or cy5-NHS ester (GE Healthcare) following the manufacturer’s instructions.

growth_protocol: Cultures of P. aerophilum were grown in media containing (per liter) 10g NaCl, 1.3g (NH4)2SO4, 0.28g KH2PO4, 0.25g MgSO4•7H2O, 1mg NaSeO4, 0.1mg Na2WO4•2H2O, 70mg CaCl2•2H2O, 0.5g yeast extract, 1mg (NH4)2Fe(SO4)2•6H2O, 0.5mg resazurin, and 10ml of a trace element solution. The trace element solution (DSM141) was prepared by combining the following components (per liter) in a 78.5µM solution of nitriloacetic acid adjusted to pH6.5: 3g MgSO4•7H2O, 0.5g MnSO4•H2O, 1g NaCl, 0.1g FeSO4•7H2O, 0.18g CoSO4•7H2O, 0.1g CaCl2•2H2O, 0.18g ZnSO4•7H2O, 0.01g CuSO4•5H2O, 0.02g KAl(SO4)2•12H2O, 0.01g H3BO3, 0.01g Na2MoO4•2H2O, 0.025g NiCl2•6H2O, and 0.0003g NaSeO3•5H2O. The complete media preparation was adjusted to pH 6.8 and sterilized by autoclaving.

extract_protocol: Total RNA was extracted from frozen cell pellets using a polytron tissue homogenizer and Tri reagent (Sigma-Aldrich), following the manufacturer’s instructions. RNA samples were treated with DNase I (Ambion) to remove any residual DNA, re-extracted with Tri-reagent, and normalized to 1µg/µl before proceeding with preparation of cDNA for microarray analysis.

treatment_protocol: Cultures of P. aerophilum were incubated at 96˚C, typically with 200ml of media in 0.5 liter wide mouth bottles under a gas headspace of N2, and shaking at 200rpm. For aerobic cultures, 5% (v/v) of atmospheric air was added to the headspace for a final concentration of approximately 1% O2. Three replicate respiratory induction experiments were performed in which cultures were grown with a 1% O2 gas headspace, followed by amendment with different respiratory substrates when the cultures became anoxic. No reducing agents were used. Depletion of O2 in cultures was monitored by recording changes in the redox-indicator dye resazurin from pink to clear. After depletion of O2 cultures were cooled to ambient temperature, diluted with a 25% volume of fresh growth media and dispensed in 200ml volumes to bottles in an anaerobic chamber. Separate bottles were prepared for collection at each of three time points. Bottles received either 1% (v/v) additions from 1M stocks of NaNO3, Na2HAsO4, or Fe(III)-citrate pH 6, 5% (v/v) of atmospheric air in the gas headspace, or no added electron acceptor in each induction experiment. These were re-equilibrated to growth temperature (96˚C), and after 2.5 hours (T1), 4.5 hours (T2) or 7.5 hours (T3) one bottle from each respiratory condition was collected for RNA preparation. Cells were collected for RNA analysis by centrifugation at 10,000g for 10 minutes. Cell pellets were frozen in liquid N2 and stored at -80˚C.

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with Fe(III) (See "Channel 1 Treatment Protocol"). Time point 2 (T2) samples were collected 4.5 hours after this shift.

label_protocol: Same as Channel 1

growth_protocol: Same as Channel 1

extract_protocol: Same as Channel 1

treatment_protocol: Same as Channel 1, with differences described in "Channel 2 Characteristics"

tag: A reference pool of RNA prepared from 45 cultures of P. aerophilum grown under aerobic conditions, then shifted to anoxic growth with different terminal electron acceptors, and collected at three time points (See "Channel 1 Treatment Protocol" and "Channel 1 Growth Protocol"). RNA from each of the 45 different samples used individually for Channel 1 were combined in equal amounts to create the reference pool used in Channel 2.


title: Fe(III), Experiment 3, Time point 1

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with Fe(III) (See "Channel 1 Treatment Protocol"). Time point 1 (T1) samples were collected 2.5 hours after this shift.


title: Fe(III), Experiment 2, Time point 2


title: Fe(III), Experiment 3, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with Fe(III) (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 7.5 hours after this shift.


title: Fe(III), Experiment 2, Time point 3


title: Control (C) - rep1


title: Fe(III), Experiment 2, Time point 1


title: Fe(III), Experiment 1, Time point 3


title: Fe(III), Experiment 1, Time point 1


title: Fe(III), Experiment 1, Time point 2


title: As(V), Experiment 3, Time point 2

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with As(V) (See "Channel 1 Treatment Protocol"). Time point 2 (T2) samples were collected 4.5 hours after this shift.


title: H3K4me3_ENCODE_ChIPchip_mouseNPC_1

hyb_protocol: Samples were hybridized according to Nimblegen established protocol

scan_protocol: Samples were scanned according to Nimblegen established protocol

data_processing: Ratios computed and biweight mean normalized using NimbleScan software package

source_name: H3K4 trimethyl ChIP in Mouse Neural Precursor cells

tag: ChIP from NPC extract

source_name: Genomic DNA in Mouse Neural Precursor cells

treatment_protocol: No immunoprecipitation

tag: Isolated NPC genomic DNA


title: CHD7_ENCODE_ChIPchip_mouseNPC_1

source_name: CHD7 ChIP in Mouse Neural precursor cells


title: As(V), Experiment 3, Time point 1

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with As(V) (See "Channel 1 Treatment Protocol"). Time point 1 (T1) samples were collected 2.5 hours after this shift.


title: As(V), Experiment 3, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with As(V) (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 7.5 hours after this shift.


title: GM12878_Input_1

source_name: Input RNA


title: CHD7_ENCODE_ChIPchip_mouseNPC_2


title: H3K4me2_ENCODE_ChIPchip_mouseNPC_1

source_name: H3K4 dimethyl ChIP in Mouse Neural Precursor cells


title: H3K4me1_ENCODE_ChIPchip_mouseES_1

source_name: H3K4 monomethyl ChIP in Mouse ES

tag: ChIP from ES extract

source_name: Genomic DNA in Mouse ES

tag: Isolated ES genomic DNA


title: As(V), Experiment 2, Time point 1

source_name: Total RNA from P. aerophilum cultures


title: As(V), Experiment 1, Time point 2


title: As(V), Experiment 1, Time point 1


title: H3K4me1_ENCODE_ChIPchip_mouseNPC_1

source_name: H3K4 monomethyl ChIP in Mouse Neural Precursor cells


title: NO3, Experiment 3, Time point 2

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with NO3 (See "Channel 1 Treatment Protocol"). Time point 2 (T2) samples were collected 4.5 hours after this shift.


title: NO3, Experiment 3, Time point 1

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with NO3 (See "Channel 1 Treatment Protocol"). Time point 1 (T1) samples were collected 2.5 hours after this shift.


title: As(V), Experiment 2, Time point 2


title: As(V), Experiment 1, Time point 3


title: As(V), Experiment 2, Time point 3


title: NO3, Experiment 2, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with NO3 (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 7.5 hours after this shift.


title: NO3, Experiment 3, Time point 3


title: NO3, Experiment 2, Time point 1


title: H3K4me2_ENCODE_ChIPchip_mouseES_1

source_name: H3K4 dimethyl ChIP in Mouse ES


title: Control (C) - rep2

source_name: leaf: Control (C)

tag: cultivar Hamidiye (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007098 LP.02 two leaves visible (Development Stage); 13 days old (Age); hydroponic 1/2 strength hoagland's solution (Growth Media).


title: CHD7_ENCODE_ChIPchip_mouseES_1

source_name: CHD7 ChIP in Mouse ES

tag: Isolated genomic DNA


title: H3K9me3_ENCODE_ChIPchip_mouseES_1

source_name: H3K9 trimethyl ChIP in Mouse ES


title: NO3, Experiment 1, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with NO3 (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 4.5 hours after this shift.


title: NO3, Experiment 1, Time point 2


title: H3K4me3_ENCODE_ChIPchip_mouseES_1

source_name: H3K4 trimethyl ChIP in Mouse ES


title: CHD7_ENCODE_ChIPchip_mouseES_2


title: NO3, Experiment 2, Time point 2


title: CHD7_ENCODE_ChIPchip_mouseES_3


title: whole cerebellum postnatal day 60, replicate a, chip Mu11K_sub_A

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: human fetal lung 133 dpc biological replicate 2

hyb_protocol: 25 micrograms of each biotin-labeled cRNA was hybridized to an Affymetrix Mu11K sub A and B chip according to the manufacturer's protocol. Four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) were included in each hybridization reaction to verify consistent hybridization efficiency. Hybridization is carried out according the Affymetrix GeneChip® Manual. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Standard Affymetrix protocol.

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

source_name: Whole cerebella pooled mouse

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

growth_protocol: Not applicable.

extract_protocol: 10 micrograms of total RNA was used to generate target cRNA for hybridization to Affymetrix Mu11K chipset subA and subB oligonucleotide microarrays. A single chip set was used for each time-point. Before target generation, individual RNA samples were pooled so that each target was derived from a minimum of 3 individual cerebella. This step was performed to minimize both biologic variability and the number of microarrays necessary to generate informative data. After pooling, RNA was re-purified using Qiagen purification kits (Valencia, CA). Target cRNA was synthesized according to manufacturer's protocol. Briefly, total RNA was reverse transcribed into a complete cDNA library (SuperScript Choice kit; Invitrogen) using a T7/T24 primer (Genset Corp., La Jolla, CA). This cDNA was subsequently in vitro transcribed into biotin-labeled cRNA (High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY). The resulting cRNA was fragmented and assessed for quality by gel electrophoresis. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols.

treatment_protocol: Not applicable.

tag: microarray hybridization date


title: O2, Experiment 3, Time point 2

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with additional O2 (See "Channel 1 Treatment Protocol"). Time point 2 (T2) samples were collected 4.5 hours after this shift.

tag: A reference pool of RNA prepared from 45 cultures of P. aerophilum grown under aerobic conditions, then shifted to anoxic growth with different terminal electron acceptors, and collected at three time points (See "Channel 1 Treatment Protocol" and "Channel 1 Growth Protocol"). RNA from each of the 45 different samples used individually for Channel 1 were combined in equal amounts to create the reference pool used in Channel 2.


title: whole cerebellum postnatal day 60, replicate b, chip Mu11K_sub_A

description: human fetal lung 140 dpc biological replicate 2


title: whole cerebellum postnatal day 7, replicate a, chip Mu11K_sub_A

description: human fetal lung 133 dpc biological replicate 3


title: O2, Experiment 2, Time point 2


title: O2, Experiment 1, Time point 1

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with additional O2 (See "Channel 1 Treatment Protocol"). Time point 1 (T1) samples were collected 2.5 hours after this shift.


title: whole cerebellum postnatal day 5, replicate b, chip Mu11K_sub_A

description: human fetal lung 130 dpc


title: O2, Experiment 3, Time point 1


title: whole cerebellum postnatal day 5, replicate a, chip Mu11K_sub_A

description: human fetal lung 133 dpc biological replicate 1


title: O2, Experiment 2, Time point 1


title: O2, Experiment 2, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with additional O2 (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 7.5 hours after this shift.


title: NO3, Experiment 1, Time point 1


title: whole cerebellum postnatal day 7, replicate b, chip Mu11K_sub_A

description: human fetal lung 133 dpc biological replicate 4


title: O2, Experiment 1, Time point 2


title: whole cerebellum postnatal day 3, replicate b, chip Mu11K_sub_A

description: human fetal lung 154 dpc


title: whole cerebellum postnatal day 30, replicate a, chip Mu11K_sub_A

description: human fetal lung 105 dpc


title: O2, Experiment 1, Time point 3


title: whole cerebellum postnatal day 3, replicate a, chip Mu11K_sub_A

description: human fetal lung 140 dpc biological replicate 1


title: whole cerebellum postnatal day 21, replicate a, chip Mu11K_sub_A

description: human fetal lung 76 dpc biological replicate 2


title: No Addition, Experiment 3, Time point 3

tag: Cultures of P. aerophilum grown under aerobic conditions, then shifted to growth with no added terminal electron acceptor (See "Channel 1 Treatment Protocol"). Time point 3 (T3) samples were collected 7.5 hours after this shift.