title: Sample 27P_ependymoma-250knsp

description:
primary ependymoma, female, SP, 8.9yrs
S0398FL0019 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 27


title: Sample 24P_blood sample-250knsp

status: Public on Feb 09 2012

type: genomic

city: Nottingham

first: John-Paul

last: Kilday

address: Derby Road

department: CBTRC

country: United Kingdom

institute: University of Nottingham

description:
blood
S0398FL0038 nsp
Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labelled and hybridised to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files and CHP files (generated by Affymetrix GTYPE using the BRLMM algorithm) were processed by CNAG. Normalization was performed using the constitutional samples. Data processing was performed as described in Miller et al Neuro Oncol 2011;13(8):866-79.
Primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall;

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: blood DNA sample from patient 24

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted snap frozen tumour tissue and mononuclear cell preparations  from peripheral blood, using a standard phenol/chloroform/isoamyl alcohol method. DNA quality and quantity was assessed using a Nandrop spectrophotometer and agarose gel electrophoresis.

tag: patient

tag: disease state

value: blood

tag: gender

value: male

tag: age

tag: tumour grade

tag: patient outcome

value: Alive and no disease progression

tag: tumour 1q gain status


title: Sample 29P_blood sample-250knsp

description:
blood
S0398FL0025 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 29

value: female


title: Sample 24P_ependymoma-250knsp

description:
primary ependymoma, male, SP, 7.1yrs
S0398FL0015 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 24

value: ependymoma

tag: ependymoma status

value: primary

tag: location

value: spinal (SP)

value: World Health Organisation Grade II

value: No 1q gain


title: Sample 26R1_ependymoma-250knsp

description:
recurrent ependymoma, PF
ept017 nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 26

value: recurrent

value: posterior fossa (PF)

value: Dead of disease

value: 1q gain


title: Sample 26P_blood sample-250knsp

description:
blood
epn017 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 26


title: Sample 21P_ependymoma-250knsp

description:
primary ependymoma, sex unknown, PF, 6.5yrs
S0398FL0009 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 21

value: unknown


title: Sample 23P_ependymoma-250knsp

description:
primary ependymoma, female, ST, 7.1yrs
ept125d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 23

value: supratentorial (ST)

value: World Health Organisation Grade III


title: Sample 25P_blood sample-250knsp

description:
blood
epn250 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 25

value: 8 yrs.


title: Sample 40P_blood sample-250ksty

description:
blood
S0398FL0027 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 40

value: blood

value: Alive with disease progression


title: Sample 43R1_blood sample-250ksty

description:
blood
epn061 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 43

value: male


title: Sample 23P_blood sample-250knsp

description:
blood
epn125 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 23

value: female


title: Sample 25P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 8 yrs.
ept250 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 25

value: ependymoma

value: Alive and no disease progression


title: Sample 41P_blood sample-250ksty

description:
blood
epn152 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 41


title: Sample 43R1_ependymoma-250ksty

description:
recurrent ependymoma, male, ST, 15.5yrs
ept061 sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 43


title: Sample 42P_ependymoma-250ksty

description:
primary ependymoma, male, SP, 15.3yrs
S0398FL0047 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 42

value: primary

value: spinal (SP)

value: World Health Organisation Grade I


title: Sample 22P_blood sample-250knsp

description:
blood
epn109d nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 22


title: Sample 40P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 14.7yrs
S0398FL0005 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 40

value: No 1q gain


title: Sample 41P_ependymoma-250ksty

description:
primary ependymoma, female, ST, 14.8yrs
ept152r sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 41

value: World Health Organisation Grade II


title: Sample 26P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 8.8yrs
ept253 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 26

value: posterior fossa (PF)

value: Dead of disease


title: Sample 38P_ependymoma-250ksty

description:
primary ependymoma, male, SP, 14.6yrs
S0398FL0002 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 38


title: Sample 38P_blood sample-250ksty

description:
blood
S0398FL0024 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 38


title: Sample 37P_blood sample-250ksty

description:
blood
S0398FL0040 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 37


title: Sample 39P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 14.7yrs
ept047r sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 39

value: 1q gain


title: Sample 20R1_ependymoma-250knsp

description:
recurrent ependymoma, ST
ept116d nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 20

value: recurrent

value: supratentorial (ST)


title: Sample 37P_ependymoma-250ksty

description:
primary ependymoma, female, ST, 13.8yrs
S0398FL0017 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 37


title: Sample 21P_blood sample-250knsp

description:
blood
S0398FL0030 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 21

value: unknown


title: Sample 20P_blood sample-250knsp

description:
blood
epn057 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 20

value: blood


title: Sample 22P_ependymoma-250knsp

description:
primary ependymoma, female, ST, 6.7yrs
ept109d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 22


title: Sample 34P_blood sample-250ksty

description:
blood
S0398FL0039 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 34


title: Sample 20P_ependymoma-250knsp

description:
primary ependymoma, male, ST, 5.6yrs
ept057 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 20


title: Sample 36P_ependymoma-250ksty

description:
primary ependymoma, male, ST, 12.7yrs
ept134d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 36

value: World Health Organisation Grade III

value: Alive with disease progression


title: Sample 18R1_ependymoma-250knsp

description:
recurrent ependymoma, ST
ept115d nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 18

value: male


title: Sample 15P_blood sample-250knsp

description:
blood
S0398FL0033 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 15

value: female


title: Sample 32P_blood sample-250ksty

description:
blood
S0398FL0042 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 32

value: Alive and no disease progression


title: Sample 19R1_ependymoma-250knsp

description:
recurrent ependymoma, male, PF, 4.5yrs
S0296FL0018 nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 19

value: ependymoma

value: Unknown


title: Sample 34P_ependymoma-250ksty

description:
primary ependymoma, female, ST, 12yrs
S0398FL0016 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 34

value: primary


title: Sample 31P_ependymoma-250ksty

description:
primary ependymoma, male, SP, 10.3yrs
S0398FL0010 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 31

value: spinal (SP)

value: World Health Organisation Grade I

value: No 1q gain


title: Sample 17P_ependymoma-250knsp

description:
primary ependymoma, sex unknown, ST, 3.8 yrs
ept151 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 17

value: 3.8 yrs

value: World Health Organisation Grade II


title: Sample 33R1_blood sample-250ksty

description:
blood
epn130r sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 33


title: Sample 18P_blood sample-250knsp

description:
blood
epn051r nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 18

value: Dead of disease


title: Sample 36P_blood sample-250ksty

description:
blood
epn134r sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 36


title: Sample 31P_blood sample-250ksty

description:
blood
S0398FL0031 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 31


title: Sample 17R1_ependymoma-250knsp

description:
recurrent ependymoma, ST
ept112d nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 17

value: recurrent

value: supratentorial (ST)


title: Sample 32P_ependymoma-250ksty

description:
primary ependymoma, female, ST, 11.4yrs
S0398FL0018 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 32


title: Sample 35P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 12.2yrs
ept046 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 35

value: posterior fossa (PF)

value: 1q gain


title: Sample 13P_blood sample-250knsp

description:
blood
epn132r nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 13

value: blood


title: Sample 14P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 2.9 yrs.
ept055r nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 14

value: male

value: Alive with disease progression


title: Sample 29P_blood sample-250ksty

description:
blood
S0398FL0025 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 29

value: female

value: Alive and no disease progression


title: Sample 12P_blood sample-250knsp

description:
blood
epn124 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 12


title: Sample 16P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 3.8 yrs.
ept139d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 16

value: ependymoma


title: Sample 33R1_ependymoma-250ksty

description:
recurrent ependymoma, female, ST, 12yrs
ept130d sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 33

value: World Health Organisation Grade III


title: Sample 16P_blood sample-250knsp

description:
blood
epn139 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 16


title: Sample 18P_ependymoma-250knsp

description:
primary ependymoma, male, ST, 4.2yrs
ept051 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 18

value: primary


title: Sample 30P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 10yrs
S0398FL0011 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 30


title: Sample 28P_blood sample-250ksty

description:
blood
S0398FL0028 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 28


title: Sample 12P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 2.6 yrs.
ept124d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 12


title: Sample 35R1_ependymoma-250ksty

description:
recurrent ependymoma, PF
S0296FL0023 sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 35


title: Sample 15P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 3.5 yrs.
S0296FL0012 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 15


title: Sample 30P_blood sample-250ksty

description:
blood
S0398FL0032 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 30


title: Sample 27P_blood sample-250ksty

description:
blood
S0398FL0043 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 27


title: Sample 10P_blood sample-250knsp

description:
blood
epn117r nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 10

value: unknown

value: 2.5 yrs


title: Sample 28P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 9.8yrs
S0398FL0007 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 28

value: No 1q gain


title: Sample 11P_blood sample-250knsp

description:
blood
epn062 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 11

value: 2.6 yrs


title: Sample 27P_ependymoma-250ksty

description:
primary ependymoma, female, SP, 8.9yrs
S0398FL0019 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 27

value: spinal (SP)

value: World Health Organisation Grade I


title: Sample 10P_ependymoma-250knsp

description:
primary ependymoma, (sex and locn unknown), 2.5 yrs
ept117d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 10

value: World Health Organisation Grade II

value: Dead of disease


title: Sample 11P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 2.6 yrs
ept062 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 11

value: posterior fossa (PF)


title: Sample 16R1_ependymoma-250knsp

description:
recurrent ependymoma, PF
S0296FL0022 nsp
Hybridized to 250K_Nsp

source_name: recurrent ependymoma DNA sample from patient 16

value: recurrent

value: 1q gain


title: PAO6359-RpoN-4

type: RNA

city: Syracuse

first: Christopher

last: Nomura

state: NY

address: 1 Forestry Dr.

department: Chemistry

country: USA

institute: SUNY-ESF

description:
Gene expression from mid-exponential cells grown in rich media
PA06359 is the name for the rpoN-deficient PA01 strain.

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 50C 60 rpm on GeneChip P. aeruginosa Genome Array with rotation at 60 rpm. GeneChips were processed with an Affymetrix Fluidics Station 450 using the modified Flex FS450_0002 P. aeruginosa array protocol (as specified in the Affymetrix GeneChip Expression Analysis Technical Manual), using stains from the Affymetrix Hybridization, Wash, and Stain Kit.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 7G Plus

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.

label: biotin

molecule: total RNA

organism: Pseudomonas aeruginosa PAO1

source_name: Cells with RpoN molecular roadblock

label_protocol: Samples were processed according to the Prokaryotic Target Preparation Protocol in Affymetrix GeneChip Expression Analysis Technical Manual.  Briefly, 10 ug of RNA was used to synthesize cDNA via random primers and SuperScript II reverse transcriptase.  cDNA was purified using Qiagen MinElute PCR purification columns.  The resulting cDNA was fragmented and labeled with biotin.

growth_protocol: P. aeruginosa PAO1 harboring either empty plasmid or the plasmid encoding the RpoN molecular roadblock were grown in Difco Lennox broth (50 mL in a 500-mL baffled shake flask with gentamicin at 30 mg per liter) at 37 celsius with shaking at 200 rpm

extract_protocol: RNA was isolated using the enzymatic lysis and proteinase K digestion method of Qiagen Rneasy with on-column DNA digestion.

treatment_protocol: At an optical density (600 nm) of 0.5, cells were induced with 1 mM IPTG and grown for two more hours.  At this time, 0.5 mL of culture was removed and added to 1.0 mL of RNAprotect Bacterial Reagent (Qiagen) to stabilize the RNA.

tag: genotype/variation

value: rpoN-deficient

tag: strain

tag: plasmid

value: pBRL348 (RpoN molecular roadblock)


title: Sample 24P_ependymoma-250ksty

description:
primary ependymoma, male, SP, 7.1yrs
S0398FL0015 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 24

value: male

value: Alive and no disease progression


title: Sample 29P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 10yrs
S0398FL0003 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 29

value: ependymoma

value: female


title: Sample 9P_blood sample-250knsp

description:
blood
epn023 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 9

value: blood


title: Sample 24P_blood sample-250ksty

description:
blood
S0398FL0038 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 24


title: Sample 9P_ependymoma-250knsp

description:
primary ependymoma, male, PF 2.5 yrs
ept023 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 9

value: primary

value: 2.5 yrs

value: World Health Organisation Grade III


title: Sample 6P_blood sample-250knsp

description:
blood
S0398FL0045 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 6


title: Sample 25P_blood sample-250ksty

description:
blood
epn250b sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 25

value: 8 yrs.


title: Sample 26R1_ependymoma-250ksty

description:
recurrent ependymoma, PF
ept017 sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 26


title: PAO6359-RpoN-3


title: Sample 26P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 8.8yrs
ept253 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 26


title: Sample 5P_blood sample-250knsp

description:
blood
S0398FL0041 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 5


title: PAO6359-RpoN-2


title: Sample 8P_blood sample-250knsp

description:
blood
epn060 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 8

value: 2.4 yrs


title: Sample 7P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 2 yrs.
ept056r nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 7

value: 2 yrs.

value: No 1q gain


title: Sample 7P_blood sample-250knsp

description:
blood
epn056 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 7

value: Dead of disease


title: PAO6359-empty-4

source_name: Cells with empty plasmid

value: pBRL344 (empty)


title: Sample 25P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 8 yrs.
ept250 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 25

value: posterior fossa (PF)

value: World Health Organisation Grade II


title: Sample 23P_blood sample-250ksty

description:
blood
epn125r sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 23


title: Sample 4P_blood sample-250knsp

description:
blood
epn146 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 4


title: Sample 26P_blood sample-250ksty

description:
blood
epn017 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 26


title: Sample 8P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 2.4 yrs
ept060 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 8


title: Sample 13P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 2.8 yrs.
ept132d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 13


title: Sample 21P_ependymoma-250ksty

description:
primary ependymoma, sex unknown, PF, 6.5yrs
S0398FL0050 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 21

value: unknown

value: 1q gain


title: Sample 22P_blood sample-250ksty

description:
blood
epn109b sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 22

value: Alive and no disease progression


title: PAO6359-empty-3

description:
Gene expression from mid-exponential cells grown in rich media
PA06359 is the name for the rpoN-deficient PA01 strain.

value: rpoN-deficient


title: PAO6359-RpoN-1

source_name: Cells with RpoN molecular roadblock

value: pBRL348 (RpoN molecular roadblock)


title: PAO6359-empty-1


title: PAO1-RpoN-4

description: Gene expression from mid-exponential cells grown in rich media

value: wild-type


title: Sample 23P_ependymoma-250ksty

description:
primary ependymoma, female, ST, 7.1yrs
ept125d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 23

value: ependymoma

value: primary

value: female

value: supratentorial (ST)


title: Sample 21P_blood sample-250ksty

description:
blood
S0398FL0030 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 21

value: blood


title: PAO1-RpoN-3


title: PAO1-RpoN-2


title: Sample 20P_ependymoma-250ksty

description:
primary ependymoma, male, ST, 5.6yrs
ept057 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 20

value: male


title: Sample 20R1_ependymoma-250ksty

description:
recurrent ependymoma, ST
ept116d sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 20

value: recurrent

value: No 1q gain


title: Sample 18R1_ependymoma-250ksty

description:
recurrent ependymoma, ST
ept115d sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 18

value: World Health Organisation Grade III

value: Dead of disease


title: PAO6359-empty-2

value: pBRL344 (empty)


title: Sample 4P_ependymoma-250knsp

description:
primary ependymoma, male, ST, 1.8yrs
ept146c nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 4

value: World Health Organisation Grade II


title: Sample 15P_blood sample-250ksty

description:
blood
S0398FL0033 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 15


title: Sample 3P_ependymoma-250knsp

description:
primary ependymoma, male, (locn unknown),1.5yrs
ept119d nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 3

value: unknown


title: PAO1-empty-4

source_name: Cells with empty plasmid


title: Sample 19R1_ependymoma-250ksty

description:
recurrent ependymoma, male, PF, 4.5yrs
S0296FL0018 sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 19

value: posterior fossa (PF)

value: Unknown


title: Sample 5P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 1.8yrs
ept058 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 5

value: Alive and no disease progression


title: Sample 1P_blood sample-250knsp

description:
blood
epn063 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 1


title: Sample 6P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 1.8yrs
S0398FL0021 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 6


title: Sample 22P_ependymoma-250ksty

description:
primary ependymoma, female, ST, 6.7yrs
ept109d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 22


title: Sample 18P_ependymoma-250ksty

description:
primary ependymoma, male, ST, 4.2yrs
ept051 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 18


title: Sample 16P_blood sample-250ksty

description:
blood
epn139 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 16

value: Alive with disease progression


title: PAO1-RpoN-1

source_name: Cells with RpoN molecular roadblock

value: wild-type

value: pBRL348 (RpoN molecular roadblock)


title: Sample 18P_blood sample-250ksty

description:
blood
epn051 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 18


title: Sample 16R1_ependymoma-250ksty

description:
recurrent ependymoma, PF
S0296FL0022 sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 16

value: ependymoma

value: female

value: 1q gain


title: Sample 17P_ependymoma-250ksty

description:
primary ependymoma, sex unknown, ST, 3.8 yrs
ept151 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 17

value: primary

value: supratentorial (ST)

value: 3.8 yrs


title: Sample 2P_ependymoma-250knsp

description:
primary ependymoma, female, PF, 1.3yrs
ept138 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 2

value: World Health Organisation Grade III

value: No 1q gain


title: Sample 1P_ependymoma-250knsp

description:
primary ependymoma, male, PF, 1.0yrs
ept063 nsp
Hybridized to 250K_Nsp

source_name: primary ependymoma DNA sample from patient 1

value: male

value: Dead of disease


title: Sample 3P_blood sample-250knsp

description:
blood
epn119 nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 3

value: blood


title: PAO1-empty-2

description: Gene expression from mid-exponential cells grown in rich media

value: pBRL344 (empty)


title: Sample 17R1_ependymoma-250ksty

description:
recurrent ependymoma, ST
ept112d sty
Hybridized to 250K_Sty

source_name: recurrent ependymoma DNA sample from patient 17

value: recurrent

value: unknown

value: World Health Organisation Grade II


title: Sample 13P_blood sample-250ksty

description:
blood
epn132 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 13

value: 2.8 yrs

value: Alive and no disease progression


title: Sample 20P_blood sample-250ksty

description:
blood
epn057r sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 20


title: Sample 15P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 3.5 yrs.
S0296FL0012 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 15

value: ependymoma

value: posterior fossa (PF)


title: Sample 16P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 3.8 yrs.
ept139d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 16

value: female

value: Alive with disease progression


title: Sample 2P_blood sample-250knsp

description:
blood
epn138r nsp
Hybridized to 250K_Nsp

source_name: blood DNA sample from patient 2


title: PAO1-empty-1

source_name: Cells with empty plasmid

value: wild-type


title: Identification of miR-133a target genes in prostate cancer (PC3)

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1 Inohana,Chuo-ku

department: School of Medicine

country: Japan

institute: Chiba University

description:
Differentially expressed genes by miR-133a transfection
Cy5(PC133)vsCy3(PCN2).txt

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: miR-133a transfected in prostate cancer cell line (PC3)

label_protocol: Agilent two-color Low Input Quick Amp Labeling Kit labeling protocol

growth_protocol: normal cell culture medium RPMI1640 or MEM

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: microRNA transfection using Lipofectamine RNiMAX (Invitrogen)

tag: cell type

value: prostate cancer

tag: cell line

source_name: control microRNA transfected cell line


title: Identification of miR-133a target genes in prostate cancer (DU145)

description:
Differentially expressed genes by miR-133a transfection
Cy5(DU133)vsCy3(DUN2).txt

source_name: miR-133a transfected in prostate cancer cell line (DU145)


title: Sample 14P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 2.9 yrs
ept055 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 14

value: primary

value: 2.9 yrs


title: Identification of miR-1 target genes in prostate cancer  (PC3)

description:
Differentially expressed genes by miR-1 transfection
Cy5(PCmi1)vsCy3(PCN2).txt

source_name: miR-1 transfected in prostate cancer cell line (PC3)


title: Sample 11P_blood sample-250ksty

description:
blood
epn062b sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 11

value: male

value: 2.6 yrs


title: Identification of miR-1 target genes in prostate cancer  (DU145)

description:
Differentially expressed genes by miR-1 transfection
Cy5(DUmi1)vsCy3(DUN2).txt

source_name: miR-1 transfected in prostate cancer cell line (DU145)


title: Identification of miR-1 target genes in bladder cancer, T24

description: Differentially expressed genes by miR-1 transfection.

hyb_protocol: Agilent two-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 9.5.3.

data_processing: LOWESS-normalized, background-subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent Feature Extraction software version 9.5.3 was used.

source_name: miR-1 transfected in bladder cancer cell line (T24)

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol.

growth_protocol: Normal cell culture medium RPMI 1640 or MEM.

extract_protocol: Total RNA extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA transfection using Lipofectamine RNiMAX (Invitrogen).

value: bladder cancer

tag: miRNA

source_name: control microRNA-transfected cell line (T24)

value: control


title: Identification of miR-375 target genes in HNSCC (SAS)

description:
Differentially expressed genes by miR-375 transfection
Cy5(SA375)vsCy3(SAcon).txt

source_name: miR-375 transfected in HNSCC cell line (SAS)

value: head and neck squamous cell carcinoma

value: SAS


title: Sample 12P_blood sample-250ksty

description:
blood
epn124 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 12

value: blood


title: 8165-37-rep4

city: shanghai

first: hang

last: wu

address: Huashan Road

country: China

institute: sjtu

description: Gene expression at 37C

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

data_processing:
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
The values were log2 transformed.

organism: Streptomyces avermitilis

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

growth_protocol: Strain NRRL8165 was pre-cultured at 30°C for 48 h in 50 ml TSB liquid medium plus 1 % yeast extract in 250 ml shaking flasks with reciprocal shaking (220 rpm). 0.5 ml of each culture was inoculated into 50 ml liquid fermentation medium in three 250 ml shaking flasks. The batch cultures were incubated at 30°C or 37°C for 48 h (220 rpm).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The mycelia was collected from the fermentation medium by centrifugation at 12,000 rpm for 5 min, resuspended in 1 mL TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US), and broken in a precellys homogenizer (6,500 rpm, 1×30 s; Peqlab) with glass beads (150–212 μm, Sigma). Cell debris was removed by centrifugation at 12,000 rpm for 5 min, and the extracted supernatants were stored at -80°C.

tag: tissue

value: Mycelia


title: Identification of miR-1 target genes in bladder cancer, BOY

source_name: miR-1 transfected in bladder cancer cell line (BOY)

value: BOY

source_name: control microRNA-transfected cell line (BOY)


title: Sample 13P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 2.8 yrs
ept132d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 13

value: ependymoma

value: 2.8 yrs

value: World Health Organisation Grade II

value: Alive and no disease progression

value: No 1q gain


title: Identification of miR-375 target genes in HNSCC (FaDu)

description:
Differentially expressed genes by miR-375 transfection
Cy5(FA375)vsCy3(FAcon).txt

source_name: miR-375 transfected in HNSCC cell line (FaDu)

value: FaDu


title: 8165-37-rep3

description: Gene expression at 37C


title: Sample 5P_blood sample-250ksty

description:
blood
S0398FL0041 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 5

value: female


title: Sample 10P_ependymoma-250ksty

description:
primary ependymoma, (sex and locn unknown), 2.5 yrs
ept117d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 10

value: primary

value: unknown

value: 2.5 yrs

value: Dead of disease

value: 1q gain


title: 8165-37-rep2

description: Gene expression at 37C


title: Identification of miR-517a target genes in bladder cancer, T24

description: Differentially expressed genes by miR-517a transfection.

source_name: miR-517a transfected in bladder cancer cell line (T24)

value: bladder cancer

value: control


title: Sample 7P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 2 yrs.
ept056 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 7

value: posterior fossa (PF)

value: 2 yrs.

value: World Health Organisation Grade III


title: Sample 6P_blood sample-250ksty

description:
blood
S0398FL0045 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 6

value: blood

value: male


title: Sample 9P_blood sample-250ksty

description:
blood
epn023 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 9


title: Sample 8P_blood sample-250ksty

description:
blood
epn060 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 8

value: 2.4 yrs


title: Sample 11P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 2.6 yrs
ept062 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 11

value: ependymoma

value: 2.6 yrs

value: World Health Organisation Grade II

value: Alive and no disease progression


title: 8165-37-rep1

description: Gene expression at 37C

value: Mycelia


title: Identification of miR-517a target genes in bladder cancer, BOY

source_name: miR-517a transfected in bladder cancer cell line (BOY)

value: BOY


title: Sample 9P_ependymoma-250ksty

description:
primary ependymoma, male, PF 2.5 yrs
ept023 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 9

value: primary

value: 2.5 yrs

value: No 1q gain


title: Sample 6P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 1.8yrs
S0398FL0021 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 6


title: Total RNA from Inosine RNA treated human primary cells-4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner using recommended defaults.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.  The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using the Rosetta Resolver® system (version 7.2) (Rosetta Biosoftware, Kirkland, WA).

label: cy 3

source_name: primary human bronchial epithelial (PHBE)

label_protocol: Gene expression analysis was conducted using Agilent Whole Human Genome 4x44 multiplex format oligo arrays (014850) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: TRIzol total RNA isolation reagent (Invitrogen, Carlsbad, CA) was used for RNA extraction.

treatment_protocol: Primary human bronchial epithelial cells were treated with 20 ug/ml of normal or Ino-RNA (10% inosines). After 2 hr, total cellular RNA was isolated.

value: clonetics normal human airway epithelial cell

value: lung


title: Identification of miR-133a target genes in HNSCC (IMC3)

description:
Differentially expressed genes by miR-133a transfection
Cy5(IMC13)vsCy3(IMCco).txt

source_name: miR-133a transfected in HNSCC cell line (IMC3)

value: head and neck squamous cell carcinoma

source_name: control microRNA transfected cell line


title: Identification of miR-218 target genes in bladder cancer, T24

description: Differentially expressed genes by miR-218 transfection.

source_name: miR-218 transfected in bladder cancer cell line (T24)

value: bladder cancer

source_name: control microRNA-transfected cell line (T24)

value: control


title: PAO1-empty-3

description: Gene expression from mid-exponential cells grown in rich media

source_name: Cells with empty plasmid

value: wild-type

value: pBRL344 (empty)


title: Identification of miR-135a target genes in renal cell carcinoma (A498)

description:
Differentially expressed genes by miR-135a transfection
Cy5(A498135a)vsCy3(A498N2).txt

source_name: miR-135a transfected in RCC cell line (A489)

value: renal cell carcinoma


title: Identification of miR-1 target genes in HNSCC (IMC3)

description:
Differentially expressed genes by miR-1 transfection
Cy5(IMCm1)vsCy3(IMCco).txt

source_name: miR-1 transfected in HNSCC cell line (IMC3)


title: Sample 10P_blood sample-250ksty

description:
blood
ept117r sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 10

value: blood

value: unknown

value: Dead of disease


title: Sample 8P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 2.4 yrs
ept060 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 8

value: ependymoma

value: male

value: posterior fossa (PF)

value: 2.4 yrs

value: World Health Organisation Grade III

value: Alive and no disease progression


title: 8165-30-rep4

description: Gene expression at 30C

value: Mycelia


title: 8165-30-rep2

description: Gene expression at 30C


title: 5008-37-rep4

description: Gene expression at 37C

organism: Streptomyces hygroscopicus subsp. jinggangensis 5008

growth_protocol: Strain 5008 was pre-cultured at 30°C for 48 h in 50 ml TSB liquid medium plus 1 % yeast extract in 250 ml shaking flasks with reciprocal shaking (220 rpm). 0.5 ml of each culture was inoculated into 50 ml liquid fermentation medium in three 250 ml shaking flasks. The batch cultures were incubated at 30°C or 37°C for 48 h (220 rpm).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).


title: 8165-30-rep3

description: Gene expression at 30C


title: Sample 4P_blood sample-250ksty

description:
blood
epn146 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 4


title: Identification of miR-133a target genes in lung cancer (P10)

description:
Differentially expressed genes by miR-133a transfection
Cy5(P10133a)vsCy3(P10N2).txt

source_name: miR-133a transfected in lungcancer cell line (P10)

value: lung cancer


title: 8165-30-rep1

description: Gene expression at 30C


title: 5008-37-rep3

description: Gene expression at 37C


title: Identification of miR-133a target genes in lung cancer (H157)

description:
Differentially expressed genes by miR-133a transfection
Cy5(H157133a)vsCy3(H157N2).txt

source_name: miR-133a transfected in lung cancer cell line (H157)


title: Identification of miR-133a target genes in renal cell carcinoma (A498)

description:
Differentially expressed genes by miR-133a transfection
Cy5(A498133a)vsCy3(A498N2).txt

source_name: miR-133a transfected in RCC cell line (A498)


title: Total RNA from Inosine RNA treated human primary cells-3

value: clonetics normal human airway epithelial cell

value: lung


title: Total RNA from Inosine RNA treated human primary cells-2


title: Total RNA from Inosine RNA treated human primary cells-1


title: Sample 7P_blood sample-250ksty

description:
blood
epn056 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 7

value: female

value: 2 yrs.


title: Sample 4P_ependymoma-250ksty

description:
primary ependymoma, male, ST, 1.8yrs
ept146c sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 4

value: primary

value: supratentorial (ST)

value: World Health Organisation Grade II

value: No 1q gain


title: 5008-37-rep2

description: Gene expression at 37C


title: Total RNA from normal RNA treated human primary cells-4


title: Identification of miR-183 target genes in bladder cancer (T24)

description:
Differentially expressed genes by miR-183 transfection
Cy5(T183)vsCy3(Tcon).txt

source_name: miR-183 over expressed in baldder cancer cell line(T24)

value: bladder cancer


title: 5008-37-rep1

description: Gene expression at 37C


title: Sample 3P_ependymoma-250ksty

description:
primary ependymoma, male, (locn unknown),1.5yrs
ept119d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 3

value: ependymoma

value: unknown


title: 5008-30-rep4

description: Gene expression at 30C


title: Sample 5P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 1.8yrs
ept058r sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 5

value: posterior fossa (PF)


title: Sample 3P_blood sample-250ksty

description:
blood
epn119r sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 3

value: blood

value: male


title: 5008-30-rep1

description: Gene expression at 30C


title: 5008-30-rep2

description: Gene expression at 30C


title: Identification of miR-183 target genes in bladder cancer (KK47)

description:
Differentially expressed genes by miR-183 transfection
Cy5(KK183)vsCy3(KKcon).txt

source_name: miR-183 over expressed in baldder cancer cell line (KK47)

source_name: control microRNA transfected cell line


title: Total RNA from normal RNA treated human primary cells-3

source_name: primary human bronchial epithelial (PHBE)


title: IMCD cells, 300mOsmol/KgH2O, 24 h hypo-osmolality, rep3

city: Daegu

first: Hyo-Jung

last: Choi

address: Dongin-dong 101

department: Biochemistry and Cell Biology

country: South Korea

institute: Kyungpook National  University

description:
340-3
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with reduced (300 mOsm/KgH2O) osmolality for 1 d more.

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on the Rat Gene 1.0 ST array. The hybridized probe arrays were stained and washed with the GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450 (Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) at 570 nm.

data_processing: The Robust Multichip Average (RMA) algorithm was used for background correction, sketch-quantile normalization and summarization. The probe-level data to expression values was generated from the CEL files using Affymetrix Power Tools (APT).

organism: Rattus norvegicus

source_name: Primary cultured kidney IMCD cells, hyperosmolar culture medium (640 mOsm/KgH2O) for 4d, then hypo-osmolar medium (300 mOsm/KgH2O) for 1d

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription was performed according to the manufacturer's instructions from 300ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol was performed using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).

extract_protocol: Total RNA from IMCD cells were extracted by using Trizol reagent. RNA that had high RNA integrity number (RIN > 9.0) and A260/A280 absorbance ratio ranging from 1.8 to 2.1 was used for cDNA synthesis.

treatment_protocol: Primary cultured IMCD cells of rat kidney were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with either reduced (300 mOsm/KgH2O) or the same osmolality for 1 or 2 d more.

value: SD

value: 7 weeks

value: kidney

value: primary cultured kidney inner medullary collecting duct (IMCD) cells

tag: treatment

value: 300mOsmol/KgH2O (hypo-osmolar)

tag: treatment duration

value: 24 hours


title: Identification of miR-96 target genes in bladder cancer (KK47)

description:
Differentially expressed genes by miR-96 transfection
Cy5(KK96)vsCy3(KKcon).txt

source_name: miR-96 over expressed in baldder cancer cell line (KK47)


title: Sample 2P_blood sample-250ksty

description:
blood
epn138 sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 2

tag: patient

tag: disease state

value: female

value: Alive and no disease progression


title: IMCD cells, 300mOsmol/KgH2O, 24 h hypo-osmolality, rep2

description:
340-2
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with reduced (300 mOsm/KgH2O) osmolality for 1 d more.

tag: gender

tag: age


title: 5008-30-rep3

description: Gene expression at 30C

value: Mycelia


title: Identification of miR-96 target genes in bladder cancer (T24)

description:
Differentially expressed genes by miR-96 transfection
Cy5(T96)vsCy3(Tcon).txt

source_name: miR-96 over expressed in baldder cancer cell line (T24)


title: Total RNA from normal RNA treated human primary cells-1

value: clonetics normal human airway epithelial cell

value: lung


title: Sample 12P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 2.6 yrs
ept124d sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 12

value: primary

value: 2.6 yrs

tag: tumour grade

value: World Health Organisation Grade III

tag: patient outcome

value: No 1q gain


title: IMCD cells, 640mOsmol/KgH2O, 24 h hypo-osmolality control, rep3

description:
640-3
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 5 days.

source_name: Primary cultured kidney IMCD cells, hyperosmolar culture medium (640 mOsm/KgH2O) for 5d

value: 640mOsmol/KgH2O (hyperosmolar)


title: Total RNA from untreated RNA  human primary cells-3


title: Identification of miR-145 target genes in prostate cancer, PC3

description: Differentially expressed genes by miR-145 transfection.

source_name: miR-145 transfected in prostate cancer cell line (PC3)

value: prostate cancer

source_name: control microRNA-transfected cell line (PC3)

value: control


title: IMCD cells, 300mOsmol/KgH2O, 24 h hypo-osmolality, rep1

description:
340-1
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with reduced (300 mOsm/KgH2O) osmolality for 1 d more.

value: SD

value: male

value: 7 weeks


title: Identification of miR-145 target genes in prostate cancer, DU145

source_name: miR-145 transfected in prostate cancer cell line (DU145)

source_name: control microRNA-transfected cell line (DU145)


title: IMCD cells, 640mOsmol/KgH2O, 24 h hypo-osmolality control, rep2

description:
640-2
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 5 days.

value: kidney

value: primary cultured kidney inner medullary collecting duct (IMCD) cells


title: Slide 6

city: Stratford

first: Eric

last: Moss

state: NJ

address: 2 Medical Center Dr.

department: Molecular Biology

institute: UMDNJ

description: wildtype biological replicate 3

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 Other Species (Exiqon, Denmark), which contains capture probes targeting all miRNAs for other species than human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

organism: Caenorhabditis elegans

source_name: Wildtype 3/30

label_protocol: One µg total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: nematodes were grown on solid NGM media with E. coli as food source for 18 hours at 20°C

extract_protocol: Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA). The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

value: wild type

tag: developmental stage

value: late L1 stage

source_name: common reference pool

tag: reference

value: common reference pool


title: Sample 2P_ependymoma-250ksty

description:
primary ependymoma, female, PF, 1.3yrs
ept138 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 2

value: ependymoma

tag: ependymoma status

value: female

tag: location

value: posterior fossa (PF)

value: Alive and no disease progression

tag: tumour 1q gain status


title: Total RNA from untreated RNA  human primary cells-2

tag: strain

value: clonetics normal human airway epithelial cell

value: lung


title: Total RNA from normal RNA treated human primary cells-2


title: Slide 5

description: wildtype biological replicate 2

source_name: Wildtype 3/19

tag: genotype/variation


title: Slide 4

description: mutant biological replicate 3

source_name: mutant 3/30


title: Total RNA from untreated RNA  human primary cells-4


title: Slide 3

description: mutant biological replicate 2

source_name: mutant 3/19


title: Identification of miR-874 target genes in HNSCC, SAS

description: Differentially expressed genes by miR-874 transfection.

source_name: miR-874 transfected in HNSCC cell line (SAS)

tag: cell line

value: SAS

tag: cell type

value: head and neck squamous cell carcinoma

tag: miRNA

source_name: control microRNA-transfected cell line (SAS)


title: Identification of miR-874 target genes in HNSCC, IMC3

source_name: miR-874 transfected in HNSCC cell line (IMC3)

source_name: control microRNA-transfected cell line (IMC3)

value: control


title: IMCD cells, 640mOsmol/KgH2O, 24 h hypo-osmolality control, rep1

description:
640-1
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 5 days.

value: SD

tag: tissue

tag: treatment

value: 640mOsmol/KgH2O (hyperosmolar)

tag: treatment duration

value: 24 hours


title: Slide 1

description: mutant biological replicate 1

source_name: mutant 11/13


title: Slide 2

description: wildtype biological replicate 1

source_name: wildtype 11/13


title: Identification of miR-1 target genes in renal cell carcinoma, A498

description: Differentially expressed genes by miR-1 transfection.

source_name: miR-1 transfected in RCC cell line (A498)

value: renal cell carcinoma

source_name: control microRNA-transfected cell line (A498)


title: IMCD cells, 300mOsmol/KgH2O, 48 h hypo-osmolality, rep3

description:
300-3
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with reduced (300 mOsm/KgH2O) osmolality for 2 d more.

source_name: Primary cultured kidney IMCD cells, hyperosmolar culture medium (640 mOsm/KgH2O) for 4d, then hypo-osmolar medium (300 mOsm/KgH2O) for 2d

tag: gender

value: male

value: 7 weeks

value: kidney

value: primary cultured kidney inner medullary collecting duct (IMCD) cells

value: 300mOsmol/KgH2O (hypo-osmolar)

value: 48 hours


title: Total RNA from untreated RNA  human primary cells-1

source_name: primary human bronchial epithelial (PHBE)


title: Sample 1P_blood sample-250ksty

description:
blood
epn063b sty
Hybridized to 250K_Sty

source_name: blood DNA sample from patient 1

tag: patient

tag: disease state

value: blood

tag: age

value: Dead of disease


title: IMCD cells, 300mOsmol/KgH2O, 48 h hypo-osmolality, rep1

description:
300-1
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with reduced (300 mOsm/KgH2O) osmolality for 2 d more.


title: Identification of miR-218 target genes in bladder cancer, BOY

description: Differentially expressed genes by miR-218 transfection.

source_name: miR-218 transfected in bladder cancer cell line (BOY)

value: BOY

value: bladder cancer

source_name: control microRNA-transfected cell line (BOY)


title: Sample 1P_ependymoma-250ksty

description:
primary ependymoma, male, PF, 1.0yrs
ept063 sty
Hybridized to 250K_Sty

source_name: primary ependymoma DNA sample from patient 1

value: ependymoma

value: primary

value: posterior fossa (PF)

tag: tumour grade

value: World Health Organisation Grade II

tag: patient outcome

value: No 1q gain


title: IMCD cells, 640mOsmol/KgH2O, 48 h hypo-osmolality control, rep2

description:
600-2
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 6 days.

source_name: Primary cultured kidney IMCD cells, hyperosmolar culture medium (640 mOsm/KgH2O) for 6d

value: SD

value: 640mOsmol/KgH2O (hyperosmolar)


title: IMCD cells, 640mOsmol/KgH2O, 48 h hypo-osmolality control, rep3

description:
600-3
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 6 days.

value: male


title: IMCD cells, 640mOsmol/KgH2O, 48 h hypo-osmolality control, rep1

description:
600-1
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 6 days.

value: 7 weeks


title: Drosophila_melanogaster_WT_PGC_5-7h_1

status: Public on Feb 08 2012

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the first of four  biological replicates.

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

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

data_processing: The raw data (.pair file) was subjected to Arraystar software (RMA normlization). See www.arraystar.com

organism: Drosophila melanogaster

source_name: Drosophila melanogaster 5-to-7 hour PGCs, wild type

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

growth_protocol: The following fly strains were used: w1118, VASA-GFP/CyO ; PrDr/TM3,Sb [82], VASA-GFP/CyO ; smg1/TM3,Sb and Df(3L)Scf-R6/TM3,Sb (Bloomington Stock #4500). All stocks were maintained at 25oC. To collect embryos for pole cell isolation, flies were grown in cages made from 500 ml plastic beakers fitted with a 10 cm petri-dish agar plate (25% apple juice, 0.15% methyl paraben, 0.625% sucrose and 2% agar) on the open side of the beaker. To prevent over-crowding of flies in the cage, each cage was seeded with a monolayer of anesthetized flies covering the bottom of the beaker. One- to two-day old flies of the desired genotype were kept in fresh bottles supplemented with dry yeast for 2-3 days before transferring to the cages. To improve egg lay efficiency, approximately a 70% : 30% female : male ratio was maintained by removing excess males. Fresh room temperature plates with wet yeast paste were used for all embryo collections. The first 2-hour embryo collection plate was discarded to maximize embryos synchronized in development during subsequent collections.

extract_protocol: Total RNA was extracted by TRIzol according to the manufacturer’s protocol. RNA quality and quantity was determined using the Bioanalyzer-RNA Pico kit (Agilent Technologies). Typical RNA yield ranged from 0.5 - 2 ng/l

value: wild type


title: Drosophila_melanogaster_WT_PGC_3-5h_4

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the fourth of four biological replicates.

source_name: Drosophila melanogaster 3-to-5 hour PGCs, wild type


title: Drosophila_melanogaster_WT_PGC_3-5h_1

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the first of four biological replicates.


title: Drosophila_melanogaster_WT_PGC_5-7h_2

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the second of four  biological replicates.


title: Drosophila_melanogaster_WT_PGC_5-7h_3

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the third of four 5-to-7 hour biological replicates.


title: Drosophila_melanogaster_WT_PGC_3-5h_2

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the second of four biological replicates.


title: Identification of miR-1 target genes in HNSCC, HSC3

source_name: miR-1 transfected in HNSCC cell line (HSC3)

value: head and neck squamous cell carcinoma

source_name: control microRNA-transfected cell line (HSC3)

value: control


title: IMCD cells, 300mOsmol/KgH2O, 48 h hypo-osmolality, rep2

description:
300-2
Primary cultured kidney IMCD cells were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with reduced (300 mOsm/KgH2O) osmolality for 2 d more.

value: kidney

value: primary cultured kidney inner medullary collecting duct (IMCD) cells

value: 300mOsmol/KgH2O (hypo-osmolar)

value: 48 hours


title: Drosophila_melanogaster_WT_PGC_1-3h_3

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the third of four biological replicates.

source_name: Drosophila melanogaster 1-to-3 hour PGCs, wild type


title: Identification of miR-1 target genes in HNSCC, FaDu

description: Differentially expressed genes by miR-1 transfection.

source_name: miR-1 transfected in HNSCC cell line (FaDu)

value: FaDu

source_name: control microRNA-transfected cell line (FaDu)


title: Drosophila_melanogaster_WT_PGC_1-3h_4


title: Drosophila_melanogaster_WT_PGC_1-3h_2


title: Drosophila_melanogaster_WT_PGC_1-3h_1


title: Drosophila_melanogaster_WT_somatic_cell_1-3h_3

description: This sample is of wild-type Drosophila melanogaster somatic cells. It is the third of four biological replicates.

source_name: Drosophila melanogaster 1-to-3 hour somatic cells, wild type


title: Drosophila_melanogaster_WT_somatic_cell_1-3h_4

description: This sample is of wild-type Drosophila melanogaster somatic cells. It is the fourth of four  biological replicates.


title: Drosophila_melanogaster_WT_somatic_cell_1-3h_2

description: This sample is of wild-type Drosophila melanogaster somatic cells. It is the second of four biological replicates.


title: Drosophila_melanogaster_WT_somatic_cell_1-3h_1

description: This sample is of wild-type Drosophila melanogaster somatic cells. It is the first of four biological replicates.


title: Drosophila_melanogaster_smaug_PGC_3-5h_1

description: This sample is of smaug mutant Drosophila melanogaster PGCs. It is the first of three biological replicates.

source_name: Drosophila melanogaster 3-to-5 hour PGCs, smaug mutant

value: smaug mutant


title: Drosophila_melanogaster_smaug_PGC_3-5h_2

description: This sample is of smaug mutant Drosophila melanogaster PGCs. It is the second of three biological replicates.


title: Drosophila_melanogaster_smaug_PGC_5-7h_1

description: This sample is of smaug mutant Drosophila melanogaster PGCs. It is the first of four biological replicates.

source_name: Drosophila melanogaster 5-to-7 hour PGCs, smaug mutant


title: Drosophila_melanogaster_smaug_PGC_5-7h_4

description: This sample is of smaug mutant Drosophila melanogaster PGCs. It is the fourth of four biological replicates.


title: Drosophila_melanogaster_smaug_PGC_1-3h_3

description: This sample is of smaug mutant Drosophila melanogaster PGCs. It is the third of three biological replicates.

source_name: Drosophila melanogaster 1-to-3 hour PGCs, smaug mutant


title: Oocyte_GV versus Oocyte_MII

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description: Each channel consists of one replicate with pools of oocytes.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Raw intensities experienced the adjustments of data-filtering, log 2 transformation, gene centering and global normalization. MiRNAs with all samples intensities larger than the intensity threshold of 22 were considered detectable.

organism: Bos taurus

label_protocol: The microarray assay was performed using a service provider (LC Sciences). The assay started from 200 ng total RNA sample, which was amplified in-house then size fractionated using a YM-100 Microcon centrifugal filter (Millipore), and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining

growth_protocol: Follicles of 5 mm in diameter were aspirated from ovaries of slaughtered dairy cattle. The collected cumulus-oocyte complexes (COCs) were washed 4 times in TLH and selected to be placed in 50-µl drops of maturation medium covered with mineral oil. The oocytes at the germinal vesicle stage (GVs) were collected after the TLH washes. The COCs was matured in TCM-199 medium supplemented with 10% fetal calf serum (FCS), pyruvate and gentamycin. The dishes were placed for at 39°C under 5% CO2 with a maximum humidity level. After 22h of maturation, oocytes at MII stage were collected. All the GVs and MII collected were mechanically denuded by agitation for about 5 minutes in PBS to remove their cumulus cells before the freezing step.

extract_protocol: Total RNA was extracted using miRNeasy kit from Qiagen according to the manufacturer's protocol.

tag: developmental stage

value: Germinal vesicule

value: metaphase II


title: Drosophila_melanogaster_smaug_PGC_5-7h_3

description: This sample is of smaug mutant Drosophila melanogaster PGCs. It is the third of four  biological replicates.


title: Drosophila_melanogaster_WT_PGC_5-7h_4

description: This sample is of wild-type Drosophila melanogaster PGCs. It is the fourth of four 5-to-7 hour biological replicates.


title: Drosophila_melanogaster_smaug_PGC_1-3h_1


title: Drosophila_melanogaster_smaug_PGC_1-3h_2


title: Drosophila_melanogaster_smaug_PGC_5-7h_2

description: This sample is of smaug mutant Drosophila melanogaster PGCs. It is the second of four biological replicates.


title: Drosophila_melanogaster_smaug_PGC_3-5h_3


title: Primary melanoma tissue RG8 rep1

city: Edinburgh

first: Yan

last: Xu

address: Crewe Road South

department: MRC

institute: The University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R 2.8.1 software.

source_name: Human skin

label_protocol: Biotinylated cDNA  were prepared for the Illumina microRNA microarray (Catalogue # MI 501-1001, Part # 11297743) assay which was carried out on RNA extracted from FFPE and cultured cell samples using the manufacturer’s protocol.

extract_protocol: RNA from mammalian cell lines was isolated using the reagent RNAzolB and RNA from melanocytic tissue samples was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion) with the guidance of protocol.

value: FFPE tissue

value: Primary


title: Primary melanoma tissue RG9 rep1


title: Primary melanoma tissue RG7 rep1


title: Primary melanoma tissue RG6 rep1


title: young needles_rep7

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

description:
JB001-3408.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Microarray Scanner: ScanArray Express (Perkin Elmer, Waltham MA, USA) Image Analysis Program: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA) Slide scanning was performed at 5 micron resolution.

data_processing: Data analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach.   A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem juvenile). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

label: Alexa 555

organism: Picea glauca

source_name: young needles

label_protocol: Total RNA (1 µg) or mRNA (10 ng) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Nursery planting stock (from open-pollinated seed lots) were obtained as 3-year-old seedlings of P. glauca, were transferred to 8-inch pots and grown in a greenhouse under natural light conditions. Sampling of tissues was timed with the ending of primary shoot elongation, i.e. after 6 to 8 weeks of growth, and was as described (Pavy et al. 2008). For each tissue type five biological samples were prepared by pooling 6 independent trees.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees, the seed or tissue culture vessels, and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the sample types, except for megagametophytes where poly A+ RNA was extracted directly by using the Dynabeads mRNA Mikro kit (Dynal/Invitrogen, Oslo, Norway) following manufacturers instructions.

value: young needles

tag: age of trees

tag: replicate

tag: slide batch


title: Drosophila_melanogaster_WT_PGC_3-5h_3

tag: genotype/variation


title: Primary melanoma tissue RG5 rep1


title: young needles_rep3

description:
JB001-3360.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: young needles_rep8

description:
JB001-3409.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: young needles_rep10

description:
JB001-3444.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: young needles_rep5

description:
JB001-3383.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: young needles_rep9

description:
JB001-3414.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: young needles_rep4

description:
JB001-3367.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Primary melanoma tissue RG4 rep1


title: young needles_rep6

description:
JB001-3394.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Primary melanoma tissue RG3 rep1


title: Primary melanoma tissue RG20 rep1


title: young needles_rep1

description:
JB001-3336.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep20

description:
JB001-3481.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: phelloderm, juvenile

value: phelloderm


title: Primary melanoma tissue RG19 rep1


title: phelloderm, juvenile_rep19

description:
JB001-3462.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Primary melanoma tissue RG18 rep1


title: Primary melanoma tissue RG17 rep1


title: Primary melanoma tissue RG16 rep1


title: young needles_rep2

description:
JB001-3343.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Primary melanoma tissue RG2 rep1


title: phelloderm, juvenile_rep18

description:
JB001-3461.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep17

description:
JB001-3440.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Primary melanoma tissue RG14 rep1


title: Primary melanoma tissue RG15 rep1


title: Primary melanoma tissue RG12 rep1


title: Primary melanoma tissue RG13 rep1


title: Primary melanoma tissue RG11 rep1


title: Primary melanoma tissue RG10 rep1


title: phelloderm, juvenile_rep16

description:
JB001-3431.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep15

description:
JB001-3429.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep14

description:
JB001-3417.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep10

description:
JB001-3382.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Primary melanoma tissue RG1 rep1


title: phelloderm, juvenile_rep13

description:
JB001-3398.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep12

description:
JB001-3397.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep11

description:
JB001-3385.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep8

description:
JB001-3368.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep6

description:
JB001-3362.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep7

description:
JB001-3364.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep5

description:
JB001-3359.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep9

description:
JB001-3380.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep4

description:
JB001-3357.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep3

description:
JB001-3349.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Ovarian cancer cell PO23 rep1

source_name: Human ovary

tag: cell line

value: Malignant ovarian cancer cell


title: Ovarian cancer cell PO14 rep1


title: Ovarian cancer cell PO1 rep1


title: Benign naevus N9 rep1

value: Benign Naevus


title: Ovarian cancer cell PEA2 rep1


title: Benign naevus N9 rep2


title: Benign naevus N8 rep1


title: Benign naevus N7 rep1


title: Benign naevus N4 rep1


title: Benign naevus N6 rep1


title: Benign naevus N5 rep1


title: Benign naevus N3 rep1


title: xylem, juvenile_rep20

description:
JB001-3465.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: xylem, juvenile

value: xylem (juvenile)


title: phelloderm, juvenile_rep1

description:
JB001-3338.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep19

description:
JB001-3464.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Metastatic melanoma tissue ME rep1

value: Metastatic


title: Benign naevus N10 rep1


title: Benign naevus N1 rep1


title: Benign naevus N2 rep1


title: xylem, juvenile_rep16

description:
JB001-3457.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep15

description:
JB001-3438.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep17

description:
JB001-3458.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep13

description:
JB001-3430.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: phelloderm, juvenile_rep2

description:
JB001-3348.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep18

description:
JB001-3463.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep14

description:
JB001-3435.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep9

description:
JB001-3406.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep12

description:
JB001-3427.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep11

description:
JB001-3421.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep10

description:
JB001-3412.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep7

description:
JB001-3378.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Metastatic melanoma tissue M7 rep1


title: Metastatic melanoma tissue M54 rep1


title: Metastatic melanoma tissue M6 rep1


title: Metastatic melanoma tissue M5 rep1


title: Metastatic melanoma tissue M44 rep1


title: Metastatic melanoma tissue M48 rep1


title: Metastatic melanoma tissue M4 rep1


title: Metastatic melanoma tissue M39 rep1


title: Metastatic melanoma tissue M42 rep1


title: Metastatic melanoma tissue M57 rep1


title: xylem, juvenile_rep5

description:
JB001-3365.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep6

description:
JB001-3376.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep4

description:
JB001-3361.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Metastatic melanoma tissue M53 rep1


title: xylem, juvenile_rep8

description:
JB001-3386.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Metastatic melanoma tissue M38 rep1


title: adventitious roots_rep18

description:
000000019924-635-2011-07-13.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.

scan_protocol: Microarray Scanner: PowerScanner (Tecan Group Ltd., Männedorf, Switzerland) Image Analysis Program: ArrayPro Analyzer v. 6.3 (Media Cybernetics, Bethesda, MD, USA) Slide scanning was performed at 5 micron resolution.

organism: Picea abies

source_name: adventitious roots

growth_protocol: Norway spruce (P. abies) seedlings were grown in the experimental nursery of Finnish Forest Research Institute for about one and a half years before sampling. They were grown in standard nursery growing media, light Sphagnum peat, and fertilized with mineral nutrients. Roots were washed under tap water to remove surrounding peat and approximately 1 cm of the root ends was collected for analysis. Between two and four biological samples comprised of several root ends were analysed for each of eight different genotypes.

value: adventitious roots

tag: genotype


title: adventitious roots_rep20

description:
000000019930-635-2011-09-22.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep19

description:
000000019927-635-2011-06-30.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: xylem, juvenile_rep2

description:
JB001-3352.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: adventitious roots_rep17

description:
000000019918-635-2011-06-23.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep16

description:
000000019916-635-2011-06-23.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Metastatic melanoma tissue M34 rep1


title: Metastatic melanoma tissue M41 rep1


title: xylem, juvenile_rep3

description:
JB001-3356.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, juvenile_rep1

description:
JB001-3342.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: adventitious roots_rep13

description:
000000019902-635-2011-06-21.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep14

description:
000000019903-635-2011-06-21.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Metastatic melanoma tissue M33 rep1


title: Metastatic melanoma tissue M31 rep1


title: Metastatic melanoma tissue M36 rep1


title: Metastatic melanoma tissue M11 rep1


title: Metastatic melanoma tissue M17 rep1


title: Melanocyte Hermes1 rep1

description: Immortalised

value: Cell

tag: developmental stage:


title: Melanocyte Hermes4 rep1

description: Immortalised

tag: tissue


title: Melanoma cell WM115 rep1

value: Metastatic melanoma cell


title: Metastatic melanoma tissue M29 rep1


title: adventitious roots_rep12

description:
000000019899-635-2011-06-21.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Melanoma cell G361 rep1


title: Melanoma cell EDMEL3 xenograft 2 rep1


title: adventitious roots_rep15

description:
000000019907-635-2011-06-22.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep10

description:
000000019893-635-2011-06-17.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Melanoma cell EDMEL3 subclone 4 rep1


title: adventitious roots_rep8

description:
000000019888-635-2011-06-16.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep9

description:
000000019890-635-2011-06-16.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep11

description:
000000019897-635-2011-06-17.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Melanoma cell EDMEL3 subclone 5 rep1


title: adventitious roots_rep7

description:
000000019887-635-2011-06-16.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep5

description:
000000019884-635-2011-06-15.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Melanoma cell HBL rep1

value: HBL


title: Melanoma cell EDMEL3 subclone 2 rep1


title: adventitious roots_rep4

description:
000000019879-635-2011-06-15.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep2

description:
000000019875-635-2011-06-14.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Melanoma cell EDMEL3 subclone 1 rep1


title: Melanoma cell EDMEL3 passage 2 rep1


title: Melanoma cell EDMEL3 rep1


title: megagametophytes_rep2

description:
JF003-000000008141-635-2011-03-04.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.

molecule: polyA RNA

source_name: megagametophytes

growth_protocol: Control-pollinated seed (cross C962856) were obtained from P. glauca tree (80112) described in Pelgas et al. (2011) were surface-sterilized for 1 minute in 70% EtOH and ten minutes in 3% Na-hypochlorite, washing the seeds with sterile water three times in after and between treatments. The seeds were then immersed at 4°C sterile water for 24 hours and stratified at 4°C for 28 days. Next, the seeds were, moved to 26 Celsius on petri dishes with a moist paper and kept in the dark °C for 16h to start the germination process. After four hours of incubation the seeds were opened and the embryo was separated from the megagametophyte under a dissecting microscope. A total of 3 biological samples comprised of a single megagametophyte were used for analysis.

value: megagametophytes


title: megagametophytes_rep3

description:
JF-000000008142-635-2011-03-04.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep6

description:
000000019886-635-2011-06-16.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: adventitious roots_rep1

description:
000000019665-635-2011-06-14.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Melanoma cell C32 rep1


title: megagametophytes_rep1

description:
JF003-000000008138-635-2011-03-04.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: Melanoma cell A375 rep1


title: SET2_INC424_800nM_3h_1

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

description: SET2 cells exposed to 800 nM INC424  for 3h (replicate #1)

hyb_protocol: Total labeled RNA was hybridized to the Affymetrix Genechip miRNA array 1.0 using manufacturer's protocols.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: Signal reconstruction was performed using the RMA algorithm as implemented in Bioconductor affy package. All chip probes were used for background estimation but only human probes were considered for normalization and summarization phases.

source_name: SET2 cell line

label_protocol: Total RNA (500ng for samples) was labeled using the FlashTag Biotin HSR kit (Genisphere)

extract_protocol: Total cellular RNA, including small RNAs, was extracted using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: treatment group

value: MUTATED FOR JAK2V617F


title: SET2_INC424_800nM_3h_3

description: SET2 cells exposed to 800 nM INC424  for 3h (replicate #3)


title: embryonic cells_rep5

description:
JF003-8066.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: embryonic cells

growth_protocol: Cells were prepared as described in Zhao et al. (Tree Phys. 28 [2009]).

value: embryonic cells


title: embryonic cells_rep6

description:
JF003-8068.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: embryonic cells_rep3

description:
JF003-8059.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: vegetative buds_rep10

description:
JF003-8047.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: vegetative buds

growth_protocol: Buds were collected from branches of several clonal replicates of 9-year-old trees of P. glauca regenerated from two genetically distinct somatic embryogenesis lines as described (Klimaszewska et al. 2011) during the mid-Spring when the buds were just beginning to grow. For each genotype, five biological samples each consisting of 6 buds (approximately 80 mg fresh weight) were used for analysis.

value: vegetative buds


title: adventitious roots_rep3

description:
000000019878-635-2011-06-15.txt
Sample label Alexa647 is accurate.  However, the raw data file contains '532'-labeled columns because the image processing software labels the ch1 columns as '532' by default, whatever the actual dye used.


title: embryonic cells_rep1

description:
JF003-8054.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: embryonic cells_rep2

description:
JF003-8056.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: SET2_INC424_800nM_3h_2

description: SET2 cells exposed to 800 nM INC424  for 3h (replicate #2)


title: SET2_INC424_160nM_6h_3

description: SET2 cells exposed to 160 nM INC424  for 6h (replicate #3)


title: SET2_INC424_160nM_6h_2

description: SET2 cells exposed to 160 nM INC424  for 6h (replicate #2)


title: SET2_INC424_1600nM_3h_3

description: SET2 cells exposed to 1600 nM INC424  for 3h (replicate #3)


title: SET2_INC424_1600nM_6h_3

description: SET2 cells exposed to 1600 nM INC424  for 6h (replicate #3)


title: SET2_INC424_1600nM_3h_2

description: SET2 cells exposed to 1600 nM INC424  for 3h (replicate #2)


title: embryonic cells_rep4

description:
JF003-8065.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: SET2_INC424_160nM_6h_1

description: SET2 cells exposed to 160 nM INC424  for 6h (replicate #1)


title: SET2_ctr_6h_1

description: SET2 control cells collected at 6h (replicate #1)


title: SET2_INC424_1600nM_3h_1

description: SET2 cells exposed to 1600 nM INC424  for 3h (replicate #1)


title: SET2_ctr_6h_3

description: SET2 control cells collected at 6h (replicate #3)


title: SET2_ctr_6h_2

description: SET2 control cells collected at 6h (replicate #2)


title: SET2_INC424_800nM_6h_2

description: SET2 cells exposed to 800 nM INC424  for 6h (replicate #2)


title: SET2_INC424_800nM_6h_3

description: SET2 cells exposed to 800 nM INC424  for 6h (replicate #3)


title: in vitro spleen cells 72hr IM(+)_rep2

city: Tokyo

first: toyotaka

last: kawamata

department: Hematology-Oncology/Molecular therapy

institute: The Institute of Medical Science,The University of Tokyo

description:
Gene expression in spleen cells cultured with 10 µM Imatinib in conditioning medium containing IL-4 and LPS for 72 h
US14702391_252665512076_S01_GE1-v5_91_0806_1_4.txt

hyb_protocol: 1650.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using Agilent G2565AA Microarray Scanner System.

data_processing: Data processed with FeatureExrtraction v9.1. For normalization of raw microarray data, 75 percentile shift normalization was applied with GeneSpring GX v11.2.

organism: Mus musculus

source_name: spleen,72hr,IM(+), replicate 2

label_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent)

extract_protocol: QIAGEN RNeasy kit

treatment_protocol: The mouse splenocytes were cultured for 72 h with or without 10 µM Imatinib (IM) .

tag: strain

value: female

value: 8 weeks

value: splenocytes

tag: agent

value: Imatinib (IM)


title: in vitro spleen cells 72hr IM(-)_rep2

description:
Gene expression in spleen cells cultured without 10 µM Imatinib in conditioning medium containing IL-4 and LPS for 72 h
US14702391_252665512076_S01_GE1-v5_91_0806_1_3.txt

source_name: spleen,72hr,IM(-), replicate 2

tag: gender

value: control


title: in vitro spleen cells 72hr IM(+)_rep1

description:
Gene expression in spleen cells cultured with 10 µM Imatinib in conditioning medium containing IL-4 and LPS for 72 h
US14702391_252665512076_S01_GE1-v5_91_0806_1_2.txt

source_name: spleen,72hr,IM(+), replicate 1


title: xylem, mature_tree50741

description:
JF003-8024.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: xylem, mature

growth_protocol: For a complete description of experimental site and sample collection see Beaulieu et al. (Genetics 188 [2011])

value: xylem (mature)


title: xylem, mature_tree41245

description:
JF003-8026.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: in vitro spleen cells 72hr IM(-)_rep1

description:
Gene expression in spleen cells cultured without 10 µM Imatinib in conditioning medium containing IL-4 and LPS for 72 h
US14702391_252665512076_S01_GE1-v5_91_0806_1_1.txt

source_name: spleen,72hr,IM(-), replicate 1


title: SET2_INC424_800nM_6h_1

description: SET2 cells exposed to 800 nM INC424  for 6h (replicate #1)