title: M_PM_BOBAK040


title: M_PM_BAKA0925r

status: Public on Nov 29 2014

type: genomic

city: Vancouver

first: Carolyn

middle: J

last: Brown

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

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

scan_protocol: BeadChips were imaged using HiScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: final male sample from PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA mini kit according to manufacturer's instructions.

value: M

tag: ethnicity

value: Baka

value: healthy

value: redone sample

value: PM

value: PBMC

tag: sample in final analysis

value: final male sample


title: M_PM_BAKA0928


title: M_PM_BAKA0927


title: M_PM_BOBAK153


title: M_PM_BAKA0920


title: M_PM_BAKA0909


title: M_PM_BAKA0908


title: M_PM_BAKA0917


title: M_PM_BAKA0906


title: M_PM_BAKA0912


title: M_PM_BAKA0907


title: M_PM_BAKA0904


title: M_B7_BA794

source_name: final male sample from brain7


title: M_B7_BA7250

value: sample replicated as .rep


title: M_B7_BA764


title: M_B7_BA7250_rep

value: replicated sample


title: M_B7_BA7245


title: M_B7_BA7216


title: M_PM_BAKA0918


title: M_B7_BA7234


title: M_B7_BA7173


title: M_B2_BA20250

source_name: final male sample from brain20


title: M_B7_BA7169


title: M_B2_BA20234


title: M_B7_BA7104


title: M_B2_BA2094


title: M_B7_BA7133


title: M_B7_BA7135


title: M_B7_BA7163


title: M_B2_BA20216


title: M_B2_BA20173


title: M_B7_BA7101


title: M_B2_BA20169


title: M_B2_BA20163


title: M_B2_BA20133


title: M_B2_BA20135


title: M_B2_BA2064


title: M_B1_BA1064

source_name: final male sample from brain10


title: M_B1_BA10250


title: M_B2_BA20101


title: M_B2_BA20245


title: M_B1_BA1094


title: M_B1_BA10173


title: M_B1_BA10216


title: M_B1_BA10169


title: M_B1_BA10163


title: M_B2_BA20104


title: M_B1_BA10133


title: M_B1_BA10234


title: M_B1_BA10104


title: M_PM_B177H_2


title: M_B1_BA10245


title: M_PM_B218D


title: M_PM_B195D


title: M_PM_B177H_1


title: M_PM_B187D


title: M_PM_B204D


title: M_PM_B179F


title: M_PM_B107F


title: M_B1_BA10135


title: M_B1_BA10101


title: M_PM_B072D


title: M_PM_B071L


title: M_PM_B219D


title: M_PM_B120L


title: M_PM_B105F


title: M_PM_B080F


title: M_PM_B084L


title: M_PM_B159F


title: M_PM_B128F


title: M_PM_B175D


title: M_PM_B041L


title: M_PM_B069F


title: M_PM_B071D


title: M_PM_B125F


title: M_PM_B029D_1


title: M_PM_B006D


title: M_PM_B006L


title: M_PM_B009D


title: M_PM_A079L_2


title: M_PM_B003L


title: M_PM_B102F


title: M_PM_A217D


title: M_PM_A051D


title: M_PM_C016D


title: F_PM_PBMC248

source_name: outlier female sample, not in analysis from PBMC

value: F

value: outlier female sample, not in analysis


title: M_PM_B029D_2


title: M_PM_A042D


title: M_PM_A035L


title: M_PM_A023D


title: M_PM_A007D


title: M_PM_A005F


title: M_PM_B004D


title: F_PM_MEBAK124


title: M_PM_A065L


title: M_PM_B039D


title: F_BS_X31_BS

source_name: final female sample from blood_spot

extract_protocol: Genomic DNA from WhatmanTM 903 Protein Saver Cards was isolated using GenSolve DNA Recovery Kit (GVR100, IntegenX), cleaned with the QiAmp DNA Micro Kit (Qiagen). and concentrated using Microcon DNA Fast Flow Devices, MRCF0R100 (Millipore).

value: BS

value: final female sample


title: M_PM_A079L_1


title: F_BS_X64_BS


title: F_BS_X255_BS


title: F_BS_X278_BS


title: F_BS_X252_BS


title: F_BS_X45_BSV


title: F_BS_X280_BS


title: F_BS_X56_BS


title: F_BS_X230_BS


title: F_BS_X216_BS


title: M_PM_A034L


title: F_BU_X190i

source_name: final female sample from buccal

extract_protocol: Genomic DNA was isolated using Isohelix Buccal DNA Isolation Kits (Cell Projects) and purified and concentrated using DNA Clean & Concentrator (Zymo Research) according to manufacturer's instruction.

value: BU

value: buccal


title: F_BS_X69_BS


title: F_BU_X189i


title: F_BS_X209_BS


title: F_BS_X183_BS


title: F_BU_X186i


title: F_BU_X187i


title: F_BU_X176i


title: F_BU_X179i


title: F_BU_X175i


title: F_BU_X171i


title: F_BU_X180i


title: F_BU_X166i


title: F_BU_X169i


title: F_BU_X173i


title: F_BS_X164_BS


title: F_BU_X162i


title: F_BU_X182i


title: F_BU_X163i


title: F_BU_X174i


title: F_BU_X161i


title: F_BU_X157i


title: F_BU_X160i


title: F_BS_X157_BS


title: F_BU_X158i


title: F_BU_X152i


title: F_BU_X148i


title: F_BU_X155i


title: F_BS_X152_BS


title: F_BU_X156i


title: F_BU_X159i


title: F_BU_X153i


title: F_BU_X149i


title: F_BU_X138i


title: F_BU_X143i


title: F_BU_X145i


title: F_BU_X131i


title: F_BU_X128i


title: F_BU_X123i


title: F_BU_X119i


title: F_BU_X144i


title: F_BS_X131_BS


title: F_BU_X130i


title: F_BU_X121i


title: F_BU_X122i


title: F_BU_X133i


title: F_BU_X147i


title: F_BU_X117i


title: F_BU_X114i


title: F_BU_X115i


title: F_BU_X142i


title: F_BU_X112i


title: F_BU_X110i


title: F_BU_X117r


title: F_BU_X107i


title: F_BU_X106i


title: F_BU_X102i


title: F_BS_X1097_BS


title: F_BU_X103i


title: F_BS_X1005_BS


title: F_BS_X1059_BS


title: F_BU_X099i


title: F_BU_X084i


title: F_BU_X086i


title: F_BU_X074i


title: F_BU_X087i


title: F_BU_X076i


title: F_BU_X095i


title: F_BU_X078r


title: F_BU_X072i


title: F_BU_X070i


title: F_BU_X097i


title: F_BU_X065i


title: F_BU_X068i


title: F_BU_X071i


title: F_BU_X078i


title: F_BU_X063i


title: F_BU_X082i


title: F_BU_X053i


title: F_BU_X060i


title: F_BU_X046i


title: F_BU_X045i


title: F_BU_X049i


title: F_BU_X051i


title: F_BU_X033i


title: F_BS_X221_BS


title: F_BU_X044i


title: F_BU_X043i


title: F_BU_X031i


title: F_BU_X029i


title: F_BU_X024i


title: F_BU_X028i


title: F_BU_X009i


title: F_BU_X010i


title: F_BU_X003i


title: F_BU_X018i


title: F_BU_X023i


title: F_BU_X011i


title: F_PM_TWA112

source_name: final female sample from PBMC

value: Batwa


title: F_PM_TWA121


title: F_BU_X001i


title: F_PM_TWA119r


title: F_BU_X005i


title: F_PM_TWA114r


title: F_BU_X014i


title: F_PM_TWA110


title: F_PM_TWA117


title: F_PM_TWA107


title: F_PM_TWA115


title: F_PM_TWA082


title: F_PM_TWA079


title: F_PM_TWA081r


title: F_PM_TWA074


title: F_PM_TWA080r


title: F_PM_TWA065


title: F_PM_TWA078


title: F_PM_TWA061


title: F_PM_TWA104


title: F_PM_TWA073


title: F_PM_TWA064


title: F_PM_TWA035


title: F_PM_TWA034


title: F_PM_TWA044


title: F_PM_PBMC242


title: F_PM_TWA036


title: F_PM_TWA002


title: F_PM_TWA069


title: F_PM_TWA050


title: F_PM_TWA032


title: F_PM_TWA071


title: F_PM_PBMC221


title: F_PM_TWA008


title: F_PM_NZE7035

value: Nzebi


title: F_PM_MEZI50

value: Nzime


title: F_PM_TWA048


title: F_PM_NZE7036


title: F_PM_PBMC189


title: F_PM_MEZI48


title: F_PM_MEZI46


title: F_PM_MEZI33r


title: F_PM_MEZI24


title: F_PM_MEZI18


title: F_PM_MEZI44


title: F_PM_MEZI17


title: F_PM_MEZI34


title: F_PM_MEZI11


title: F_PM_MEZI36


title: F_PM_MEZI38r


title: F_PM_R606


title: F_PM_MEDIV4


title: F_PM_MEZI42


title: F_PM_KIGA049

value: Bakiga


title: F_PM_KIGA050

value: healthy


title: F_PM_MEBAK051

value: Baka


title: F_PM_KIGA048

value: PM


title: F_PM_MEBAK101

value: PBMC


title: F_PM_MEBAK079r

value: redone sample


title: F_PM_MEDIV11


title: F_PM_KIGA047r


title: F_PM_KIGA044r


title: F_PM_KIGA051


title: F_PM_KIGA041


title: F_PM_KIGA045


title: F_PM_KIGA046


title: F_PM_KIGA038


title: F_PM_MEBAK054


title: F_PM_KIGA039


title: F_PM_KIGA043


title: F_PM_KIGA052


title: F_PM_KIGA037


title: F_PM_KIGA035


title: F_PM_KIGA029


title: F_PM_KIGA034r


title: F_PM_KIGA027


title: F_PM_KIGA021


title: F_PM_KIGA033


title: F_PM_KIGA022


title: F_PM_KIGA020


title: F_PM_KIGA030


title: F_PM_KIGA019


title: F_BU_EMVC083F


title: F_BU_EMVC054F


title: F_BU_EMVC077H


title: F_PM_KIGA001


title: F_PM_KIGA015


title: F_PM_KIGA008


title: F_BU_EMVC062D


title: F_PM_KIGA018


title: F_PM_KIGA009


title: F_BU_EMVC085L


title: F_PM_KIGA012


title: F_BU_EMVC049D


title: F_BU_EMVC063F


title: F_BU_EMVC080D


title: F_BU_EMVC050L


title: F_BU_EMVC074D


title: F_BU_EMVC048D


title: F_BU_EMVC038H


title: F_BU_EMVC045D_JAN5


title: F_BU_EMVC030D


title: F_BU_EMVC036H


title: F_BU_EMVC034D


title: F_PM_KIGA025


title: F_BU_EMVC019D


title: F_BU_EMVC016D


title: F_BU_EMVC022D


title: F_BU_EMVC014L


title: F_BU_EMVC011D


title: F_BU_EMVC023L


title: F_BU_EMVC010L


title: F_BU_EMVC003D


title: F_BU_EMVC009D


title: F_BU_EMVC002H


title: F_BU_EMVB189D


title: F_BU_EMVB213L


title: F_BU_EMVB190H


title: F_BU_EMVB193F


title: F_BU_EMVB201L


title: F_BU_EMVB186D


title: F_BU_EMVB212L


title: F_BU_EMVB183D


title: F_BU_EMVB209F


title: F_BU_EMVB208L


title: F_BU_EMVB181L


title: F_BU_EMVC013H


title: F_BU_EMVB182D


title: F_BU_EMVB180F_2


title: F_BU_EMVB191H


title: F_BU_EMVB180F_1


title: F_BU_EMVB176D


title: F_BU_EMVB171F


title: F_BU_EMVB173F


title: F_BU_EMVB166D


title: F_BU_EMVB164L


title: F_BU_EMVB174D


title: F_BU_EMVB177H


title: F_BU_EMVB165L


title: F_BU_EMVB162F_2


title: F_BU_EMVB158D


title: F_BU_EMVB152D


title: F_BU_EMVB162F_1


title: F_BU_EMVB132D


title: F_BU_EMVB137D


title: F_BU_EMVB155F


title: F_BU_EMVB131F


title: F_BU_EMVB142H


title: F_BU_EMVB135D


title: F_BU_EMVB121D


title: F_BU_EMVB122H


title: F_BU_EMVB136D


title: F_BU_EMVB160F


title: F_BU_EMVB149F


title: F_BU_EMVB116L


title: F_BU_EMVB119H


title: F_BU_EMVB150F


title: F_BU_EMVB124F


title: F_BU_EMVB118H


title: F_BU_EMVB110F


title: F_BU_EMVB106F


title: F_BU_EMVB104D


title: F_BU_EMVB109F


title: F_BU_EMVB091D


title: F_BU_EMVB111H


title: F_BU_EMVB088D


title: F_BU_EMVB114F


title: F_BU_EMVB115F


title: F_BU_EMVB086D


title: F_BU_EMVB089H


title: F_BU_EMVB074F


title: F_BU_EMVB083L


title: F_BU_EMVB079F


title: F_BU_EMVB067L


title: F_BU_EMVB053L


title: F_BU_EMVB062L_1


title: F_BU_EMVB065F


title: F_BU_EMVB078F


title: F_BU_EMVB057D


title: F_BU_EMVB085D


title: F_BU_EMVB077L


title: F_BU_EMVB045D


title: F_BU_EMVB050F


title: F_BU_EMVB069D


title: F_BU_EMVB047H


title: F_BU_EMVB034L


title: F_BU_EMVB037D


title: F_BU_EMVB033F


title: F_BU_EMVB052D


title: F_BU_EMVB051L


title: F_BU_EMVB054H


title: F_BU_EMVB028D


title: F_BU_EMVB036D


title: F_BU_EMVB024H


title: F_BU_EMVB023D


title: F_BU_EMVB020F


title: F_BU_EMVB022D


title: F_BU_EMVB013D


title: F_BU_EMVB040L


title: F_BU_EMVB027F


title: F_BU_EMVB015L


title: F_BU_EMVB005L_2


title: F_BU_CARE099F


title: F_BU_EMVB001L


title: F_BU_EMVB035D


title: F_BU_CARE102F


title: F_BU_EMVB018L


title: F_BU_EMVB021L


title: F_BU_CARE097F


title: F_BU_EMVB007L


title: F_BU_CARE092F


title: F_BU_EMVB011F


title: F_BU_CARE090F


title: F_BU_EMVB008F


title: F_BU_EMVB005L_1


title: F_BU_CARE088F


title: F_BU_CARE084F


title: F_BU_CARE072F


title: F_BU_CARE076F


title: F_BU_CARE086F


title: F_BU_CARE079F


title: F_BU_CARE071F


title: F_BU_CARE067F


title: F_BU_CARE096F


title: F_BU_CARE081F


title: F_BU_CARE070F


title: F_BU_CARE091F


title: F_BU_CARE065F


title: F_BU_CARE058F


title: F_BU_CARE064F


title: F_BU_CARE059F


title: F_BU_CARE039F


title: F_BU_CARE043F


title: F_BU_CARE055F


title: F_BU_CARE038F


title: F_BU_CARE051F


title: F_BU_CARE025F


title: F_BU_CARE032F


title: F_BU_CARE029F


title: F_BU_CARE035F


title: F_BU_CARE078F


title: F_BU_CARE010F


title: F_BU_CARE001F


title: F_BU_CARE062F


title: F_BU_CARE028F


title: F_PM_C097D


title: F_PM_C059L


title: F_PM_C083F


title: F_BU_CARE024F


title: F_PM_BOBAK199


title: F_BU_CARE004F


title: F_PM_BOBAK154


title: F_B7_BA7248

source_name: final female sample from brain7


title: F_PM_BOBAK057


title: F_PM_BOBAK045


title: F_B2_BA20248

source_name: final female sample from brain20


title: F_B2_BA20242


title: F_BU_CARE016F


title: F_B7_BA7189


title: F_B1_BA10248_1

source_name: final female sample from brain10

value: sample replicated as .rep


title: F_B1_BA10248_2

value: replicated sample


title: F_B2_BA20189

value: F


title: F_B7_BA7221


title: F_BU_CARE006F


title: F_B1_BA10221


title: F_B1_BA10242


title: F_B1_BA10189


title: F_PM_B180F


title: F_PM_B160F


title: F_PM_B155F_2


title: F_B7_BA7242


title: F_PM_B131F


title: F_PM_B144F


title: F_PM_B116L


title: F_PM_B109F


title: F_BU_EMVB046H


title: F_PM_B210F


title: F_BU_EMVB030D


title: F_PM_B083L


title: F_PM_B091D


title: F_PM_B130F


title: v-myc immortalized human Neural Stem Cell line 3_sample1

type: RNA

city: MADRID

first: María José

last: Pino-Barrio

state: MADRID

address: Avda Complutense, 40.

department: Hematopoietic Innovative Therapies Division.

country: Spain

institute: CIEMAT

description:
Test
hVM1_1

data_processing: The expression data were normalized taking into account the values of the genes that were expressed in all samples. The normalization formula is as follows: ΔCt(test) = (Ct(gene)- Ct(total average))/SD(Ct(total)).

label: FAM™

molecule: total RNA

source_name: v-myc hNSCs 3

extract_protocol: Total RNA was extracted using the High Pure RNA isolation Kit (Roche) following manufacturer’s guidelines.

treatment_protocol: Microfluidic RT-Q-PCR was performed in triplicate using the TaqMan® Human Stem Cell Pluripotency Array (Applied Biosystems). Regular RT- Q-PCR was performed using the ABI PRISM 7900 HT Sequence Detection System. One µg of RNA for each sample was subjected to reverse transcription using the High Capacity cDNA Achieve Kit (Applied Biosystems). For Real Time-Q-PCR 0.5 µg cDNA was amplified using TaqMan based technology (Applied Biosystems).

tag: tissue source

value: Midbrain

tag: cell line


title: v-myc immortalized human Neural Stem Cell line 3_sample2

description:
Test
hVM1_2


title: v-myc immortalized human Neural Stem Cell line 3_sample3

description:
Test
hVM1_3


title: v-myc immortalized human Neural Stem Cell line 2_sample1

description:
Test
hCTX_1

source_name: v-myc hNSCs 2

value: Cortex


title: v-myc immortalized human Neural Stem Cell line 2_sample2

description:
Test
hCTX_2


title: v-myc immortalized human Neural Stem Cell line 2_sample3

description:
Test
hCTX_3


title: v-myc immortalized human Neural Stem Cell line 2_sample4

description:
Test
hCTX_4


title: v-myc immortalized human Neural Stem Cell line 3_sample4

description:
Test
hVM1_4


title: F_PM_B074F

value: final female sample


title: F_PM_B069D


title: F_PM_B064L


title: v-myc immortalized human Neural Stem Cell line 1_sample4

description:
Test
hNS1_4

source_name: v-myc hNSCs 1

value: Forebrain


title: v-myc immortalized human Neural Stem Cell line 1_sample3

description:
Test
hNS1_3


title: v-myc immortalized human Neural Stem Cell line 1_sample2

description:
Test
hNS1_2


title: v-myc immortalized human Neural Stem Cell line 1_sample1

description:
Test
hNS1_1


title: human Neural Stem Cell line  9,5w_sample4

description:
Multipotent progenitor control
hNPCs 9.5_4

source_name: Neurospheres of 9,5 w

tag: cell type

value: neurospheres


title: F_PM_B057D_2


title: F_PM_B062L


title: human Neural Stem Cell line  9,5w_sample2

description:
Multipotent progenitor control
hNPCs 9.5_2


title: F_PM_B057D_1


title: human Neural Stem Cell line  9,5w_sample3

description:
Multipotent progenitor control
hNPCs 9.5_3


title: F_PM_B155F_1


title: human Neural Stem Cell line 10w_sample1

description:
Multipotent progenitor control
hNPCs 10_1

source_name: Neurospheres of 10 w


title: human Neural Stem Cell line 10w_sample2

description:
Multipotent progenitor control
hNPCs 10_2


title: human Neural Stem Cell line 10w_sample4

description:
Multipotent progenitor control
hNPCs 10_4


title: human Neural Stem Cell line 10w_sample3

description:
Multipotent progenitor control
hNPCs 10_3


title: human Neural Stem Cell line  9,5w_sample1

description:
Multipotent progenitor control
hNPCs 9.5_1


title: F_PM_B027F


title: human Foreskin Fibroblast_sample4

description:
Negative control, control of differentiation
hFF1_4

source_name: hFF 1

value: Foreskin


title: F_PM_B030D


title: F_PM_B052D_1


title: F_PM_B018L


title: F_PM_B008F


title: human Foreskin Fibroblast_sample3

description:
Negative control, control of differentiation
hFF1_3


title: F_PM_B011F


title: F_PM_A080L


title: F_PM_B052D_2


title: F_PM_B007L


title: BaR_2

city: Zurich

first: Maria Rita

last: Lecca

department: FGCZ

country: Switzerland

institute: University of Zurich

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Tomato Genome Oligo 4 x 44 K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent and finally air-dried before scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent  DANN Microarray C reader  using using a scan Control software version A.8.4.1 and one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Solanum lycopersicum

source_name: Basta resistant line T2

label_protocol: Cy3 cRNA were prepared according to the standard Agilent's protocol from 100 ng total RNA  (Agilent low Input (Low Input Quick Amp Labeling Kit, one-color).

growth_protocol: Tomato plants were germinated in a glass house under controlled conditions (25°C, 70% humidity), natural light regime and insect proof environment. A 1/1 mixture of peat Terraplant 2 (COMPO GmbH and Co. KG, Germany) and zeolite Litosand (natural product Tasajeras, Empresa Geominera del Centro, Cuba) was used for germination in pots. One month after germination, the plants that had reached a four leave stage were transplanted to a field area near Havana city in a randomized block design and cultivated from June to September, 2011. Temperature range in the field was between 25oC and 32oC. Both non-transgenic C plants and transgenic T1 and T2 plants were cultivated for four months under these open field conditions.

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

treatment_protocol: The KmR transgenic tomato line 126, designated here T1, has been generated previously by agrobacterium-mediated transformation of Solanum lycopersicum cv. Campbell-28 .The BaR transgenic tomato line B1, designated here T2, was generated by subcloning the RNAi hairpin expression cassette from the T1 as the Hind III fragment (Fuentes et al. 2006) into pCambia 3300 binary vector (carrying  phosphinothricin acetyl transferase marker gene for selection with Basta, designated here BaR) and transforming Campbell-28 tomato by agro-transformation

tag: cultivar

value: Campbell

tag: line

value: Transgenic line T2 (Basta-resistant (BaR) line B1)

tag: infectious agent

value: TYLCV

tag: genotype

value: TYLCV resistant


title: human Foreskin Fibroblast_sample2

description:
Negative control, control of differentiation
hFF1_2


title: F_BU_CARE017F

value: healthy

value: BU

value: buccal


title: human Embryonic Stem Cells 181_sample 4

description:
Positive control of pluripotency
HS181_4

source_name: hESCs 181

value: Inner cell mass (ICM) of human blastocyst


title: human Foreskin Fibroblast_sample1

description:
Negative control, control of differentiation
hFF1_1


title: F_PM_A064D

value: PM

value: PBMC


title: BaR_1


title: F_PM_A061D

value: F


title: human Embryonic Stem Cells 181_sample 3

description:
Positive control of pluripotency
HS181_3


title: human Embryonic Stem Cells 181_sample 2

description:
Positive control of pluripotency
HS181_2


title: F_PM_A056D


title: human Embryonic Stem Cells 181_sample 1

description:
Positive control of pluripotency
HS181_1


title: F_PM_A054L


title: F_PM_A053L


title: human Embryonic Stem Cells  9_sample3

description:
Positive control of pluripotency
H9_3

source_name: hESCs 9


title: KmR_1

source_name: Kanamycin resistant line T1

value: Transgenic line T1 (Kanamicin-resistant (KmR) line 126)


title: KmR_2


title: wt_C_2

source_name: Control tomato line C

value: control non transgenic

value: TYLCV sensitive


title: F_PM_A031D

value: final female sample


title: F_PM_A035F


title: F_PM_A026L


title: human Embryonic Stem Cells  9_sample2

description:
Positive control of pluripotency
H9_2


title: wt_C_1


title: human Embryonic Stem Cells  9_sample1

description:
Positive control of pluripotency
H9_1


title: XP+dox day7 1/21

city: Taipei

first: Liang-Ting

last: Lin

address: No.155, Sec.2, Li-Nong St., Beitou District

country: Taiwan

institute: National Yang-Ming University

description: miRNA expression of HCOXP cells with doxycycline treatment for 7 days

hyb_protocol: not provided

scan_protocol: Fluorescent images were obtained using Agilent Technologies Scanner G2505C US84303579

data_processing: Agilent Feature Extraction Software (v 10.1.1.1) was used for background subtraction and LOWESS normalization. Data analysis was performed using GenomicWorkbench v5.0(Agilent Technology)

source_name: HCOXP, doxycycline treated, 7 days

label_protocol: not provided

growth_protocol: The cells were maintained in Dulbecco modified Eagles' Medium (DMEM) with 10% fetal bovine serum supplied, and were incubated in humidified 37 degree Celsius incubator with 5% CO2.

extract_protocol: The cells were lysed by TRIzol reagent and froze. After thawing, the lysates were extracted by Zymo spin column. Total RNAs were then subjected to quantified and validated by Nanodrop ND-1000.

treatment_protocol: The cells were treated with doxycycline (1 ug/ml) for either 2 or 7 days after drug administration.

tag: tissue

value: Lung

tag: gender

value: male


title: H1299-dox day2 1/26

description: Basal miRNA expression of H1299 parental cells as negative control

source_name: H1299, doxycycline treated, 2 days


title: SKOM+Flag_Day5

city: Guangzhou

first: Yi

last: Wu

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health

description: Gene expression during reprogramming

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=3μm, 20bit.

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

organism: Mus musculus

source_name: Mouse embryonic fibroblasts infected with SKOM plus Flag, Day5

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), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

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: MEFs were infected with certain virus and then cultured in DMEM/High Glucose plus +15%FBS+NEAA+Gluta Max+Sodium Pyruvate+lif for 5 days.

value: embryonic fibroblasts

tag: day

value: 5 days


title: XP+dox day2 1/21

description: miRNA expression of HCOXP cells with doxycycline treatment for 2 days

source_name: HCOXP, doxycycline treated, 2 days


title: WT3

city: MAdrid

first: Gustavo

last: Melen

state: Madrid

address: Avda. Menendez Pelayo 65

institute: FIB Hospital NIño Jesus

description: Gene expression

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Kit.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.The signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified (using a linear T7-based amplification step) and labelled using the Agilent Low Input Quick-Amp Labelling kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from freshly sorted LSK population of NIKWT and NIKaly/aly mice using TRIzol reagent (Invitrogen) and its quality checked in the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: For LSK sorting we used a Beckman Coulter EPICS ALTRA Cell Sorter (Beckman Coulter, Inc).

tag: cell population

value: LSK

value: wild type


title: SKO+Flag_Day5

description: Gene expression during reprogramming

source_name: Mouse embryonic fibroblasts infected with SKO plus Flag, Day5


title: KO2

description: Gene expression

value: NIKaly/aly


title: H1299+dox day2 1/26

description: Basal miRNA expression of H1299 parental cells with doxycycline treatment as negative control

source_name: H1299, doxycycline treated, 7 days


title: WT1

description: Gene expression


title: SKOM+Srebp1_Day5

description: Gene expression during reprogramming

source_name: Mouse embryonic fibroblasts infected with SKOM plus Srebp1, Day5


title: WT5

description: Gene expression


title: F_PM_C098D

source_name: final female sample from PBMC

value: healthy


title: gs1;2 4th 2

status: Public on Nov 28 2014

city: Yokohama

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description: The sample was grown and harvested at the P1-green house in Tohoku university. For details, see Funayama et al. (2012) and Kamachi et al. (1991).

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 h on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suitesoftware.

data_processing: The microarray data normalization and background correction was performed using robust multi-array average (RMA) with Bioconductor package 'simpleaffy' by using R 3.1.0 for Windows (64 bit).

label: biotin

organism: Oryza sativa Japonica Group

source_name: 5-mm of basal parts, a homozygous gs1;2 plants, ammonium sufficient condition, 11 day-old sample

label_protocol: Biotinylated cRNA was labeled using a biotinylated nucleotide analog/ribonucleotide mix using GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol:
We grew samples under the following  condition. The conditions in the greenhouse at Tohoku University, Sendai, Japan were: 13h of light at 26oC and 11 h of darkness at 23oC without humidity control; light source, metal halide lamp (05:30 - 18:30) and sunlight.
Wild-type- and homozygous gs1;2 seeds were sterilized in 3 steps: (i) seeds were immersed in 60°C water for 10 min and then washed in flowing water for 10 min, (ii) immersed in 70% ethanol for 30 sec and washed immediately, and (iii) immersed in 2% hypochlorous acid for 20 min and then washed in water for 20 min. Then they were incubated at 30oC for 2 days in the dark. Germinated seeds were hydroponically grown for 7 or 11 days in one strength basal nutrient solution that lacked an N source and contained 150 μM NaH2PO4•2H2O, 75 μM K2SO4, 75 μM CaCl2•2H2O, 100 μM MgCl2•H2O, 11.25 μM Fe•EDTA, 12.5 μM H3BO3, 2.25 μM MnSO4•5H2O, 0.075 μM CuSO4•5H2O, 0.175 μM ZnSO4•7H2O, and 0.025 μM Na2MoO4•2H2O (3) and 1.0 mm NH4Cl to harvest the 5mm-of basal parts of shoots from the bottom.
Growth condition 3 for SAMPLE 13-36: We used the same growth chamber described under growth condition 2. The metal halide lamp was replaced with a non-polar lamp ‘enebright’ (TOSMO, Iwata, Japan). The average light strength and temperature in the growth chamber were 359 μmol∙m−2∙sec−1 and 30.5°C in the daytime. Plants were hydroponically grown for 18 days.

extract_protocol: Total RNA isolation was performed using RNeasy Plant Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instruction.

treatment_protocol: Germinated seeds were hydroponically grown under one strength basal nutrient solution lacking a nitrogen (N) source with 1 mM of ammonium for 7 and 11 days.

value: Nipponbare

value: 5-mm of basal parts

tag: growth period

value: 11 days

tag: treatment

value: full-strength basal nutrient solution lacking nitrogen source with 1 mM of ammonium


title: XP-dox day2 1/21

description: Basal miRNA expression of HCOXP cells

source_name: HCOXP, control, 2 days


title: KO6

description: Gene expression


title: WT 4th 14

source_name: 5-mm of basal parts, wild-type plants, ammonium sufficient condition, 11 day-old sample


title: gs1;2 4th 3


title: KO4

description: Gene expression


title: gs1;2 4th 1


title: Human umbilical cord blood CD34+CD45+ cells, biological rep1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

growth_protocol: MEF conditioned medium + 8ng/ml bFGF

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: not applicable

value: human umbilical cord blood CD34+CD45+ cells


title: hESC, biological rep3

source_name: hESC

label_protocol: In accordance with manufacturer's protocols

value: human embryonic stem cells (ESC)


title: F_PM_B121D

value: F

value: PM

value: PBMC


title: gs1;2 3rd 8

source_name: 5-mm of basal parts, a homozygous gs1;2 plants, ammonium sufficient condition, 7 day-old sample

value: 7 days


title: WT 4th 13


title: WT 3rd 9

source_name: 5-mm of basal parts, wild-type plants, ammonium sufficient condition, 7 day-old sample


title: WT 4th 15


title: Human umbilical cord blood CD34+CD45+ cells, biological rep2


title: hESC, biological rep2


title: iPSCs derived from human adult dermal fibroblasts, biological rep2_4

tag: somatic source

value: adult dermal fibroblasts (Fib)

value: Human induced pluripotent stem cells (hiPSCs)


title: gs1;2 3rd 10


title: hESC, biological rep1


title: WT 3rd 8


title: VI_14 days_S3

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

description:
DNA9182-013
miRNA Gene expression 14 days after vascular injury- Mouse carotid artery

hyb_protocol: All samples have been hybridized on one slide and extracted with Feature Extraction 9.5.1.1 from Agilent.

scan_protocol: For each sample, we analyzed the distribution of the Signal generated by the probes and those generated by the negative controls. We also looked at the average signal of the background and the % of CV.

data_processing: For each sample, and each probe of each miRNAs, we calculated the (median green signal – the median local background signal). Then we calculated the median of the median to provide the final net Signal. In order to be able to perform further comparisons between samples, we normalized the data according to the median of signal of all the miRNAs with an intensities >100 (which is considered as expressed).

source_name: Wire-injured carotid artery_14 days after injury

label_protocol: 700 ng of total RNA have been first processed according to the manufacturer's protocol. This method involves the ligation of one Cyanine 3-pCp molecule to the 3' end. The incorporation has been measured by Nanodrop for each sample. All samples were positive for the incorporation.

extract_protocol: RNA was prepared using the miRNeasy Mini Kit (Qiagen) following the manufacturer's recommendations.  The protocol includes tissue lysis, and an on-column DNase digestion. total RNA includes RNA from approximately 18 nucleotides upwards. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Wire-induced carotid injury was performed in ApoE-/- mice on western-type diet. Uninjured carotid arteries served as control. RNA was isolated after 1, 7, 14, and 28 days (n=3-4 each group) and hybridized to an Agilent microRNA microarray (Sanger v12).

tag: background strain

tag: genotype/variation

value: ApoE-/-

value: carotid artery

value: female

tag: age

value: 6 to 8 weeks


title: Ctrl_S2

description:
DNA9182-015
miRNA Gene expression- uninjured mouse carotid artery

source_name: un-injured carotid arteries


title: iPSCs derived from human adult dermal fibroblasts, biological rep2_1


title: VI_28 days_S1

description:
DNA9182-007
miRNA Gene expression 28 days after vascular injury- Mouse carotid artery

source_name: Wire-injured carotid artery_28 days after injury


title: VI_7 days_S3

description:
DNA9182-006
miRNA Gene expression 7 days after vascular injury- Mouse carotid artery

source_name: Wire-injured carotid artery_7 days after injury


title: VI_28 days_S3

description:
DNA9182-009
miRNA Gene expression 28 days after vascular injury- Mouse carotid artery


title: VI_14 days_S1

description:
DNA9182-011
miRNA Gene expression 14 days after vascular injury- Mouse carotid artery


title: VI_14 days_S2

description:
DNA9182-012
miRNA Gene expression 14 days after vascular injury- Mouse carotid artery


title: VI_28 days_S4

description:
DNA9182-010
miRNA Gene expression 28 days after vascular injury- Mouse carotid artery


title: VI_7 days_S2

description:
DNA9182-005
miRNA Gene expression 7 days after vascular injury- Mouse carotid artery


title: WT 3rd 7

value: wild type


title: iPSCs derived from human adult dermal fibroblasts, biological rep1_3


title: iPSCs derived from human adult dermal fibroblasts, biological rep1_2


title: iPSCs derived from human adult dermal fibroblasts, biological rep1_1


title: VI_28 days_S2

description:
DNA9182-008
miRNA Gene expression 28 days after vascular injury- Mouse carotid artery


title: VI_7 days_S1

description:
DNA9182-004
miRNA Gene expression 7 days after vascular injury- Mouse carotid artery


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep5_1

value: umbilical cord blood cells (CB)


title: VI_1 day_S3

description:
DNA9182-003
miRNA Gene expression 1 day after vascular injury- Mouse carotid artery

source_name: Wire-injured carotid artery_1 day after injury

value: 8 weeks


title: iPSCs derived from human adult dermal fibroblasts, biological rep2_3


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep3_2


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep3_3


title: Ctrl_S1

description:
DNA9182-014
miRNA Gene expression- uninjured mouse carotid artery


title: iPSCs derived from human adult dermal fibroblasts, biological rep2_2


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep5_2


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep5_3


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep3_1


title: Ctrl_S3

description:
DNA9182-016
miRNA Gene expression- uninjured mouse carotid artery


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep2_2


title: VI_1 day_S2

description:
DNA9182-002
miRNA Gene expression 1 day after vascular injury- Mouse carotid artery


title: 91072C2 subject ID number at time C2

status: Public on Nov 27 2014

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

description: Test

data_processing:
BioMark Real-time PCR Analysis V2.1.1, Fluidigm
Raw data obtained from the system’s software using the default global threshold were checked using the graphical representation of the plate layout. All amplification curves were displayed for each well of the calibrator sample made of the cDNA from the same total RNA sample was included in each plate for each of the 3 assay pools. When threshold for cycle did not meet quality criteria (i.e. threshold set in the linear phase of the amplification curve instead of the exponential phase), threshold value was set manually and the analysis parameters were changed to auto detector function for the corresponding gene. Wells with very high (>30) or absent (999) endogenous Ct were excluded.
Missing data were implemented using k nearest neighbour methods.

label: Taqman Fam-MGB

source_name: Subcutaneaous adipose tissue

label_protocol: cDNA was prepared from 200 ng or 500 ng of  total RNA, depending on RNA concentration and diluted in water to 5ng/µl (RNA-equivalent). Each diluted cDNA sample was split into 4 parts. The first part was used to check 18S expression level homogeneity using ABI Prism 7900HT (Applied Biosystems) to ensure good quality reverse transcription step. The 3 other parts were dedicated to target amplification for Biomark Dynamic Arrays. Inventoried TaqMan assays were pooled into 3 separate sets to a final concentration of 0.2X  for each of the assays. Each set included GUSB as reference gene. To increase sensitivity, a multiplexed preamplification process was performed for each pool on every 1.25µl cDNA using 14 cycle cDNA preamplification step (95°C for 15 s and 60°C 4 min) and Taqman PreAmp Master Mix (Applied Biosystems) in a standard PCR thermocycler. To check reproducibility and test normalization approaches a sample calibrator made of the cDNA from the same adipose tissue total RNA sample was included in each plate for each of the 3 assay pools. Preamplified cDNA was diluted 1:5 in 10 mmol/L Tris, 1 mmol/L EDTA. Diluted cDNA (2.25 µl) was added to 2.5 µl Taqman Universal PCR Master Mix (Applied Biosystems) and 0.25 µl GE Sample Loading Reagent (Fluidigm). In a separate tube, 3.5 µl of Taqman Assay was added to 3.5µl Sample Loading Reagent. Five µl cDNA samples were loaded into the sample inlet wells, and 5 µl assay samples were loaded into assay detector inlets. For each plate, 1 well was loaded with H20 as control for contamination and 1 well was loaded with the calibration sample. The chip was primed and placed into the NanoFlex Integrated fluidic circuit controller where 8 nl of cDNA and 1 nl of Assay were mixed. Real time PCR analysis was completed on the BioMark System (Fluidigm).

extract_protocol: Total RNA was extracted with the RNeasy mini lipid kit (Qiagen). Quality was checked by capillary electrophoresis (Experion, BioRad) and quantified using Nanodrop ND-1000 Spectrophotometer (Labtech).

treatment_protocol: Adipose tissue biopsies were rinsed from blood using PBS, frozen in liquid nitrogen and stored at -80°C until batch RNA extraction.

value: Female

value: Adipose

tag: time

value: After calorie restriction (C2) 8 wk


title: 91072C3 subject ID number at time C3

description: Test

value: After weight maintenance (C3) 26 wk


title: VI_1 day_S1

description:
DNA9182-001
miRNA Gene expression 1 day after vascular injury- Mouse carotid artery


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep2_1


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep1_2


title: 90992C1 subject ID number at time C1

description: Control

value: Baseline (C1)


title: 90992C3 subject ID number at time C3

description: Test


title: 90982C2 subject ID number at time C2

description: Test


title: 91072C1 subject ID number at time C1

description: Control


title: iPSCs derived from human cord blood CD34+CD45+ cells, biological rep1_1


title: 90982C3 subject ID number at time C3

description: Test


title: 90992C2 subject ID number at time C2

description: Test


title: 90972C2 subject ID number at time C2

description: Test


title: 90972C3 subject ID number at time C3

description: Test


title: 90952C2 subject ID number at time C2

description: Test


title: 90982C1 subject ID number at time C1

description: Control


title: 90972C1 subject ID number at time C1

description: Control


title: 90882C3 subject ID number at time C3

description: Test


title: 90882C2 subject ID number at time C2

description: Test


title: 90952C1 subject ID number at time C1

description: Control


title: 90882C1 subject ID number at time C1

description: Control


title: 90872C2 subject ID number at time C2

description: Test


title: 90872C3 subject ID number at time C3

description: Test


title: 90872C1 subject ID number at time C1

description: Control


title: 90812C3 subject ID number at time C3

description: Test


title: 90812C2 subject ID number at time C2

description: Test


title: 90802C3 subject ID number at time C3

description: Test


title: 90812C1 subject ID number at time C1

description: Control


title: 90802C1 subject ID number at time C1

description: Control


title: 90782C3 subject ID number at time C3

description: Test


title: 90952C3 subject ID number at time C3

description: Test


title: 90782C1 subject ID number at time C1

description: Control


title: 90752C3 subject ID number at time C3

description: Test


title: 90782C2 subject ID number at time C2

description: Test


title: 90752C2 subject ID number at time C2

description: Test


title: 90762C3 subject ID number at time C3

description: Test


title: 90762C1 subject ID number at time C1

description: Control


title: 90752C1 subject ID number at time C1

description: Control


title: 90692C2 subject ID number at time C2

description: Test


title: 90692C3 subject ID number at time C3

description: Test


title: 90572C3 subject ID number at time C3

description: Test


title: 90692C1 subject ID number at time C1

description: Control


title: 90802C2 subject ID number at time C2

description: Test


title: 90562C2 subject ID number at time C2

description: Test


title: 90572C1 subject ID number at time C1

description: Control


title: 90532C1 subject ID number at time C1

description: Control


title: 90532C2 subject ID number at time C2

description: Test


title: 90532C3 subject ID number at time C3

description: Test


title: 90562C1 subject ID number at time C1

description: Control


title: 90192C3 subject ID number at time C3

description: Test


title: 90202C2 subject ID number at time C2

description: Test


title: 90192C2 subject ID number at time C2

description: Test


title: 90202C3 subject ID number at time C3

description: Test


title: 90182C3 subject ID number at time C3

description: Test


title: 90182C1 subject ID number at time C1

description: Control


title: 90572C2 subject ID number at time C2

description: Test


title: 90192C1 subject ID number at time C1

description: Control


title: 90762C2 subject ID number at time C2

description: Test


title: 90562C3 subject ID number at time C3

description: Test


title: 70912C2 subject ID number at time C2

description: Test


title: 70912C3 subject ID number at time C3

description: Test


title: 70912C1 subject ID number at time C1

description: Control


title: 70902C3 subject ID number at time C3

description: Test


title: 70902C2 subject ID number at time C2

description: Test


title: 70902C1 subject ID number at time C1

description: Control


title: gs1;2 3rd 9

description: The sample was grown and harvested at the P1-green house in Tohoku university. For details, see Funayama et al. (2012) and Kamachi et al. (1991).

value: Nipponbare

value: 5-mm of basal parts

value: full-strength basal nutrient solution lacking nitrogen source with 1 mM of ammonium


title: 90182C2 subject ID number at time C2

description: Test


title: human Embryonic Stem Cells  9_sample4

description:
Positive control of pluripotency
H9_4

source_name: hESCs 9

tag: tissue source

value: Inner cell mass (ICM) of human blastocyst

tag: cell line


title: 70882C3 subject ID number at time C3

description: Test


title: 70882C2 subject ID number at time C2

description: Test


title: 70872C3 subject ID number at time C3

description: Test


title: 70882C1 subject ID number at time C1

description: Control


title: 70872C1 subject ID number at time C1

description: Control


title: 70852C2 subject ID number at time C2

description: Test


title: 70852C3 subject ID number at time C3

description: Test


title: 70842C3 subject ID number at time C3

description: Test


title: 70842C2 subject ID number at time C2

description: Test


title: 70842C1 subject ID number at time C1

description: Control


title: 70832C2 subject ID number at time C2

description: Test


title: 70832C1 subject ID number at time C1

description: Control


title: 70812C1 subject ID number at time C1

description: Control


title: 70762C3 subject ID number at time C3

description: Test


title: 90202C1 subject ID number at time C1

description: Control


title: 70812C2 subject ID number at time C2

description: Test


title: 70762C2 subject ID number at time C2

description: Test


title: 70762C1 subject ID number at time C1

description: Control


title: 70752C3 subject ID number at time C3

description: Test


title: 70752C1 subject ID number at time C1

description: Control


title: 70712C3 subject ID number at time C3

description: Test


title: 70712C2 subject ID number at time C2

description: Test


title: 70692C2 subject ID number at time C2

description: Test


title: 70872C2 subject ID number at time C2

description: Test


title: 70692C3 subject ID number at time C3

description: Test


title: 70592C3 subject ID number at time C3

description: Test


title: 70852C1 subject ID number at time C1

description: Control


title: 70712C1 subject ID number at time C1

description: Control


title: 70692C1 subject ID number at time C1

description: Control


title: 70832C3 subject ID number at time C3

description: Test


title: 70812C3 subject ID number at time C3

description: Test


title: 70592C1 subject ID number at time C1

description: Control


title: 70592C2 subject ID number at time C2

description: Test


title: 70572C3 subject ID number at time C3

description: Test


title: 70572C1 subject ID number at time C1

description: Control


title: 70752C2 subject ID number at time C2

description: Test


title: 70572C2 subject ID number at time C2

description: Test


title: 70502C2 subject ID number at time C2

description: Test


title: 70492C2 subject ID number at time C2

description: Test


title: 70502C1 subject ID number at time C1

description: Control


title: 70562C3 subject ID number at time C3

description: Test


title: 70492C3 subject ID number at time C3

description: Test


title: 70492C1 subject ID number at time C1

description: Control


title: 70482C3 subject ID number at time C3

description: Test


title: 70442C3 subject ID number at time C3

description: Test


title: 70442C1 subject ID number at time C1

description: Control


title: 70432C2 subject ID number at time C2

description: Test


title: 70432C3 subject ID number at time C3

description: Test


title: 70442C2 subject ID number at time C2

description: Test


title: 70422C3 subject ID number at time C3

description: Test


title: 70422C1 subject ID number at time C1

description: Control


title: 70562C1 subject ID number at time C1

description: Control


title: 70422C2 subject ID number at time C2

description: Test


title: 70562C2 subject ID number at time C2

description: Test


title: 70502C3 subject ID number at time C3

description: Test


title: 70402C3 subject ID number at time C3

description: Test


title: 70402C1 subject ID number at time C1

description: Control


title: 70482C2 subject ID number at time C2

description: Test


title: 70392C1 subject ID number at time C1

description: Control


title: 70402C2 subject ID number at time C2

description: Test


title: 70392C2 subject ID number at time C2

description: Test


title: 70482C1 subject ID number at time C1

description: Control


title: 70252C2 subject ID number at time C2

description: Test


title: 70252C1 subject ID number at time C1

description: Control


title: 70252C3 subject ID number at time C3

description: Test


title: 70432C1 subject ID number at time C1

description: Control


title: 61022C3 subject ID number at time C3

description: Test


title: 60652C3 subject ID number at time C3

description: Test


title: 61022C1 subject ID number at time C1

description: Control


title: 60792C2 subject ID number at time C2

description: Test


title: 60792C3 subject ID number at time C3

description: Test


title: 60792C1 subject ID number at time C1

description: Control


title: 60652C2 subject ID number at time C2

description: Test


title: 60652C1 subject ID number at time C1

description: Control


title: 60642C3 subject ID number at time C3

description: Test


title: 60642C2 subject ID number at time C2

description: Test


title: 70392C3 subject ID number at time C3

description: Test


title: 60642C1 subject ID number at time C1

description: Control


title: 60562C3 subject ID number at time C3

description: Test


title: 60552C3 subject ID number at time C3

description: Test


title: 60562C1 subject ID number at time C1

description: Control


title: 60552C2 subject ID number at time C2

description: Test


title: 60552C1 subject ID number at time C1

description: Control


title: 60432C1 subject ID number at time C1

description: Control


title: 60322C1 subject ID number at time C1

description: Control


title: 60432C3 subject ID number at time C3

description: Test


title: 60432C2 subject ID number at time C2

description: Test


title: 61022C2 subject ID number at time C2

description: Test


title: 60322C2 subject ID number at time C2

description: Test


title: 50942C1 subject ID number at time C1

description: Control


title: 60322C3 subject ID number at time C3

description: Test


title: 50942C3 subject ID number at time C3

description: Test


title: 50902C2 subject ID number at time C2

description: Test


title: 50942C2 subject ID number at time C2

description: Test


title: 50902C1 subject ID number at time C1

description: Control


title: 50882C3 subject ID number at time C3

description: Test


title: 60562C2 subject ID number at time C2

description: Test


title: 50872C2 subject ID number at time C2

description: Test


title: 50882C1 subject ID number at time C1

description: Control


title: 50872C3 subject ID number at time C3

description: Test


title: 50862C1 subject ID number at time C1

description: Control


title: 50862C2 subject ID number at time C2

description: Test


title: 50862C3 subject ID number at time C3

description: Test


title: 50872C1 subject ID number at time C1

description: Control


title: 50792C3 subject ID number at time C3

description: Test


title: 50902C3 subject ID number at time C3

description: Test


title: 50882C2 subject ID number at time C2

description: Test


title: 50732C2 subject ID number at time C2

description: Test


title: 50732C3 subject ID number at time C3

description: Test


title: 50792C2 subject ID number at time C2

description: Test


title: 50742C1 subject ID number at time C1

description: Control


title: 50742C3 subject ID number at time C3

description: Test


title: 50792C1 subject ID number at time C1

description: Control


title: 50482C2 subject ID number at time C2

description: Test


title: 50552C3 subject ID number at time C3

description: Test


title: 50552C1 subject ID number at time C1

description: Control


title: 50722C3 subject ID number at time C3

description: Test


title: 50572C1 subject ID number at time C1

description: Control


title: 50722C1 subject ID number at time C1

description: Control


title: 50482C3 subject ID number at time C3

description: Test


title: 50572C3 subject ID number at time C3

description: Test


title: 50572C2 subject ID number at time C2

description: Test


title: 50722C2 subject ID number at time C2

description: Test


title: 50552C2 subject ID number at time C2

description: Test


title: 50732C1 subject ID number at time C1

description: Control


title: 50432C2 subject ID number at time C2

description: Test


title: 50362C2 subject ID number at time C2

description: Test


title: 50432C3 subject ID number at time C3

description: Test


title: 50362C3 subject ID number at time C3

description: Test


title: 50412C3 subject ID number at time C3

description: Test


title: 50412C2 subject ID number at time C2

description: Test


title: 50482C1 subject ID number at time C1

description: Control


title: 50412C1 subject ID number at time C1

description: Control


title: 50742C2 subject ID number at time C2

description: Test


title: 50362C1 subject ID number at time C1

description: Control


title: 50312C3 subject ID number at time C3

description: Test


title: 50432C1 subject ID number at time C1

description: Control


title: 50252C3 subject ID number at time C3

description: Test


title: 50312C1 subject ID number at time C1

description: Control


title: 50252C1 subject ID number at time C1

description: Control


title: 50252C2 subject ID number at time C2

description: Test


title: 50312C2 subject ID number at time C2

description: Test


title: 50072C2 subject ID number at time C2

description: Test


title: 50152C3 subject ID number at time C3

description: Test


title: 50182C3 subject ID number at time C3

description: Test


title: 50062C1 subject ID number at time C1

description: Control


title: 50182C1 subject ID number at time C1

description: Control


title: 50072C1 subject ID number at time C1

description: Control


title: 40972C1 subject ID number at time C1

description: Control


title: 50182C2 subject ID number at time C2

description: Test


title: 50072C3 subject ID number at time C3

description: Test


title: 40972C2 subject ID number at time C2

description: Test


title: 50062C2 subject ID number at time C2

description: Test


title: 40932C2 subject ID number at time C2

description: Test


title: 50052C3 subject ID number at time C3

description: Test


title: 50052C2 subject ID number at time C2

description: Test


title: 50152C2 subject ID number at time C2

description: Test


title: 40932C3 subject ID number at time C3

description: Test


title: 40342C2 subject ID number at time C2

description: Test


title: 40342C3 subject ID number at time C3

description: Test


title: 50052C1 subject ID number at time C1

description: Control


title: 40342C1 subject ID number at time C1

description: Control


title: 40282C3 subject ID number at time C3

description: Test


title: 50152C1 subject ID number at time C1

description: Control


title: 40282C2 subject ID number at time C2

description: Test


title: 40282C1 subject ID number at time C1

description: Control


title: 40152C3 subject ID number at time C3

description: Test


title: 40152C2 subject ID number at time C2

description: Test


title: 31172C1 subject ID number at time C1

description: Control


title: 31022C2 subject ID number at time C2

description: Test


title: 40932C1 subject ID number at time C1

description: Control


title: 50062C3 subject ID number at time C3

description: Test


title: 31022C1 subject ID number at time C1

description: Control


title: 40972C3 subject ID number at time C3

description: Test


title: 31022C3 subject ID number at time C3

description: Test


title: 40152C1 subject ID number at time C1

description: Control


title: 31172C3 subject ID number at time C3

description: Test


title: 31172C2 subject ID number at time C2

description: Test


title: 30992C1 subject ID number at time C1

description: Control


title: 30922C2 subject ID number at time C2

description: Test


title: 30882C2 subject ID number at time C2

description: Test


title: 30902C2 subject ID number at time C2

description: Test


title: 30882C3 subject ID number at time C3

description: Test


title: 30992C2 subject ID number at time C2

description: Test


title: 30902C3 subject ID number at time C3

description: Test


title: 30882C1 subject ID number at time C1

description: Control


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description: Test


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description: Test


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description: Control


title: 30842C2 subject ID number at time C2

description: Test


title: 30842C1 subject ID number at time C1

description: Control


title: 30802C3 subject ID number at time C3

description: Test


title: 30902C1 subject ID number at time C1

description: Control


title: 30922C3 subject ID number at time C3

description: Test


title: 30802C2 subject ID number at time C2

description: Test


title: 30612C2 subject ID number at time C2

description: Test


title: 30802C1 subject ID number at time C1

description: Control


title: 30612C3 subject ID number at time C3

description: Test


title: 30502C2 subject ID number at time C2

description: Test


title: 30612C1 subject ID number at time C1

description: Control


title: 30502C3 subject ID number at time C3

description: Test


title: 30482C2 subject ID number at time C2

description: Test


title: 30472C3 subject ID number at time C3

description: Test


title: 30472C2 subject ID number at time C2

description: Test


title: 30502C1 subject ID number at time C1

description: Control


title: 30482C1 subject ID number at time C1

description: Control


title: 30482C3 subject ID number at time C3

description: Test


title: 30472C1 subject ID number at time C1

description: Control


title: 30382C3 subject ID number at time C3

description: Test


title: 30382C1 subject ID number at time C1

description: Control


title: 30372C3 subject ID number at time C3

description: Test


title: 30372C2 subject ID number at time C2

description: Test


title: 30382C2 subject ID number at time C2

description: Test


title: 30182C3 subject ID number at time C3

description: Test


title: 30332C1 subject ID number at time C1

description: Control


title: 30262C2 subject ID number at time C2

description: Test


title: 30162C3 subject ID number at time C3

description: Test


title: 30162C2 subject ID number at time C2

description: Test


title: 30332C2 subject ID number at time C2

description: Test


title: 30332C3 subject ID number at time C3

description: Test


title: 30182C2 subject ID number at time C2

description: Test


title: 30262C3 subject ID number at time C3

description: Test


title: 30372C1 subject ID number at time C1

description: Control


title: 30262C1 subject ID number at time C1

description: Control


title: 30132C3 subject ID number at time C3

description: Test


title: Kc Mcm2-7 HU Replicate 2 Array 4

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University

description: Biological Replicate 2 Array 4: Mcm2-7 ChIP relative to input

hyb_protocol: Agilent hybridization protocol; Setting up hybridization 1.Thaw samples on ice, in the dark 2.Set up hyb reaction: (Oligo aCGH/ChOP-on-Chip Hyb kit; Agilent) sample 25ul Ambion dH2O 175ul 10X Blocking Solution 50ul 2X Hybridization buffer 250ul 3.Inc 95C, 5 minutes 4.Spin down briefly and keep at 37C while getting slide ready 5.Place gasket with agilent side facing up on metal chamber 6.Pipet 490ul of hyb reaction on gasket 7.Lay down microarray on hyb reaction with Agilent side down. 8.Assemble metal chamber 9.inc. 16-20 hours in rotating hyb oven at 65C Washing microarrays 10.Dissamble arrays in tip box lid containing Buffer 1 (Agilent) 11.Wash slide in buffer 1 with stirring, 5 minutes 12.Wash slide in buffer 2 with stirring, 5 minutes 13.Wash slide in acetonitrile, 30 seconds 14.Wash slide in buffer 3, 30 seconds 15.Store in light proof holder and scan

scan_protocol: Array scanning protocol; Scanning per Agilent recommendations.

data_processing:
Data was normalized with the R package limma and log2 ratio of probe intensities were determined via MA2C.
Normalized log2 ratio (Cy5/Cy3) representing Mcm2-7 ChIP / input

organism: Drosophila melanogaster

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 2 Array 4

label_protocol: Sequenase labeling protocol; 1.Thaw DNA samples on ice 2.Transfer to 0.2ml pcr tubes. Open tubes and place inside a 1.5ml tube 3.Speed vac samples on medium heat for approx. 15-18 minutes 4.Resusp DNA in sequenase primer mix: 5X sequenase buffer 2ul (US Biochemicals) random nonamer 5ul (NNNNNNNNN; hand mixed 25,25,25,25) Ambion dH2O 1ul 5.Thaw Cy dyes (Cy 3 dUTP and Cy 5 dUTP; Perkin Elmer) on ice and in the dark 6.Add 2ul of cy dye to DNA sample 7.Start pcr program: 95C 3' 4C 2' 37C 30' ramp 95C 2' 4C 2' 37C 30' ramp 4C hold 8.At the first 4C step in program, add the following: 5X sequenase buffer 1ul Low T 1.5ul (5ul dATP, 5ul dCTP, 5ul dGTP, 2ul dTTP, 83ul ambion dH2O) 100 mM BSA 1ul 100mM DTT 0.75ul sequenase 1ul 9.At the second 4C step, add additional sequenase and finish program sequenase buffer DLT 0.7ul sequenase 0.3ul 10.Clean samples on YM-30 microcon column (Millipore) according to directions 11.Spec samples

growth_protocol: Cells were cultured in 150-mm plates at an approximate density of 1 x 10E6 cells/mL in Schneider's Insect Cell Medium (Invitrogen) supplemented with 10% heat-inactivated FBS (Hyclone) and 1% penicillin/streptomycin/glutamine (Invitrogen).

extract_protocol: ChIP crosslinking and isolation protocol; 1. Crosslink cells at room temperature with 1% formaldehyde (Ted Pella #18505) for 10 min. 2. Quench reaction with 125 mM glycine for 5 min at room temp. 3. Centrifuge cross-linked cells, 1,000 rpm, 10 min. 4. Wash cells with 2X cold 1X PBS. 5. Freeze pellet with liquid nitrogen and store at -80C for at least two hours 6. Thaw pellet on ice and prepare lysis buffers: Lysis Buffer 1: 50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1/2 mini protease tablet (Roche) per 5ml of buffer; Lysis Buffer 2: 10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 EGTA, 1/2 protease tablet per 5ml of buffer; Lysis Buffer 3: 10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1/2 mini protease tablet per 5ml buffer 7. Keep lysis buffers on ice 8. Resuspend pellet in 5ml lysis buffer 1 and incubate with rotation at 4C for 10min. 9. Centrifuge, 4C, 1350xg, 5 min 10.Resuspend pellet in 5ml lysis buffer 2 and incubate with rotation at room temperature for 10 min. 11. Centrifuge, 4C, 1350xg, 5 min 12. Resuspend in 3 mL lysis buffer 3 13. sonicate extract to an average size of 1Kb. 14. Add Triton X-100 to 1%. vortex gently 15. Centrifuge at 4C, 20,000xg, 10min. 16. Aliquot extracts into ~500ul samples.  The chromatin was immunoprecipitated with the Mcm2-7 monoclonal mouse antibody (AS1.1) and used at a 1/25 dilution.

treatment_protocol: Cells were incubated with 1 mM HU for 24 h to arrest cells in G1/S.

tag: chip antibody

source_name: Input: Kc Mcm2-7 HU Replicate 2 Array 4

value: input


title: 30112C2 subject ID number at time C2

description: Test


title: 30132C2 subject ID number at time C2

description: Test


title: 30132C1 subject ID number at time C1

description: Control


title: 30112C3 subject ID number at time C3

description: Test


title: 30182C1 subject ID number at time C1

description: Control


title: 30112C1 subject ID number at time C1

description: Control


title: 30162C1 subject ID number at time C1

description: Control


title: 30012C3 subject ID number at time C3

description: Test


title: 30012C1 subject ID number at time C1

description: Control


title: 21002C1 subject ID number at time C1

description: Control


title: 20822C2 subject ID number at time C2

description: Test


title: 20822C3 subject ID number at time C3

description: Test


title: 21002C3 subject ID number at time C3

description: Test


title: 20822C1 subject ID number at time C1

description: Control


title: 30012C2 subject ID number at time C2

description: Test


title: 21002C2 subject ID number at time C2

description: Test


title: Kc Mcm2-7 HU Replicate 1 Array 4

description: Biological Replicate 1 Array 4: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 1 Array 4

source_name: Input: Kc Mcm2-7 HU Replicate 1 Array 4


title: 20782C3 subject ID number at time C3

description: Test


title: 20782C1 subject ID number at time C1

description: Control


title: Control,CK3,biological rep1

city: Beijing

first: Jin

middle: Hui

last: Chen

state: Beijing

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Biotechnology, Beijing Forestry University

institute: Beijing Forestry University

description: Expression data from one year old leaves of Populus simonii

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Populus simonii

source_name: Populus simonii leaves from controls

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The cuttings were planted in basins (15 cm diameter × 10 cm depth) that contained sand, organic matter and vermiculite (3:1:1,v/v/v) in the greenhouse of Beijing Forestry University in March 2010. After sprouting and growth for about one year, healthy cuttings with approximately the same crown size and equal height were chosen and moved into growth chambers at the laboratory of Beijing Forestry University.

extract_protocol: Total RNA was extracted by the procedure of Chang et al(Chang, et al. 1993). mRNA was isolated from total RNA (~0.5 mg for each treatment) using the PolyAtract mRNA Isolation System (Promega). Double-stranded cDNA was then synthesized from mRNA with the Universal RiboClone cDNA Synthesis System (Promega) following the manufacturer’s protocol. The synthesized cDNA was dissolved in 50 μl TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The NaCl treatments were carried by roots exposed to 100 mMol/L NaCl 24 hours and the controls were water as normal.

value: leaves


title: Control,CK1,biological rep1

data_processing: Raw data were normalized by MAS 5.0 algorithm, Expression Console.


title: Control,CK2,biological rep1


title: 100 mMol/L NaCl treatments 24 hours,S1,biological rep1

source_name: Populus simonii leaves from NaCl treatments


title: 100 mMol/L NaCl treatments 24 hours,S2,biological rep1


title: 100 mMol/L NaCl treatments 24 hours,S3,biological rep1


title: 20732C3 subject ID number at time C3

description: Test


title: 20732C1 subject ID number at time C1

description: Control


title: 20732C2 subject ID number at time C2

description: Test


title: 20572C3 subject ID number at time C3

description: Test


title: 20572C2 subject ID number at time C2

description: Test


title: 20572C1 subject ID number at time C1

description: Control


title: 20472C3 subject ID number at time C3

description: Test


title: MUNC deprived differentiating cells

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

description:
differentiating cells
C12C12 DM3 siMUNC

hyb_protocol: The Ambion® WT Expression Kit For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays

scan_protocol: Affymetrix scanner 3000 with 7G upgrade, Fluidics Stations 450; standard scanner settings

data_processing: Affymetrix Expression Console  Console software and Microsoft Excel

source_name: C2C12 cell line_siMUNC_differentiating

label_protocol: GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit

growth_protocol: C2C12 cells were cultured in 10% FBS high glucose DMEM medium (proliferating cells)

extract_protocol: RNA was extracted using TRIZOL method

treatment_protocol: Differentiation: when cells were 80% confluent medium was changed to 2% horse serum containing DMEM medium. Cells were collected 3 days after differentiation.

tag: knockdown

value: siMUNC


title: control differentiating cells

description:
differentiating cells
C2C12 DM3 siCONTROL

source_name: C2C12 cell line_control_differentiating

value: control


title: control proliferating cells

description:
proliferating cells
C2C12 GM siCONTROL

source_name: C2C12 cell line_control_proliferating


title: MUNC deprived proliferating cells

description:
proliferating cells
C2C12 GM siMUNC

source_name: C2C12 cell line_siMUNC_proliferating


title: 20442C1 subject ID number at time C1

description: Control


title: 20442C3 subject ID number at time C3

description: Test


title: 20472C2 subject ID number at time C2

description: Test


title: 20442C2 subject ID number at time C2

description: Test


title: 20392C3 subject ID number at time C3

description: Test


title: VMH Nkx2-1 f/f rep1

city: San Francisco

first: Holly

middle: A

last: Ingraham

state: CA

address: 1550 4th St., Rock Hall 284E

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: raw data are supplied, normalized data normalized by quartile method

source_name: Mouse ventromedial hypothalamus

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

growth_protocol: Mice were housed with their parents in a breeding duo and fed a standard breeder chow

extract_protocol: Total RNA was isolated using the PureLink Total RNA kit from Invitrogen

tag: Sex

value: female

tag: developmental stage

value: VMH Nkx2-1 f/f


title: VMH Nkx2-1 f/f; Sf1Cre rep3

value: VMH Nkx2-1 f/f; Sf1Cre


title: 20392C1 subject ID number at time C1

description: Control

tag: tissue


title: VMH Nkx2-1 f/f; Sf1Cre rep4


title: 20472C1 subject ID number at time C1

description: Control

tag: gender


title: 20392C2 subject ID number at time C2

description: Test


title: Lactation day 171 [TR022-021003_635]

city: Bundoora

first: Christy

last: Vander Jagt

state: Victoria

address: 5 Ring Road, LaTrobe University

department: Computational Biology

country: Australia

institute: Department of Environment and Primary Industries

hyb_protocol: 1. Paired Cy3 and Cy5 labelled cDNA samples were combined and rotated in a Centrivap Concentrator (Labconco) at 35C until completely dried (approximately 30 minutes) 2. Samples were resuspended in 8 ul of nuclease free water (Amersham Biosciences) and denatured at 95C for 2 minutes before placing on ice for a minimum of 30 seconds 3. To reduce non-specific binding of target to the array surface, 2 uL of poly A (1 mg / 1 ml) was added to each sample and incubated at 75C for 45 minutes 4. Following the incubation, 10 ul of CyScribe kit hybrisation buffer and 20 ul of deionised formamide (Amresco) were added 5. The reaction mixtures were applied evenly across the array area of the prepared microarray slides, and coverslips were lowered with care, making sure no bubbles were present 6. Slides were placed into ArrayIt Hybridisation Cassettes (TeleChem International Inc) and 60 ul of 3 x SSC added to each well at the ends of the hybridisation cassettes 7. Slides were allowed to hybridise in the cassettes overnight in a 42C waterbath

scan_protocol: Hybridised microarray slides were scanned at 595 nm and 685 nm for detection of bound Cy3 and Cy5 cDNA respectively using the laser-induced fluorescence Agilent G2565BA Microarray Scanner System with SureScan Technology (Agilent Technologies). All slides were scanned using the default settings recommended by Agilent Technologies.

data_processing:
Spot signal intensity data was computed from the microarray images using ImaGene 5.5 Standard Edition (Biodiscovery Inc.)
Analysis of the quantified image data was performed in the R statistical environment using LIMMA (Linear Models for Microarray Data). Microarray data was background corrected using the normexp method. An offset value of 50 was used during background correction to add a constant to the intensities before log-transforming so that log-ratios are shrunk towards zero at the lower intensities. Print-tip loess normalisation was performed for each microarray slide before Aquantile normalisation was applied to allow for comparisons between slides. Following normalisation, separate channel analysis was performed by fitting a linear model. For the assessment of differential expression an empirical Bayes method was used to moderate the standard errors for the estimated log-fold changes. This data has been analysed and is submitted for publication in the Journal of Reproduction, Fertility and Development. The study described in the manuscript focuses on gene expression changes between the time-points that are closest to each adjacent phase boundary. Therefore the normalised results submitted to GEO only represent the analysis of the following linear model contrasts: pregnancy day 26 versus lactation day 2 (phase 1 versus phase 2A), lactation day 110 versus lactation day 151 (phase 2A versus phase 2B) and lactation day 151 versus lactation 216 (phase 2B versus phase 3).

molecule: polyA RNA

organism: Notamacropus eugenii

source_name: Suckled mammary gland

label_protocol: Fluorescently labelled target Cy3- and Cy5-cDNA was prepared from 250 ng of mRNA using a CyScribe First-Strand cDNA labelling kit (Amersham Biosciences) as per manufacture's instructions

extract_protocol:
1. Total RNA was isolated from mammary gland tissue by purification through a silica column using an RNeasy Midi kit (QIAGEN) as per manufacture's instruction (QIAGEN)
2. Subsequent mRNA was extracted from total RNA with poly T oligomers attached to superparamagnetic beads using the DynaBeads mRNA Purification Kit (Dynal Biotech) as per manufacture's instructions

tag: day lactation

value: Lactation day 171


title: Lactation day 266 [TR022-021003_532]

value: Lactation day 266


title: VMH Nkx2-1 f/f rep4


title: VMH Nkx2-1 f/f rep3


title: VMH Nkx2-1 f/f; Sf1Cre rep2


title: VMH Nkx2-1 f/f; Sf1Cre rep1


title: VMH Nkx2-1 f/f rep2


title: Lactation day 266 [TR021-021003_635]


title: 20282C3 subject ID number at time C3

description: Test

value: Female

value: Adipose


title: Lactation day 171 [TR021-021003_532]


title: Lactation day 171 [TR019-021003_635]


title: Lactation day 243 [TR019-021003_532]

value: Lactation day 243


title: 20282C2 subject ID number at time C2

description: Test

value: After calorie restriction (C2) 8 wk


title: 20202C3 subject ID number at time C3

description: Test

value: After weight maintenance (C3) 26 wk


title: Lactation day 171 [TR015-021003_532]


title: 20202C2 subject ID number at time C2

description: Test


title: Lactation day 216 [TR013-021003_532]

value: Lactation day 216


title: 20282C1 subject ID number at time C1

description: Control

value: Baseline (C1)


title: 20092C3 subject ID number at time C3

description: Test


title: Lactation day 243 [TR015-021003_635]


title: 20092C2 subject ID number at time C2

description: Test


title: 20092C1 subject ID number at time C1

description: Control


title: 20202C1 subject ID number at time C1

description: Control


title: Lactation day 171 [TR013-021003_635]


title: Lactation day 171 [TR012-021003_532]


title: 11272C2 subject ID number at time C2

description: Test


title: 11272C1 subject ID number at time C1

description: Control


title: Lactation day 266 [TR029-021003_532]


title: Lactation day 216 [TR012-021003_635]


title: Lactation day 151 [TR029-021003_635]

value: Lactation day 151


title: 11232C3 subject ID number at time C3

description: Test


title: Lactation day 151 [TR010-021003_635]


title: Lactation day 243 [TR010-021003_532]


title: 11232C2 subject ID number at time C2

description: Test


title: 11232C1 subject ID number at time C1

description: Control


title: Lactation day 151 [34_test_new_532]


title: 11182C3 subject ID number at time C3

description: Test


title: 11272C3 subject ID number at time C3

description: Test


title: 11182C2 subject ID number at time C2

description: Test


title: Lactation day 151 [TR024-021003-2_532]


title: 20782C2 subject ID number at time C2

description: Test


title: 11182C1 subject ID number at time C1

description: Control


title: Lactation day 216 [TR027-021003_532]


title: 11072C3 subject ID number at time C3

description: Test


title: Lactation day 216 [TR026-021003-2_635]


title: 11072C2 subject ID number at time C2

description: Test


title: Lactation day 130 [TR025-021003_635]

value: Lactation day 130


title: Lactation day 151 [TR026-021003-2_532]


title: 11072C1 subject ID number at time C1

description: Control


title: 10772C1 subject ID number at time C1

description: Control


title: 10752C3 subject ID number at time C3

description: Test


title: 10772C2 subject ID number at time C2

description: Test


title: Lactation day 130 [TR011-021003_532]


title: Lactation day 130 [TR020-021003_635]


title: 10772C3 subject ID number at time C3

description: Test


title: Lactation day 243 [TR020-021003_532]


title: 10752C1 subject ID number at time C1

description: Control


title: 10752C2 subject ID number at time C2

description: Test


title: Lactation day 266 [TR011-021003_635]


title: Lactation day 266 [TR025-021003_532]


title: 10702C2 subject ID number at time C2

description: Test


title: Lactation day 243 [TR024-021003-2_635]


title: 10702C1 subject ID number at time C1

description: Control


title: 10702C3 subject ID number at time C3

description: Test


title: Lactation day 151 [TR027-021003_635]


title: Lactation day 266 [34_test_new_635]


title: Lactation day 243 [TR08-021003_635]


title: Lactation day 130 [TR08-021003_532]


title: Lactation day 216 [TR09-021003_532]


title: Lactation day 130 [TR09-021003_635]


title: XT8M1

first: Han

state: Guangdong

address: Xinggang Rd. Haizhu District

institute: Sun Yatsen University

description: Hybridized to Affymetrix SNP6.0

hyb_protocol: Hybridization was performed according to Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (Affymetrix 702504).

scan_protocol: Arrays were then scanned by GeneChip Scanner 3000 (Affymetrix).

data_processing:
The genotype and copy number of each probe or genomic segment were calculated by Genotyping Console Software 4.1 (Affymetrix).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: metastasis tumor derived from XT8

label_protocol: Adaptors were ligated to the DNA fragments for PCR amplification.  The amplified DNA was labeled with biotin using the Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 (Affymetrix 901015).

growth_protocol: The immortalized MCF10A and MCF10A-HRAS cells were cultured in DMEM-F12 containing 5% Horse Serum (Gibco 16050-122), and with supplements of 20 ng/ml EGF (Gibco PHG0311), 0.5 mg/ml hydrocortisone (Sigma H0888), 100ng/ml cholera toxin (Sigma C8052), and 10 ug/ml insulin (Sigma I1882).  Because most of the above supplements were no longer required for the transformed XT cells, all XT cells were cultured in DMEM-F12 containing 10% FBS, with none of the above supplements.

extract_protocol: Genomic DNA was extracted from ~5x106 cells using the DNeasy Kit (Qiagen 69504)

value: Acute leukemia cell line 380

tag: cell type

value: metastasis tumor


title: Lactation day 87 [TR05_110903_W685]

value: Lactation day 87


title: Lactation day 193 [TR05_110903_W595]

value: Lactation day 193


title: 10662C1 subject ID number at time C1

description: Control


title: 10682C3 subject ID number at time C3

description: Test


title: 10682C2 subject ID number at time C2

description: Test


title: Lactation day 216 [TR07-021003-2_635]


title: 10682C1 subject ID number at time C1

description: Control


title: 10662C2 subject ID number at time C2

description: Test


title: XT6

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from XT5

value: Acute leukemia cell line Jurkat

value: xenograft tumor


title: 10662C3 subject ID number at time C3

description: Test


title: XT8

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from XT7

value: Acute leukemia cell line Kasumi-1


title: Lactation day 87 [TR011_SNR_W595]


title: Lactation day 171 [TR016_W685]

value: Lactation day 171


title: Lactation day 87 [TR016_W595]


title: 10632C2 subject ID number at time C2

description: Test

source_name: Subcutaneaous adipose tissue

value: Female


title: 10632C3 subject ID number at time C3

description: Test

value: Adipose


title: Lactation day 87 [TR011_110903_W685]


title: Lactation day 130 [TR07-021003-2_532]


title: 10502C2 subject ID number at time C2

description: Test


title: Lactation day 151 [TR04_110903_W595]


title: Lactation day 171 [TR011_110903_W595]


title: Lactation day 87 [TR04_110903_W685]


title: 10502C1 subject ID number at time C1

description: Control


title: 10442C3 subject ID number at time C3

description: Test


title: 10442C2 subject ID number at time C2

description: Test


title: 10442C1 subject ID number at time C1

description: Control


title: Lactation day 151 [TRO2_110903_W685]


title: Lactation day 87 [TRO2_110903_W595]


title: 10422C3 subject ID number at time C3

description: Test


title: XT7

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from XT6

value: Acute leukemia cell line K-562


title: Lactation day 193 [TR015_W685]


title: Lactation day 62 [TR015_W595]

value: Lactation day 62


title: MCF10A

description: Hybridized to Affymetrix SNP6.0

source_name: human breast cell line

value: cell line


title: Lactation day 62 [TR010_110903_W685]


title: XT5

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from XT4

value: Acute leukemia cell line HL-60


title: 10422C1 subject ID number at time C1

description: Control

value: Baseline (C1)


title: Lactation day 171 [TR010_SNR_W685]


title: 10422C2 subject ID number at time C2

description: Test

value: After calorie restriction (C2) 8 wk


title: 10502C3 subject ID number at time C3

description: Test

value: After weight maintenance (C3) 26 wk


title: 10392C3 subject ID number at time C3

description: Test


title: 10392C1 subject ID number at time C1

description: Control


title: 10632C1 subject ID number at time C1

description: Control


title: XT3

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from XT2

value: Acute leukemia cell line CCRF-CEM


title: Lactation day 193 [TR010_110903_W595]


title: XT2

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from XT1

value: Acute leukemia cell line BV173


title: MCF10AHRAS

description: Hybridized to Affymetrix SNP6.0

source_name: MCF10A transfected by an activated HRAS gene

value: Acute leukemia cell line 697


title: 10372C2 subject ID number at time C2

description: Test


title: Lactation day 62 [TR01_110903_W685]


title: 10372C1 subject ID number at time C1

description: Control


title: Lactation day 62 [TR010_SNR_W595]


title: 10392C2 subject ID number at time C2

description: Test


title: XT8M2

description: Hybridized to Affymetrix SNP6.0

value: metastasis tumor


title: Lactation day 171 [TR01_110903_W595]


title: Lactation day 151 [TR014_W595]

value: Lactation day 151


title: Lactation day 62 [TR014_W685]


title: XT4

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from XT3

value: Acute leukemia cell line CMK

value: xenograft tumor


title: XT1

description: Hybridized to Affymetrix SNP6.0

source_name: xenograft tumor derived from MCF10AHRAS

value: Acute leukemia cell line AT1


title: Lactation day 151 [TR013_W685]


title: 10352C2 subject ID number at time C2

description: Test

value: Female


title: 10352C3 subject ID number at time C3

description: Test

value: Adipose


title: Lactation day 110 [TR019_110903_W685]

value: Lactation day 110


title: Lactation day 62 [TR013_W595]

value: Lactation day 62


title: Lactation day 193 [TR019_110903_W595]

value: Lactation day 193


title: 10162C2 subject ID number at time C2

description: Test


title: 10352C1 subject ID number at time C1

description: Control


title: 10162C3 subject ID number at time C3

description: Test


title: Lactation day 193 [TR015_110903_W685]


title: Lactation day 110 [TR015_110903_W595]


title: Lactation day 110 [TR013_110903_W685]


title: Lactation day 171 [TR013_110903_W595]

value: Lactation day 171


title: Lactation day 171 [TR012_110903_W685]


title: 10142C3 subject ID number at time C3

description: Test


title: 10142C2 subject ID number at time C2

description: Test


title: Lactation day 110 [TR012_110903_W595]


title: 10142C1 subject ID number at time C1

description: Control

value: Baseline (C1)


title: Lactation day 110 [TRO6_110903_W595]


title: Lactation day 151 [TRO6_110903_W685]


title: 10122C2 subject ID number at time C2

description: Test

value: After calorie restriction (C2) 8 wk


title: 10122C3 subject ID number at time C3

description: Test

value: After weight maintenance (C3) 26 wk


title: 10122C1 subject ID number at time C1

description: Control


title: Lactation day 110 [TR014_110903_W685]


title: Lactation day 151 [TR014_110903_W595]


title: Pregnancy day 26 [PBC_TR016_250504_S01_Red]

source_name: Mammary gland

value: Pregnancy day 26


title: 10162C1 subject ID number at time C1

description: Control


title: Lactation day 22 [PBC_TR016_250504_S01_Green]

value: Lactation day 22


title: Lactation day 22 [PBC_TR025_S01_Red]


title: 10072C1 subject ID number at time C1

description: Control


title: 10072C3 subject ID number at time C3

description: Test


title: 10062C3 subject ID number at time C3

description: Test


title: 10062C1 subject ID number at time C1

description: Control


title: 10052C3 subject ID number at time C3

description: Test


title: 10052C2 subject ID number at time C2

description: Test


title: Pregnancy day 26 [PBC_TR025_S01_Green]


title: 10052C1 subject ID number at time C1

description: Control


title: Lactation day 2 [US22502651_TR012_250504_S01_Red]

value: Lactation day 2


title: Pregnancy day 18 [US22502651_TR013_250504_S01_Red]

value: Pregnancy day 18


title: 10072C2 subject ID number at time C2

description: Test


title: Lactation day 2 [US22502651_TR013_250504_S01_Green]


title: Lactation day 193 [TR011_SNR_W685]


title: Pregnancy day 26 [US22502651_TR05_250504_S01_Red]


title: Pregnancy day 18 [US22502651_TR012_250504_S01_Green]


title: 10042C1 subject ID number at time C1

description: Control


title: Lactation day 2 [US22502651_TR04_250504_S01_Red]


title: 10042C3 subject ID number at time C3

description: Test


title: 10022C2 subject ID number at time C2

description: Test


title: 10022C3 subject ID number at time C3

description: Test


title: Pregnancy day 26 [US22502651_TR04_250504_S01_Green]


title: Lactation day 2 [PBC_TR018_250504_S01_Red]


title: 10062C2 subject ID number at time C2

description: Test


title: 10022C1 subject ID number at time C1

description: Control


title: 10042C2 subject ID number at time C2

description: Test


title: 10012C3 subject ID number at time C3

description: Test


title: Lactation day 22 [PBC_TR018_250504_S01_Green]


title: Lactation day 2 [PBC_TR017_250504_S01_Green]


title: Lactation day 22 [PBC_TR017_250504_S01_Red]


title: Kc Mcm2-7 HU Replicate 2 Array 3

description: Biological Replicate 2 Array 3: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 2 Array 3

source_name: Input: Kc Mcm2-7 HU Replicate 2 Array 3

value: input


title: Pregnancy day 18 [PBC_TR024_S01_Red]


title: 10012C2 subject ID number at time C2

description: Test


title: Kc Mcm2-7 HU Replicate 2 Array 2

description: Biological Replicate 2 Array 2: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 2 Array 2

source_name: Input: Kc Mcm2-7 HU Replicate 2 Array 2


title: Lactation day 2 [US22502651_TR05_250504_S01_Green]

source_name: Suckled mammary gland


title: Kc Mcm2-7 HU Replicate 1 Array 3

description: Biological Replicate 1 Array 3: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 1 Array 3

source_name: Input: Kc Mcm2-7 HU Replicate 1 Array 3


title: Lactation day 22 [PBC_TR024_S01_Green]


title: Lactation day 22 [PBC_TR023_S01_Red]


title: Kc Mcm2-7 HU Replicate 1 Array 2

description: Biological Replicate 1 Array 2: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 1 Array 2

source_name: Input: Kc Mcm2-7 HU Replicate 1 Array 2


title: Pregnancy day 18 [PBC_TR023_S01_Green]


title: Pregnancy day 18 [US22502651_TR011_250504_S01_Red]


title: Pregnancy day 26 [US22502651_TR011_250504_S01_Green]


title: 10372C3 subject ID number at time C3

description: Test

source_name: Subcutaneaous adipose tissue


title: Pregnancy day 26 [US22502651_TR010_250504_S01_Red]


title: Kc Mcm2-7 HU Replicate 2 Array 1

description: Biological Replicate 2 Array 1: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 2 Array 1

source_name: Input: Kc Mcm2-7 HU Replicate 2 Array 1


title: 10012C1 subject ID number at time C1

description: Control


title: Kc Mcm2-7 HU Replicate 1 Array 1

description: Biological Replicate 1 Array 1: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 HU Replicate 1 Array 1

source_name: Input: Kc Mcm2-7 HU Replicate 1 Array 1


title: Pregnancy day 18 [US22502651_TR010_250504_S01_Green]


title: WT 3

city: Boston

first: Grace

last: Gill

state: MA

address: 136 Harrison Ave

department: Genetics Program

institute: Tufts University

data_processing: The data were normalized using quantile normalization with illumina Beadstudio software.  quantile normalized

source_name: cerebellum

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: Black Swiss X CD1

tag: genotype

value: WT

value: male

value: postnatal Day 21

value: cerebellum


title: Sp4 Hypo 2


title: Sp4 Hypo 3


title: Sp4 Hypo 1


title: GM-CSF activated monocytes 2

city: Muenster

first: Toni

last: Weinhage

address: Roentgenstraße 21

department: Department of Pediatric Rheumatology and Immunology

institute: University Hospital of Muenster

description: Gene expression data from GM-CSF activated monocytes 2

hyb_protocol: Ten micrograms of fragmented cRNA was, together with control cRNAs and grid alignment oligonucleotides, hybridized for 16 hours under constant rotation at 45°C to Affymetrix Human Genome 133 A Gene Chip arrays (Affymetrix)

scan_protocol: Fluorescent signals were detected by the HP G2500A Gene Array Scanner (Affymetrix).

data_processing: Data were processed by MicroArray Suite (MAS) Software 5.0 (Affymetrix). Signals were scaled to a target intensity of 100 and log transformed.

source_name: Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: not aplicable (human material) or Blood samples from individual healthy donors were purchased from the Department of Transfusion Medicine at the University Hospital Münster, Germany. Peripheral blood monocytes were obtained from donors by leukapheresis and isolated to greater than 90% purity

treatment_protocol: Monocytes were cultured in hydrophobic teflon bags  in McCoy’s 5a medium supplemented with 5% human AB serum, 2 mM L-glutamine, 200 IU/mL penicillin, 100 µg/mL streptomycin and 1x non-essential amino acids. Monocytes were allowed to rest for 16 hours prior to stimulation. For treatment monocytes were exposed to GM-CSF (10 ng/mL, MP Biomedicals, Aurora, USA) for 16 hours or left untreated in 3 independent sets of experiments to analyze changes in gene expression patterns induced by GM-CSF.

value: isolated monocytes


title: GM-CSF activated monocytes 3

description: Gene expression data from GM-CSF activated monocytes 3


title: Control monocytes 3

description: Gene expression data from control monocytes 3


title: Control monocytes 2

description: Gene expression data from control monocytes 2


title: WT 2


title: Control monocytes 1

description: Gene expression data from control monocytes 1


title: MEF Btg1 KO -glut 0h rep1

status: Public on Nov 26 2014

city: Nijmegen

first: Laurensia

last: Yuniati

address: Route 412 PO BOX  9101

department: Pediatric Oncology

country: Netherlands

institute: Radboud university medical center

description: biological duplicate 1

hyb_protocol: according to the Illumina Manual “Direct Hybridization Assay Guide

scan_protocol: Illumina iScan

data_processing: Illumina GenomeStudio v2011.1 Gene Expression Software  Expression software

source_name: embryos

label_protocol: Illumina Totalprep-96

growth_protocol: DMEM containing Glutamax supplemented with 10% FBS, 1% P/S and 55 µM b-mercaptoethanol.

extract_protocol: RNA was extracted with RNeasy Minikit (Qiagen), followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: untreated (normal DMEM) or glutamine starvation (DMEM without glutamine) for 16 hours.

tag: Stage

value: day 13.5 postcoitum

value: Btg1 KO

value: mouse embryonic fibroblasts (MEFs)


title: MEF Btg1 KO -glut 16h rep2

description: biological duplicate 2


title: WT 1


title: MEF WT -glut 0h rep2

description: biological duplicate 2

value: wildtype


title: MEF Btg1 KO -glut 0h rep2

description: biological duplicate 2


title: MEF WT -glut 0h rep1

description: biological duplicate 1


title: MEF Btg1 KO -glut 16h rep1

description: biological duplicate 1


title: MEF WT -glut 16h rep2

description: biological duplicate 2


title: MEF WT -glut 16h rep1

description: biological duplicate 1


title: GM-CSF activated monocytes 1

description: Gene expression data from GM-CSF activated monocytes 1