title: Dual symbiosis rep. 2

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

hyb_protocol: 1.5 μg of aRNAs were hybridized the arrays at 65 degree for 17 hr, using with Gene Expression Hybridization Kit (Agilent Technologies), using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B.

data_processing: The data were examined following using GeneSpring (v.9) (Agilent Technologies); After filtering all the bad spots and setting measurements less than 0.01 to 0.01, the chip intensities of nine microarray data were normalized to equal signal distribution using per-chip normalization at the 75th percentile.

organism: Glycine max

source_name: Dual symbiosis

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 500 ng total RNA from each sample using with Quick-Amp Labeling Kit 1 color (Agilent Technologies).

growth_protocol: Soybean seeds were then germinated in an incubator at 25ºC. Germinated soybean seeds were sown in plastic pots (12 cm diameter, 15 cm high) filled with sterilized river sand and loam soil (3:2).

extract_protocol: Total RNA extraction was performed in the three out of five independent biological replicates of each treated soybean roots using Trizol following the manufacturer’s protocol (Invitrogen, Carlsbad, CA, U.S.A.).

treatment_protocol: B. diazoefficiens was grown in a liquid yeast-mannitol medium for 7 days at 30oC. A 1 ml aliquot of a suspension of B. diazoefficiens (1 x 108 cells ml-1) was applied under each soybean seed at sowing. Pot cultures of G. rosea were obtained after mass multiplying on soybean grown in sterilized sand. AM fungal inoculum in the form of 200 spores was applied to each pot. The inoculated soybeans were grown in a glasshouse under natural conditions (maximum day temperature 26—31oC, minimum night temperature 16—21oC and day length 14—16 h) and watered regularly for 6 weeks.

tag: condition

value: Dual symbiosis

tag: cultivar

value: Enrei


title: Rhizobium symbiosis rep. 2

status: Public on Oct 01 2017

type: RNA

country: Japan

molecule: total RNA

source_name: Rhizobium symbiosis

value: Rhizobium symbiosis


title: UoCB6-contr-2

status: Public on Aug 01 2017

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

description: UocB6 treated with DMSO

hyb_protocol: Labeled ssDNA was hybridized to Human Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were scanned with a Affymetrix GeneChip Scanner 3000 according to the Affimetrix protocol.

data_processing: The microarray data were processed using GeneSifter software (http://www.geospiza.com) using RMA normalization protocol.

label: biotin

organism: Homo sapiens

label_protocol: The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com).

growth_protocol: RS4;11 and UoCB6 BCP-ALL cells were grown in  RPMI1640 medium with addition of 10% FBS, glutamine and antibiotics at 37 ºC, 5% CO2

extract_protocol: Total RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturers instruction.

treatment_protocol: RS4;11 and UoCB6 BCP-AL cells were treated with  AS1842856 at concentrations of 40 and 80 nM, respectively. 24 h later total RNA was isolated with RNeasy mini kit (QIAGEN). The experiment was done in duplicate.

tag: cell line

value: BCP-ALL cell line


title: Control-1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 2000ng ng of labeled cRNA sample were fragmented at 60° C and hybridized on to a Agilent Microarray Gene expression 8x15k Array (AMADID: 019439). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift .Gene based analysis was performed.

organism: Escherichia coli

source_name: BLR

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: E.coli cells (BLR and 4FR clones in BLR) were grown till late expression phase from overnight culture. One percent of overnight culture was transferred to 10 ml of LB and incubated at 37C. Samples were harvested at 0.6-0.7 OD at 600nm. Finally, pelleted at 4000rpm for 10 min. and pellets were washed with water (thrice) and pelleted again. All samples were prepared in triplicate.

extract_protocol: RNA Extraction was perforemd using Qiagen RNeasy Mini kit (Cat. No. 74106) as per the manufacturer's recommendations.

treatment_protocol: PCR amplified linear fragments with overhang regions for homologous recombination were transformed into BLR by electroporation (treated BLR-4FR).

tag: genotype

value: RecA deleted


title: Control-3


title: AM symbiosis rep. 1

source_name: AM symbiosis

value: AM symbiosis


title: AM symbiosis rep. 2


title: Rhizobium symbiosis rep. 1


title: Control rep. 2

source_name: uninoculated control

value: uninoculated control


title: UoCB6-contr-1

description: UocB6 treated with DMSO

value: BCP-ALL cell  line


title: KL_4_RS4_11_24h_Fi_2

description: RS4;11 treated with 40 nM AS1842856


title: UoCB6 AS1842856-1

description: UocB6 treated with 80 nM AS1842856


title: Dual symbiosis rep. 1


title: AM symbiosis rep. 3


title: UoCB6 AS1842856-2

description: UocB6 treated with 80 nM AS1842856


title: Control rep. 1


title: KL_1_RS4_11_24h_Ctr_1

description: RS4;11 treated with DMSO

source_name: RS4;11 contr-1


title: KL_2_RS4_11_24h_Ctr_2

description: RS4;11 treated with DMSO

source_name: RS4;11 contr-2


title: Control-2


title: SLFN5 KO + IFNβ 1

status: Public on Jan 31 2017

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description:
replicate 1
WT-3-IFN

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile method with the Illumina function provided by beadarray Bioconductor package

source_name: SLFN5 KO + IFNβ 1

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) according to the manufacturer’s protocol and starting with 150 ng of total RNA

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) per the manufacturer’s instructions. Quantity and quality of each RNA sample was assessed using Nanodrop and Bioanalyzer (Agilent)

treatment_protocol: 6 hours treatment with human IFNβ (5000 IU/ml)

tag: genotype/variation

value: SLFN5 KO

tag: agent

value: IFNbeta

tag: tissue

value: Glioblastoma


title: Rhizobium symbiosis rep. 3


title: KL_3_RS4_11_24h_Fi_1

description: RS4;11 treated with 40 nM AS1842856


title: Control rep. 3


title: Dual symbiosis rep. 3


title: SLFN5 KO Untreated 3

description:
replicate 3
WT-3-UT

source_name: SLFN5 KO Untreated 3


title: SLFN5 KO + IFNβ 2

description:
replicate 2
KO-3-UT

source_name: SLFN5 KO + IFNβ 2


title: Stress induced-1

description: Stress induced-1


title: SLFN5 WT + IFNβ 1

description:
replicate 1
KO-1-IFN

source_name: SLFN5 WT + IFNβ 1

value: SLFN5 WT


title: SLFN5 KO + IFNβ 3

description:
replicate 3
KO-3-IFN

source_name: SLFN5 KO + IFNβ 3


title: SLFN5 WT Untreated 2

description:
replicate 2
WT-1-IFN

source_name: SLFN5 WT Untreated 2


title: SLFN5 WT + IFNβ 3

description:
replicate 3
WT-2-IFN

source_name: SLFN5 WT + IFNβ 3


title: Patient Male M121 Pre-vaccine

status: Public on Jul 20 2016

city: Edinburgh

first: Paul

last: Dickinson

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

country: United Kingdom

institute: University of Edinburgh

description: Sample name: M121A

data_processing: Raw scan data were background subtracted, VST transformed and subsequently robust spline normalised as performed by the lumi package of Bioconductor.  Array probe features that had a present count in one or more samples were retained.

source_name: peripheral blood

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

extract_protocol: RNA was extracted from whole blood samples with PAXgene blood RNA reagent, followed by clean-up and DNase I treatment with QIAGEN PAXgene blood RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: peripheral blood

tag: Sex

value: Male

tag: age

value: 9 months

tag: vaccine group

value: DTP vaccine

tag: vaccine challenge

value: Pre-vaccine


title: Blood sample from healthy donor, rep 80

status: Public on Jul 06 2016

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

description: Gene expression data from human blood samples

hyb_protocol: Hybridization was processed onto Affymetrix GeneChip® Human Exon 1.0 ST oligonucleotide arrays according to the manufacturer's instructions.

scan_protocol: Probe arrays were scanned using the Affymetrix GCOS 3000 7G and the GeneChip Operating Software v1.4 to obtain .CEL files.

data_processing:
Raw data were pre-filtered by selection of core-annotated probesets then RMA-normalized with adjustment for GC content. The probesets were then mean-summarized to transcripts. Data were processed with Partek® Genomics Suite (version 6.5, Partek Inc., St Louis, MO, USA).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Healthy donor, blood

label_protocol: Ribosomal RNA reduction, first and second strand cDNA synthesis, cRNA synthesis, second round single-strand (ss) cDNA synthesis, ss-cDNA fragmentation and labelling were processed following the manufacturer's instructions (Affymetrix).

growth_protocol: Blood samples from 76 DLBCL patients and 87 healthy donors were obtained.

extract_protocol: The blood samples were collected in PAXgene tubes and stored at -80°C until RNA extraction.Total RNA was extracted using the PAXgene Blood RNA kit (Qiagen, Valencia, CA, USA). Globin mRNA was depleted using the GLOBINclear Human kit (Ambion, Austin, TX, USA). Quality control was performed using the Bioanalyzer 2100 (Agilent).

treatment_protocol: not applicable

value: blood

value: HD

tag: gender

value: Female


title: SLFN5 KO Untreated 1

description:
replicate 1
KO-2-UT

source_name: SLFN5 KO Untreated 1


title: SLFN5 KO Untreated 2

description:
replicate 2
KO-2-IFN

source_name: SLFN5 KO Untreated 2


title: SLFN5 WT Untreated 1

description:
replicate 1
WT-1-UT

source_name: SLFN5 WT Untreated 1


title: Blood sample from healthy donor, rep 79


title: SLFN5 WT + IFNβ 2

description:
replicate 2
WT-2-UT

source_name: SLFN5 WT + IFNβ 2


title: Blood sample from healthy donor, rep 84


title: Patient Female M103 Post-vaccine

description: Sample name: M103B

value: 10 months

value: Post-vaccine


title: SLFN5 WT Untreated 3

description:
replicate 3
KO-1-UT

source_name: SLFN5 WT Untreated 3


title: Blood sample from healthy donor, rep 85


title: Blood sample from healthy donor, rep 83


title: Blood sample from healthy donor, rep 82


title: Patient Male M121 Post-vaccine

description: Sample name: M121B


title: Blood sample from healthy donor, rep 86


title: Blood sample from healthy donor, rep 77


title: Blood sample from healthy donor, rep 76


title: Blood sample from healthy donor, rep 78


title: Blood sample from healthy donor, rep 72


title: Blood sample from healthy donor, rep 71


title: Blood sample from healthy donor, rep 87


title: Blood sample from healthy donor, rep 73


title: Blood sample from healthy donor, rep 81


title: Blood sample from healthy donor, rep 74


title: Blood sample from healthy donor, rep 75


title: Blood sample from healthy donor, rep 70


title: Blood sample from healthy donor, rep 69


title: Patient Female M103 Pre-vaccine

description: Sample name: M103A


title: Blood sample from healthy donor, rep 68


title: Blood sample from healthy donor, rep 66


title: Blood sample from healthy donor, rep 67


title: Blood sample from healthy donor, rep 58


title: Blood sample from healthy donor, rep 59


title: Blood sample from healthy donor, rep 61


title: Blood sample from healthy donor, rep 60


title: Blood sample from healthy donor, rep 62


title: Blood sample from healthy donor, rep 55


title: Blood sample from healthy donor, rep 56


title: Blood sample from healthy donor, rep 65


title: Blood sample from healthy donor, rep 64


title: Blood sample from healthy donor, rep 63


title: Blood sample from healthy donor, rep 48


title: Blood sample from healthy donor, rep 50


title: Blood sample from healthy donor, rep 46


title: Blood sample from healthy donor, rep 51


title: Blood sample from healthy donor, rep 52


title: Blood sample from healthy donor, rep 44


title: Blood sample from healthy donor, rep 43


title: Blood sample from healthy donor, rep 57


title: Blood sample from healthy donor, rep 40


title: Blood sample from healthy donor, rep 54


title: Blood sample from healthy donor, rep 39


title: Blood sample from healthy donor, rep 41


title: Blood sample from healthy donor, rep 45


title: Blood sample from healthy donor, rep 53


title: Blood sample from healthy donor, rep 42


title: Blood sample from healthy donor, rep 49


title: Blood sample from healthy donor, rep 35


title: Blood sample from healthy donor, rep 37


title: Blood sample from healthy donor, rep 38


title: Blood sample from healthy donor, rep 34


title: Blood sample from healthy donor, rep 36


title: Blood sample from healthy donor, rep 28


title: Blood sample from healthy donor, rep 47


title: Blood sample from healthy donor, rep 33


title: Blood sample from healthy donor, rep 30


title: Blood sample from healthy donor, rep 21


title: Blood sample from healthy donor, rep 23


title: Blood sample from healthy donor, rep 24


title: Blood sample from healthy donor, rep 27


title: Blood sample from healthy donor, rep 22


title: Blood sample from healthy donor, rep 25


title: Blood sample from healthy donor, rep 26


title: Blood sample from healthy donor, rep 20


title: Blood sample from healthy donor, rep 29


title: Blood sample from healthy donor, rep 31


title: Blood sample from healthy donor, rep 15


title: Blood sample from healthy donor, rep 18


title: Blood sample from healthy donor, rep 11


title: Blood sample from healthy donor, rep 9


title: Blood sample from healthy donor, rep 19


title: Blood sample from healthy donor, rep 16


title: Blood sample from healthy donor, rep 32


title: Blood sample from healthy donor, rep 13


title: Blood sample from healthy donor, rep 14


title: Blood sample from healthy donor, rep 8


title: Blood sample from healthy donor, rep 12


title: Blood sample from healthy donor, rep 7


title: Blood sample from healthy donor, rep 5


title: Blood sample from healthy donor, rep 2


title: Blood sample from healthy donor, rep 3


title: Blood sample from healthy donor, rep 4


title: Blood sample from healthy donor, rep 17


title: Blood sample from healthy donor, rep 10


title: Blood sample from DLBCL patient, rep 74

source_name: DLBCL, blood

value: DLBCL at diagnosis


title: Blood sample from DLBCL patient, rep 76


title: Blood sample from healthy donor, rep 1


title: Blood sample from DLBCL patient, rep 75


title: Blood sample from DLBCL patient, rep 70


title: Blood sample from DLBCL patient, rep 73


title: Blood sample from healthy donor, rep 6


title: Blood sample from DLBCL patient, rep 72


title: Blood sample from DLBCL patient, rep 67


title: Blood sample from DLBCL patient, rep 71


title: Blood sample from DLBCL patient, rep 69


title: Blood sample from DLBCL patient, rep 68


title: Blood sample from DLBCL patient, rep 66


title: Blood sample from DLBCL patient, rep 61


title: Blood sample from DLBCL patient, rep 62


title: Blood sample from DLBCL patient, rep 60


title: Blood sample from DLBCL patient, rep 57


title: Blood sample from DLBCL patient, rep 56


title: Blood sample from DLBCL patient, rep 54


title: Blood sample from DLBCL patient, rep 63


title: Blood sample from DLBCL patient, rep 49


title: Blood sample from DLBCL patient, rep 50


title: Blood sample from DLBCL patient, rep 64


title: Blood sample from DLBCL patient, rep 65


title: Blood sample from DLBCL patient, rep 51


title: Blood sample from DLBCL patient, rep 52


title: Blood sample from DLBCL patient, rep 48


title: Blood sample from DLBCL patient, rep 47


title: Blood sample from DLBCL patient, rep 55


title: Blood sample from DLBCL patient, rep 53


title: Blood sample from DLBCL patient, rep 58


title: Blood sample from DLBCL patient, rep 59


title: Blood sample from DLBCL patient, rep 44


title: Blood sample from DLBCL patient, rep 43


title: Blood sample from DLBCL patient, rep 46


title: Blood sample from DLBCL patient, rep 45


title: Blood sample from DLBCL patient, rep 42


title: Blood sample from DLBCL patient, rep 37


title: Blood sample from DLBCL patient, rep 40


title: Blood sample from DLBCL patient, rep 38


title: Blood sample from DLBCL patient, rep 39


title: Blood sample from DLBCL patient, rep 34


title: Blood sample from DLBCL patient, rep 36


title: Blood sample from DLBCL patient, rep 32


title: Blood sample from DLBCL patient, rep 27


title: Blood sample from DLBCL patient, rep 33


title: Blood sample from DLBCL patient, rep 28


title: Blood sample from DLBCL patient, rep 31


title: Blood sample from DLBCL patient, rep 29


title: Blood sample from DLBCL patient, rep 30


title: Blood sample from DLBCL patient, rep 24


title: Blood sample from DLBCL patient, rep 25


title: Blood sample from DLBCL patient, rep 23


title: Blood sample from DLBCL patient, rep 22


title: Blood sample from DLBCL patient, rep 35


title: Blood sample from DLBCL patient, rep 21


title: Blood sample from DLBCL patient, rep 20


title: Blood sample from DLBCL patient, rep 15


title: Blood sample from DLBCL patient, rep 19


title: Blood sample from DLBCL patient, rep 18


title: Blood sample from DLBCL patient, rep 14


title: Blood sample from DLBCL patient, rep 17


title: Blood sample from DLBCL patient, rep 11


title: Blood sample from DLBCL patient, rep 41


title: Blood sample from DLBCL patient, rep 12


title: Blood sample from DLBCL patient, rep 26


title: Blood sample from DLBCL patient, rep 13


title: Blood sample from DLBCL patient, rep 5


title: Blood sample from DLBCL patient, rep 4


title: Blood sample from DLBCL patient, rep 3


title: Blood sample from DLBCL patient, rep 6


title: Blood sample from DLBCL patient, rep 9


title: Blood sample from DLBCL patient, rep 10


title: Blood sample from DLBCL patient, rep 16


title: Blood sample from DLBCL patient, rep 7


title: Blood sample from DLBCL patient, rep 2


title: Blood sample from DLBCL patient, rep 1


title: Blood sample from DLBCL patient, rep 8


title: 50D

status: Public on Mar 29 2016

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

hyb_protocol: Hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip or Illumina HumanWG-6 v3.0 expression BeadChip using the standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol of iScan.

data_processing: The data were transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.

source_name: breast tumour, LumA, diagnostic

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

extract_protocol: mRNA from untreated paired biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

value: female

tag: disease

value: primary ER+ breast carcinoma

tag: subtype

value: LumA

value: breast tumour

tag: sampling time

value: diagnosis

tag: group

value: untreated


title: 10D


title: 13D


title: 56D

source_name: breast tumour, LumB, diagnostic

value: LumB


title: 6D


title: 54S

source_name: breast tumour, LumA, surgical

value: surgery


title: 53D


title: 51S


title: 55S


title: 52D

source_name: breast tumour, normal, diagnostic

value: Normal


title: 56S

source_name: breast tumour, LumB, surgical


title: 47D


title: 48D


title: 53S


title: 49D


title: 51D


title: 46S


title: 45D


title: 49S


title: 46D


title: 48S


title: 52S


title: 54D


title: 55D


title: 47S


title: 1D


title: 44D


title: 45S


title: 44S


title: 50S


title: 4D


title: 42D


title: 41D


title: 41S


title: 42S


title: 43D


title: 40D


title: 39S


title: 43S


title: 31S


title: 40S


title: 37D


title: 38D


title: 36S


title: 30S


title: 39D


title: 34S


title: 32S


title: 33S


title: 38S


title: 31D


title: 34D


title: 35D


title: 33D


title: 35S


title: 36D


title: 29S


title: 30D


title: 37S


title: 29D


title: 32D


title: 28S


title: 27D


title: 28D


title: 23S


title: 26S


title: 27S


title: 25D


title: 22S


title: 21S


title: 26D


title: 24S


title: 25S


title: 20S


title: 24D


title: 22D


title: 15D


title: 23D

source_name: breast tumour, Her2, diagnostic


title: 20D


title: 21D


title: 19D


title: 18D


title: 15S


title: 17D


title: 13S


title: 14S


title: 18S


title: 17S


title: 16S


title: 12S


title: 19S


title: 14D


title: 16D


title: 12D


title: 11D


title: 11S


title: 10S


title: 9S

source_name: breast tumour, normal, surgical


title: 9D


title: KO_control_Forebrain 1

status: Public on Jan 29 2016

city: Montreal

first: Valerie

last: Mongrain

state: QC

address: 333 rue Saint-Antoine Est

department: Research center

country: Canada

institute: CRCHUM

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Normalized expression signals were calculated from Affymetrix CEL files using the RMA function of the oligo Bioconductor package
Differential expressions were computed using the Bioconductor package “limma”
Linear model was fit for each gene, and comparisons of interest were extracted as contrasts (KO-control, KO-SD, WT-control, WT-SD)
P values were adjusted for multiple testing with the Benjamini and Hochberg method to control the false discovery rate (FDR)
*** WARNING : The Sample data tables report incomplete data.***

organism: Mus musculus

source_name: KO, CTRL

label_protocol: Standard Affymetrix protocol

extract_protocol:
RNA extraction with RNeasy Lipid Tissue Mini kit (QIAgen)
Affymetrix, Santa Clara, CA, USA

tag: strain

value: Mixed BL6/10

value: EphA4 knockout

tag: stress

value: control

value: Forebrain


title: 3D


title: 8D


title: 7D


title: 4S


title: WT_sleep deprived_Forebrain 5

source_name: WT, SD

value: WT

value: sleep-deprived


title: 5S


title: 6S


title: WT_sleep deprived_Forebrain 6


title: WT_sleep deprived_Forebrain 4


title: 8S


title: 3S


title: 5D


title: KO_control_Forebrain 3


title: KO_control_Forebrain 2


title: KO_sleep deprived_Forebrain 2

source_name: KO, SD


title: KO_sleep deprived_Forebrain 5


title: KO_sleep deprived_Forebrain 1


title: 2S


title: 1S


title: KO_control_Forebrain 4


title: KO_sleep deprived_Forebrain 3


title: KO_sleep deprived_Forebrain 4


title: 2D


title: 7S


title: WT_sleep deprived_Forebrain 1


title: WT_sleep deprived_Forebrain 3


title: kuppe-00390: T1

status: Public on Jun 27 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

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

source_name: skin

value: Cutaneous T-cell lymphoma

value: skin

value: IIB


title: WT_sleep deprived_Forebrain 2


title: kuppe-00390: M67

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

value: IB


title: kuppe-00390: M66

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


title: kuppe-00390: M65

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

value: III


title: kuppe-00390: M64

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

value: IA


title: kuppe-00390: M61


title: kuppe-00390: M63


title: kuppe-00390: M62


title: WT_control_Forebrain 4

source_name: WT, CTRL


title: kuppe-00390: M60


title: kuppe-00390: M59


title: kuppe-00390: M56


title: kuppe-00390: M57


title: kuppe-00390: M53


title: WT_control_Forebrain 3


title: kuppe-00390: M54


title: kuppe-00390: M55


title: kuppe-00390: M49


title: kuppe-00390: M51


title: WT_control_Forebrain 1


title: kuppe-00390: M50a


title: WT_control_Forebrain 2


title: kuppe-00390: M52


title: kuppe-00390: M47


title: kuppe-00390: M48


title: kuppe-00390: M45


title: kuppe-00390: M46


title: kuppe-00390: M44


title: kuppe-00390: M43


title: kuppe-00390: M38


title: kuppe-00390: M40


title: kuppe-00390: M41


title: kuppe-00390: M37


title: kuppe-00390: M34


title: kuppe-00390: M58


title: kuppe-00390: M36


title: kuppe-00390: M35


title: kuppe-00390: M31


title: kuppe-00390: M30


title: kuppe-00390: M29


title: kuppe-00390: M28


title: kuppe-00390: M27


title: kuppe-00390: M25


title: kuppe-00390: M23


title: kuppe-00390: M21


title: kuppe-00390: M22


title: kuppe-00390: M24


title: kuppe-00390: M20


title: kuppe-00390: M19


title: kuppe-00390: M18


title: kuppe-00390: M17


title: kuppe-00390: M42


title: kuppe-00390: M14


title: kuppe-00390: M16


title: kuppe-00390: M12


title: kuppe-00390: M13


title: kuppe-00390: M11


title: kuppe-00390: M10


title: kuppe-00390: M9


title: kuppe-00390: M33


title: kuppe-00390: M8


title: kuppe-00390: M7


title: kuppe-00390: M5-1


title: kuppe-00390: M2


title: kuppe-00390: M1


title: kuppe-00390: M15


title: kuppe-00390: M5-2


title: Small RNAs from Carica papaya leaves

status: Public on Apr 30 2011

type: SRA

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

library_source: transcriptomic

data_processing: Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artifacts.

organism: Carica papaya

source_name: Leaves

extract_protocol: Total RNA was extracted with the TriReagent (Molecular Research Center). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000). Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.

value: leaves

value: 1-2 weeks

tag: cultivar

value: SunUp


title: Small RNAs from Carica papaya flowers

source_name: Flowers

value: flowers

value: female

value: 1-3 weeks


title: Small RNAs from Carica papaya infected leaves

source_name: Virus-infected Leaves

value: male

value: 2-3 weeks

tag: treatment

value: infected with PRSV