title: MEF_ATF6bWT_Tun_12hr_rep1

description:
Gene expression of MEF (ATF6bWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_1_2_ATF6bWT_Tun12hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6bWT, Tun, 12hr, rep1


title: MEF_ATF6bKO_Tun_24hr_rep2

status: Public on Jan 18 2015

type: RNA

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

country: Japan

institute: Institute for Genome Research

description:
Gene expression of MEF (ATF6bKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_2_1_ATF6bKO_Tun24hr_MEF_2.txt

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent Fragmentation buffer and 2x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4852A) for 17.5 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20100422) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic fibroblast, ATF6bKO, Tun, 24hr, rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: MEFs were cultured in DMEM supplemented with 10% fetal bovine serum, 55uM 2-mercaptoethanol, 1x MEM non-essential amino acids, 100units/ml penicillin and 100ug/ml streptomycin at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored by agarose gel electrophoresis of RNA under denaturing conditions.

treatment_protocol: MEFs were treated with DMEM supplemented with 10% fetal bovine serum, 55uM 2-mercaptoethanol, 1x MEM non-essential amino acids, 100units/ml penicillin and 100ug/ml streptomycin containing 2ug/mL tunicamycin for 12 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: embryonic fibroblast

tag: background strain

tag: genotype

tag: treatment

value: tunicamycin

tag: time


title: MEF_ATF6bWT_Tun_12hr_rep2

description:
Gene expression of MEF (ATF6bWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_1_3_ATF6bWT_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6bWT, Tun, 12hr, rep2


title: MEF_ATF6bKO_Tun_12hr_rep2

description:
Gene expression of MEF (ATF6bKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_2_3_ATF6bKO_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6bKO, Tun, 12hr, rep2


title: MEF_ATF6bKO_UT_rep1

description:
Gene expression of untreated MEF (ATF6bKO)
Raw data file: 101120_2_4_ATF6bKO_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6bKO, UT, rep1

value: untreated

value: control


title: MEF_ATF6bWT_Tun_24hr_rep1

description:
Gene expression of MEF (ATF6bWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_1_4_ATF6bWT_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6bWT, Tun, 24hr, rep1


title: MEF_ATF6bKO_Tun_24hr_rep1

description:
Gene expression of MEF (ATF6bKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_2_4_ATF6bKO_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6bKO, Tun, 24hr, rep1


title: MEF_ATF6aKO_Tun_12hr_rep2

description:
Gene expression of MEF (ATF6aKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_2_4_ATF6aKO_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6aKO, Tun, 12hr, rep2


title: MEF_ATF6aKO_Tun_24hr_rep2

description:
Gene expression of MEF (ATF6aKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_2_2_ATF6aKO_Tun24hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6aKO, Tun, 24hr, rep2


title: MEF_ATF6aWT_Tun_24hr_rep2

description:
Gene expression of MEF (ATF6aWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_1_2_ATF6aWT_Tun24hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6aWT, Tun, 24hr, rep2


title: MEF_ATF6bWT_Tun_24hr_rep2

description:
Gene expression of MEF (ATF6bWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_1_1_ATF6bWT_Tun24hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6bWT, Tun, 24hr, rep2


title: MEF_ATF6bKO_UT_rep2

description:
Gene expression of untreated MEF (ATF6bKO)
Raw data file: 101215_2_1_ATF6bKO_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6bKO, UT, rep2


title: MEF_ATF6aWT_Tun_12hr_rep1

description:
Gene expression of MEF (ATF6aWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_1_1_ATF6aWT_Tun12hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6aWT, Tun, 12hr, rep1


title: MEF_ATF6aKO_UT_rep2

description:
Gene expression of untreated MEF (ATF6aKO)
Raw data file: 101215_2_3_ATF6aKO_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6aKO, UT, rep2


title: MEF_ATF6aKO_Tun_12hr_rep1

description:
Gene expression of MEF (ATF6aKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_2_1_ATF6aKO_Tun12hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6aKO, Tun, 12hr, rep1


title: MEF_ATF6bWT_UT_rep1

description:
Gene expression of untreated MEF (ATF6bWT)
Raw data file: 101120_1_4_ATF6bWT_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6bWT, UT, rep1


title: MEF_ATF6aWT_Tun_12hr_rep2

description:
Gene expression of MEF (ATF6aWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101215_1_4_ATF6aWT_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6aWT, Tun, 12hr, rep2


title: MEF_ATF4WT_Tun_24hr_rep2

description:
Gene expression of MEF (ATF4WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_1_1_ATF4WT_Tun24hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF4WT, Tun, 24hr, rep2


title: MEF_ATF6aKO_UT_rep1

description:
Gene expression of untreated MEF (ATF6aKO)
Raw data file: 101120_2_2_ATF6aKO_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6aKO, UT, rep1


title: MEF_ATF6aKO_Tun_24hr_rep1

description:
Gene expression of MEF (ATF6aKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_2_3_ATF6aKO_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6aKO, Tun, 24hr, rep1


title: MEF_ATF6aWT_Tun_24hr_rep1

description:
Gene expression of MEF (ATF6aWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_1_3_ATF6aWT_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6aWT, Tun, 24hr, rep1


title: MEF_ATF6aWT_UT_rep2

description:
Gene expression of untreated MEF (ATF6aWT)
Raw data file: 101215_1_3_ATF6aWT_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6aWT, UT, rep2


title: MEF_ATF4WT_Tun_12hr_rep2

description:
Gene expression of MEF (ATF4WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_1_3_ATF4WT_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF4WT, Tun, 12hr, rep2


title: MEF_ATF4KO_Tun_24hr_rep2

description:
Gene expression of MEF (ATF4KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_2_1_ATF4KO_Tun24hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF4KO, Tun, 24hr, rep2


title: MEF_ATF4WT_UT_rep2

description:
Gene expression of untreated MEF (ATF4WT)
Raw data file: 101215_1_2_ATF4WT_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF4WT, UT, rep2


title: MEF_ATF6aWT_UT_rep1

description:
Gene expression of untreated MEF (ATF6aWT)
Raw data file: 101120_1_2_ATF6aWT_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF6aWT, UT, rep1


title: MEF_ATF4KO_UT_rep2

description:
Gene expression of untreated MEF (ATF4KO)
Raw data file: 101215_2_2_ATF4KO_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF4KO, UT, rep2


title: MEF_ATF4KO_Tun_12hr_rep2

description:
Gene expression of MEF (ATF4KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_2_3_ATF4KO_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF4KO, Tun, 12hr, rep2


title: MEF_ATF4WT_Tun_24hr_rep1

description:
Gene expression of MEF (ATF4WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_1_4_ATF4WT_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF4WT, Tun, 24hr, rep1


title: MEF_XBP1KO_Tun_12hr_rep2

description:
Gene expression of MEF (XBP1KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_2_4_XBP1KO_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, XBP1KO, Tun, 12hr, rep2


title: MEF_XBP1KO_Tun_24hr_rep2

description:
Gene expression of MEF (XBP1KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_2_2_XBP1KO_Tun24hr_MEF_2.txt

source_name: mouse embryonic fibroblast, XBP1KO, Tun, 24hr, rep2


title: MEF_XBP1WT_Tun_24hr_rep2

description:
Gene expression of MEF (XBP1WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_1_2_XBP1WT_Tun24hr_MEF_2.txt

source_name: mouse embryonic fibroblast, XBP1WT, Tun, 24hr, rep2


title: MEF_ATF4KO_Tun_24hr_rep1

description:
Gene expression of MEF (ATF4KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_2_4_ATF4KO_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF4KO, Tun, 24hr, rep1


title: MEF_ATF4KO_Tun_12hr_rep1

description:
Gene expression of MEF (ATF4KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_2_2_ATF4KO_Tun12hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF4KO, Tun, 12hr, rep1


title: MEF_XBP1KO_Tun_24hr_rep1

description:
Gene expression of MEF (XBP1KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_2_3_XBP1KO_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, XBP1KO, Tun, 24hr, rep1


title: MEF_XBP1KO_Tun_12hr_rep1

description:
Gene expression of MEF (XBP1KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_2_1_XBP1KO_Tun12hr_MEF_1.txt

source_name: mouse embryonic fibroblast, XBP1KO, Tun, 12hr, rep1


title: Hp-12

status: Public on Jan 17 2015

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

description:
Hippocampus; Biol. Rep. 1, dye swap
Technical replicate of Hp-11

hyb_protocol: cRNA was hybridized using Gene Expression Hybridization Kit (Agilent). Hybridized microarrays were washed using standard Washing Buffer kit (Agilent). All procedures were performed according to manufacturer's protocol

scan_protocol: Data were extracted using G2565CA Microarray Scanner (Agilent, USA) and Agilent Feature Extraction Software (Agilent, USA) on default settings (GE2_1010_Sep10).

data_processing: Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.

organism: Rattus norvegicus

source_name: Hippocampus, WLP

label_protocol: RNA was labeled using Two-Color Low Input Quick Amp Labeling Kits (Agilent) according to manufacturer's protocol

growth_protocol: Before the brain extraction, male rats were kept in kept in cages with their brothers (3-4 in cage) at ambient temperature of 22±1°C and 60±2% humidity

extract_protocol: RNA was extracted using column-based RNeasy kit (Qiagen) according to manufacturer protocol

treatment_protocol: Alcohol-naive rats from both strains were rapidly sacrificed by decapitation

tag: strain

value: WLP

tag: brain area

value: Hippocampus

source_name: Hippocampus, WHP

value: WHP


title: MEF_XBP1WT_Tun_12hr_rep2

description:
Gene expression of MEF (XBP1WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101202_1_4_XBP1WT_Tun12hr_MEF_2.txt

source_name: mouse embryonic fibroblast, XBP1WT, Tun, 12hr, rep2


title: MEF_ATF4WT_Tun_12hr_rep1

description:
Gene expression of MEF (ATF4WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_1_2_ATF4WT_Tun12hr_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF4WT, Tun, 12hr, rep1


title: Hp-21

description:
Hippocampus; Biol. Rep. 2
Technical replicate of Hp-22


title: MEF_ATF4WT_UT_rep1

description:
Gene expression of untreated MEF (ATF4WT)
Raw data file: 101120_1_3_ATF4WT_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF4WT, UT, rep1


title: MEF_ATF4KO_UT_rep1

description:
Gene expression of untreated MEF (ATF4KO)
Raw data file: 101120_2_3_ATF4KO_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, ATF4KO, UT, rep1


title: MEF_XBP1KO_UT_rep2

description:
Gene expression of untreated MEF (XBP1KO)
Raw data file: 101215_2_4_XBP1KO_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, XBP1KO, UT, rep2


title: Pf-32

description:
Prefrontal medial cortex; Biol. Rep. 3, dye swap
Technical replicate of Pf-31

source_name: Prefrontal medial cortex, WLP

value: Prefrontal medial cortex

source_name: Prefrontal medial cortex, WHP


title: Pf-22

description:
Prefrontal medial cortex; Biol. Rep. 2, dye swap
Technical replicate of Pf-21


title: Pf-31

description:
Prefrontal medial cortex; Biol. Rep. 3
Technical replicate of Pf-32


title: MEF_XBP1WT_Tun_12hr_rep1

description:
Gene expression of MEF (XBP1WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_1_1_XBP1WT_Tun12hr_MEF_1.txt

source_name: mouse embryonic fibroblast, XBP1WT, Tun, 12hr, rep1


title: Hp-11

description:
Hippocampus; Biol. Rep. 1
Technical replicate of Hp-12


title: Hp-32

description:
Hippocampus; Biol. Rep. 3, dye swap
Technical replicate of Hp-31


title: Hp-22

description:
Hippocampus; Biol. Rep. 2, dye swap
Technical replicate of Hp-21


title: MEF_XBP1WT_Tun_24hr_rep1

description:
Gene expression of MEF (XBP1WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101112_1_3_XBP1WT_Tun24hr_MEF_1.txt

source_name: mouse embryonic fibroblast, XBP1WT, Tun, 24hr, rep1


title: MEF_XBP1KO_UT_rep1

description:
Gene expression of untreated MEF (XBP1KO)
Raw data file: 101120_2_1_XBP1KO_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, XBP1KO, UT, rep1


title: Pf-12

description:
Prefrontal medial cortex; Biol. Rep. 1, dye swap
Technical replicate of Pf-11


title: Hp-31

description:
Hippocampus; Biol. Rep. 3
Technical replicate of Hp-32


title: Pf-11

description:
Prefrontal medial cortex; Biol. Rep. 1
Technical replicate of Pf-12


title: MEF_XBP1WT_UT_rep2

description:
Gene expression of untreated MEF (XBP1WT)
Raw data file: 101215_1_4_XBP1WT_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, XBP1WT, UT, rep2


title: MEF_XBP1WT_UT_rep1

description:
Gene expression of untreated MEF (XBP1WT)
Raw data file: 101120_1_1_XBP1WT_UT_MEF_1.txt

source_name: mouse embryonic fibroblast, XBP1WT, UT, rep1


title: Pf-21

description:
Prefrontal medial cortex; Biol. Rep. 2
Technical replicate of Pf-22


title: Ac-32

description:
Nucleus accumbens; Biol. Rep. 3, dye swap
Technical replicate of Ac-31

source_name: Nucleus accumbens, WLP

value: Nucleus accumbens

source_name: Nucleus accumbens, WHP


title: Ac-22

description:
Nucleus accumbens; Biol. Rep. 2, dye swap
Technical replicate of Ac-21


title: Post-natal day 5 replicate 3

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

country: USA

institute: Stony Brook University

description: Biological replicate 2 of 2.

hyb_protocol: Hybridization procedure followed manufacturer direction

scan_protocol: Scanned on  Axon Instruments (V1.00) GenePix 4000B scanner

data_processing: Microarray data for liver samples used in this study was normalized and analyzed with limma R package

source_name: Mouse liver from post-natal day 5

label_protocol: 2 µg of total RNA was reverse transcribed and amplified by using an RNA amplification kit from Ambion.  Fifteen micrograms of amplified RNA were labeled by direct chemical coupling to the Cy5 NHS ester (Amersham Biosciences). Normal adult mouse liver (Agilent) was used as control and Cy3 labeled. Labeled RNAs were purified, fragmented, and used as probes to hybridize microarrays.

extract_protocol: Total RNA from whole livers taken at different developmental timepoints (embryonic day 14, embryonic day 18, post-natal day 5 and post-natal day 56) along with hepatoblasts isolated from E14 livers and immature hepatocytes isolated from E18 livers was extracted and purified using the Qiagen RNeasy Mini Kit.

tag: Stage

value: Postnatal

tag: age

value: post-natal day 5

value: hepatocytes

source_name: Normal adult mouse liver

tag: tissue

value: Liver


title: ventricular single cell (Sample206)

status: Public on Jan 16 2015

city: Pittsburgh

first: Guang

state: PA

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

description:
ventricular-CM.csv
single cell derived total RNA

data_processing:
Gene expression Ct value were exported from Fluidigm gene expression analysis software.
25 was used as the cutoff Ct value and given for those reactions with a Ct value higher than 25.
Without normalization, those processed Ct values were directly used to make heatmaps.

label: FAM

source_name: ventricular chamber

label_protocol: Single cell derived cDNA were pre-amplified in regulat PCR machine (Biorad) with the superscrip III (Direct one step qPCR kit) and Taqman assays (Life technology), then the pre-amplified cDNA were used to quantify the expression level of each taqman assay with 48x48 Fluidigm chips in the Biomark machine.

extract_protocol: Single cells were sorted to single well of 8-well strips, and lysated and reverse transcribed with the direct one step qPCR kits (Life technology).

value: cardiac


title: ventricular single cell (Sample208)


title: ventricular single cell (Sample209)


title: ventricular single cell (Sample200)


title: ventricular single cell (Sample202)


title: ventricular single cell (Sample212)


title: ventricular single cell (Sample205)


title: ventricular single cell (Sample203)


title: ventricular single cell (Sample207)


title: ventricular single cell (Sample201)


title: ventricular single cell (Sample211)


title: ventricular single cell (Sample210)


title: Post-natal day 56 replicate 2

description: Biological replicate 2 of 3.

source_name: Mouse liver from post-natal day 56

value: post-natal day 56


title: Ac-21

description:
Nucleus accumbens; Biol. Rep. 2
Technical replicate of Ac-22


title: Ac-11

description:
Nucleus accumbens; Biol. Rep. 1
Technical replicate of Ac-12


title: Post-natal day 56 replicate 3

description: Biological replicate 3 of 3.


title: Post-natal day 5 replicate 2

description: Biological replicate 1 of 2.


title: Embryonic day 18 replicate 1

description: Biological replicate 1 of 3.

source_name: Mouse liver from embryonic day 18

value: Embryonic

value: embryonic day 18

value: immature hepatocytes


title: Post-natal day 56 replicate 1

description: Biological replicate 1 of 3.


title: Ac-12

description:
Nucleus accumbens; Biol. Rep. 1, dye swap
Technical replicate of Ac-11


title: ventricular single cell (Sample204)


title: Ac-31

description:
Nucleus accumbens; Biol. Rep. 3
Technical replicate of Ac-32


title: Embryonic day 14 replicate 2

description: Biological replicate 2 of 3.

source_name: Mouse liver from embryonic day 14

value: embryonic day 14

value: hepatoblasts


title: Embryonic day 18 replicate 3

description: Biological replicate 3 of 3.


title: Embryonic day 18 replicate 2

description: Biological replicate 2 of 3.


title: Embryonic day 14 replicate 3

description: Biological replicate 3 of 3.


title: ventricular single cell (Sample199)


title: ventricular single cell (Sample198)


title: Embryonic day 14 replicate 1

description: Biological replicate 1 of 3.


title: ventricular single cell (Sample197)


title: atrial single cell (Sample195)

description:
atrial-CM.csv
single cell derived total RNA

source_name: atrial chamber


title: ventricular single cell (Sample196)


title: atrial single cell (Sample189)


title: atrial single cell (Sample193)


title: atrial single cell (Sample194)


title: atrial single cell (Sample187)


title: atrial single cell (Sample190)


title: atrial single cell (Sample192)


title: atrial single cell (Sample188)


title: atrial single cell (Sample179)


title: atrial single cell (Sample191)


title: atrial single cell (Sample180)


title: atrial single cell (Sample184)


title: atrial single cell (Sample183)


title: atrial single cell (Sample181)


title: atrial single cell (Sample185)


title: atrial single cell (Sample182)


title: embryo derived cell (Sample178)

description:
E10.5.csv
single cell derived total RNA

source_name: mouse embryo


title: embryo derived cell (Sample176)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample175)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample172)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample173)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample174)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample171)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample169)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample168)

description:
E10.5.csv
single cell derived total RNA


title: atrial single cell (Sample186)


title: embryo derived cell (Sample167)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample166)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample164)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample165)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample162)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample163)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample161)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample177)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample160)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample157)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample152)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample155)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample158)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample150)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample153)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample154)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample156)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample151)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample149)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample147)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample148)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample170)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample146)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample143)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample142)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample140)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample141)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample139)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample159)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample137)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample133)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample135)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample134)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample132)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample130)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample136)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample131)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample144)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample128)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample124)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample126)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample145)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample123)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample120)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample129)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample119)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample125)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample121)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample122)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample118)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample115)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample117)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample113)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample112)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample114)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample138)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample111)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample127)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample110)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample107)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample108)

description:
E10.5.csv
single cell derived total RNA


title: embryo derived cell (Sample109)

description:
E10.5.csv
single cell derived total RNA


title: ES derived cell at late stages (Sample106)

description:
E7.5-E10.5.csv
single cell derived total RNA

source_name: embryoid body (EB)


title: ES derived cell at late stages (Sample105)


title: ES derived cell at late stages (Sample102)


title: embryo derived cell (Sample116)

description:
E10.5.csv
single cell derived total RNA


title: ES derived cell at late stages (Sample100)


title: ES derived cell at late stages (Sample101)


title: ES derived cell at late stages (Sample94)


title: ES derived cell at late stages (Sample95)


title: ES derived cell at late stages (Sample91)


title: ES derived cell at late stages (Sample98)


title: ES derived cell at late stages (Sample90)


title: ES derived cell at late stages (Sample99)


title: ES derived cell at late stages (Sample96)


title: ES derived cell at late stages (Sample89)


title: ES derived cell at late stages (Sample93)


title: ES derived cell at late stages (Sample88)


title: ES derived cell at late stages (Sample97)


title: ES derived cell at late stages (Sample87)


title: ES derived cell at late stages (Sample85)


title: ES derived cell at late stages (Sample84)


title: ES derived cell at late stages (Sample83)


title: ES derived cell at late stages (Sample104)


title: ES derived cell at late stages (Sample103)


title: ES derived cell at late stages (Sample82)


title: ES derived cell at early stages  (Sample77)

description:
D23-D29.csv
single cell derived total RNA


title: ES derived cell at early stages  (Sample78)


title: ES derived cell at early stages  (Sample79)


title: ES derived cell at early stages  (Sample80)


title: ES derived cell at late stages (Sample81)


title: ES derived cell at early stages  (Sample75)


title: ES derived cell at late stages (Sample92)


title: ES derived cell at early stages  (Sample74)


title: ES derived cell at early stages  (Sample69)


title: ES derived cell at early stages  (Sample72)


title: ES derived cell at early stages  (Sample68)


title: ES derived cell at early stages  (Sample67)


title: ES derived cell at early stages  (Sample71)


title: ES derived cell at early stages  (Sample66)


title: ES derived cell at early stages  (Sample73)


title: ES derived cell at late stages (Sample86)


title: ES derived cell at early stages  (Sample64)


title: ES derived cell at early stages  (Sample65)


title: ES derived cell at early stages  (Sample61)


title: ES derived cell at early stages  (Sample59)


title: ES derived cell at early stages  (Sample62)


title: ES derived cell at early stages  (Sample60)


title: E10.5 cell (Sample58)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample57)

description:
D5-D8.csv
single cell derived total RNA


title: ES derived cell at early stages  (Sample76)


title: E10.5 cell (Sample54)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample55)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample52)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample53)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample56)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample51)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample47)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample48)

description:
D5-D8.csv
single cell derived total RNA


title: ES derived cell at early stages  (Sample70)


title: E10.5 cell (Sample43)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample42)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample44)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample41)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample46)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample40)

description:
D5-D8.csv
single cell derived total RNA


title: ES derived cell at early stages  (Sample63)


title: E10.5 cell (Sample45)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample35)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample36)

description:
D5-D8.csv
single cell derived total RNA


title: Reference single cell (Sample32)

description:
Reference cells.csv
single cell derived total RNA

source_name: embryoid body (EBs), mouse embryo

value: CPC,CM,SMC,FB,EDC and ESC


title: E10.5 cell (Sample37)

description:
D5-D8.csv
single cell derived total RNA


title: Reference single cell (Sample30)


title: Reference single cell (Sample29)


title: E10.5 cell (Sample49)

description:
D5-D8.csv
single cell derived total RNA


title: Reference single cell (Sample28)


title: Reference single cell (Sample27)


title: Reference single cell (Sample24)


title: E10.5 cell (Sample38)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample50)

description:
D5-D8.csv
single cell derived total RNA


title: E10.5 cell (Sample34)

description:
D5-D8.csv
single cell derived total RNA


title: Reference single cell (Sample23)


title: Reference single cell (Sample31)


title: Reference single cell (Sample20)


title: Reference single cell (Sample21)


title: E10.5 cell (Sample39)

description:
D5-D8.csv
single cell derived total RNA


title: Reference single cell (Sample22)


title: Reference single cell (Sample19)


title: Reference single cell (Sample15)


title: Reference single cell (Sample12)


title: Reference single cell (Sample18)


title: Reference single cell (Sample17)


title: Reference single cell (Sample13)


title: E10.5 cell (Sample33)

description:
D5-D8.csv
single cell derived total RNA


title: Reference single cell (Sample16)


title: Reference single cell (Sample11)


title: Reference single cell (Sample9)


title: Reference single cell (Sample7)


title: Reference single cell (Sample26)


title: Reference single cell (Sample8)


title: Reference single cell (Sample3)


title: Reference single cell (Sample6)


title: Reference single cell (Sample2)


title: Reference single cell (Sample1)


title: Reference single cell (Sample5)


title: Reference single cell (Sample4)


title: Reference single cell (Sample14)


title: Reference single cell (Sample10)


title: HaCaT_unirradiated_6 h_rep3

city: Debrecen

first: Gabor

last: Boros

address: Nagyerdei krt. 98.

department: Department of Dermatology

country: Hungary

institute: University of Debrecen

description: Gene expression of non-irradiated, non-photoreactivated samples 6 h after the exposure

hyb_protocol: For each sample, 1650 ng one-color labeled cRNA was hybridized to Agilent 4x44 K Whole Human Genome Oligo (Agilent Technologies) microarray platform at 65°C for 17 h. All further steps were carried out according to the manufacturer (Agilent Technologies). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
Data were then normalized by the Feature Extraction software version 9.5 (Agilent Technologies) with default settings for one-color oligonucleotide microarrays and then transferred to GeneSpringGX program (Agilent Technologies) for further statistical evaluation. In GeneSpring the normalization and data transformation steps recommended by Agilent Technologies for one-color data were applied at each time point. Total gene signal normalization at the 75th percentile of raw signal values and baseline transformation at the median of all samples was performed by GeneSpring software following Agilent's recommendation. Genes were filtered by flag values (100% of samples are present or marginal in at least one group) and raw data (expression is higher than 100 in 100% of samples in at least one group).
Default one-color high density protocol utilizing Feature Extraction software version 9.5. Identification of genes differentially expressed in microarray experiment was carried out by the unpaired, Student t-test followed by Benjamini-Hochberg correction.

organism: Homo sapiens

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, unirradiated, replicate 3

label_protocol: Cyanine 3-labeled cRNA was synthesized from 200 ng total RNA of each sample by the QickAmp Labeling Kit (Agilent Technologies) according to the manufacturer. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HaCaT keratinocytes were maintained in high glucose DMEM (Lonza, Verviers, Belgium) supplemented with 2 mM L-glutamine (Lonza), 10% fetal bovine serum (Lonza) and 0.5% antibiotic/antimycotic solution (Sigma-Aldrich, St. Louis, MO, USA) at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from HaCaT cells using Trizol reagent (MRC, Cincinnati, OH, USA) according to the manufacturer’s instructions. RNA samples were treated by DNase I (Fermentas, St. Leon-Rot, Germany) and their quality were checked using Agilent 2100 Bionalayzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: HaCaT cells were seeded into 96-well plates at a density of 2 × 104 cells per well one day prior to transfection. Aliquots of RNA samples (0.25 µg) were complexed with 1.0 µl Lipofectamine LTX-PLUS (Life Technologies) in a final volume of 100 µl of EpiLife and the complexed RNA was added to each well. After two hours the lipofectamine-RNA complex was replaced with 100 µl culture medium. At 12 h post transfection, the cell monolayer in a well of a 96-well plate, was covered with 50 µl Dulbecco’s phosphate buffer saline (Life Technologies) and subjected to 20 mJ/cm2 UVB using two TL-20W/12 bulbs (Philips). Immediately thereafter, cells were exposed to visible light ("photoreactivation") using F18W Daylight fluorescent bulbs (Sylvania) or kept in the dark for one hour.

value: unirradiated 6 h

value: immortalized keratinocytes

tag: cell line

value: HaCaT


title: HaCaT_PHR_24 h_rep2

description: Gene expression of UVB-irradiated plus photoreactivated samples 24 h after the exposure

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, photoreactivated, replicate 2

value: PHR 24 h


title: Ind4_F-iPSC

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Ind4 Fibroblast-derived iPSC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probes whose genomic mapping coordinates overlap a known common SNP, as well as probes with low detection values in at most two samples from each cell type were excluded. The gene expression data was then quantile normalized using the lumiExpresso function in the R package lumi.

label: biotin

source_name: iPSC

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

extract_protocol: All RNA was isolated using Zymo dual extraction kits (Zymo Research) with a DNase treatment during RNA extraction (Qiagen) according to the manufacturer's protocol. RNA quality was confirmed by quantifying sample’s RNA Integrity Number (RIN) on an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: gender

value: Female


title: HaCaT_PHR_24 h_rep1

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, photoreactivated, replicate 1


title: Ind3_L-iPSC_repC

description: Ind3 L-iPSC replicate C

value: Male


title: HaCaT_UVB_6 h_rep1

description: Gene expression of UVB-irradiated, non-photoreactivated samples 6 h after the exposure

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, UVB-irradiated, replicate 1

value: UVB 6 h


title: HaCaT_UVB_24 h_rep3

description: Gene expression of UVB-irradiated, non-photoreactivated samples 24 h after the exposure

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, UVB-irradiated, replicate 3

value: UVB 24 h


title: HaCaT_UVB_6 h_rep2

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, UVB-irradiated, replicate 2


title: HaCaT_unirradiated_24 h_rep3

description: Gene expression of non-irradiated, non-photoreactivated samples 24 h after the exposure

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, unirradiated, replicate 3

value: unirradiated 24 h


title: HaCaT_PHR_6 h_rep3

description: Gene expression of UVB-irradiated plus photoreactivated samples 6 h after the exposure

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, photoreactivated, replicate 3

value: PHR 6 h


title: HaCaT_unirradiated_24 h_rep2

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, unirradiated, replicate 2


title: HaCaT_PHR_24 h_rep3

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, photoreactivated, replicate 3


title: HaCaT_UVB_6 h_rep3

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, UVB-irradiated, replicate 3


title: HaCaT_UVB_24 h_rep2

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, UVB-irradiated, replicate 2


title: HaCaT_PHR_6 h_rep1

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, photoreactivated, replicate 1


title: HaCaT_unirradiated_6 h_rep1

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, unirradiated, replicate 1


title: HaCaT_unirradiated_6 h_rep2

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, unirradiated, replicate 2


title: HaCaT_unirradiated_24 h_rep1

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, unirradiated, replicate 1


title: HaCaT_PHR_6 h_rep2

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 6 h, photoreactivated, replicate 2


title: Ind1_L-iPSC_repB

description: Ind1 L-iPSC replicate B


title: HaCaT_UVB_24 h_rep1

source_name: HaCaT cell line transfected with CPD-photolyase mRNA, 24 h, UVB-irradiated, replicate 1


title: Ind4_L-iPSC_repB

description: Ind4 L-iPSC replicate B

source_name: iPSC


title: Gelatin, no serum Repeat 5 1_5

city: Bethesda

first: Kenneth

middle: M.

last: Yamada

state: MD

address: 30 Convent Dr.

department: LCDB

institute: NIDCR, NIH

description: Gelatin, no serum

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of2 X GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent 4x44K Whole Human Genome Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity. The readouts of multiple chips were normalized using the quantile normalization method. All probe sets corresponding to one gene were summarized into a single value using RMA. Unpaired t-test and Benjamini-Hochberg FDR corrected p-values of <= 0.05 and fold changes >= 2 were used as cutoff for array comparison for different conditions. Gene expression data were analyzed with GeneSpring Software.

source_name: Gelatin, no serum

label_protocol: Samples were labeled with an Ambion Amino Alyl MessageAmp II aRNA Amplification Kit.

growth_protocol: Breast carcinoma MDA-MB-231 cells were maintained in high glucose-DMEM (HyClone) supplemented with 10% fetal bovine serum (HyClone), 2 mM L-glutamine, 10 U/ml penicillin, and 10 μg/ml streptomycin (Life Technologies).

extract_protocol: mRNA was isolated using an RNAqueous-4PCR kits (Ambion)

treatment_protocol: 35mm glass-bottom MatTek dishes were coated with gelatin or HDFC matrix. Cells were plated on gelatin or HDFC matrices at density of 3X105 cells/35mm plate for overnight incubation in serum-free or plus serum medium. For serum free conditions, cells were wash in serum-free medium and spun before plating on the matrix.

value: Gelatin, no serum


title: Gelatin, serum Repeat 5 3_5

description: Gelatin, serum

source_name: Gelatin, serum

value: Gelatin, serum


title: HDFC, no serum Repeat 5 2_5

description: HDFC, no serum

source_name: HDFC, no serum

value: HDFC, no serum


title: HDFC, serum Repeat 5 4_5

description: HDFC, serum

source_name: HDFC, serum

value: HDFC, serum


title: Gelatin, serum Repeat 4 3_4

description: Gelatin, serum


title: Ind3_L-iPSC_repA

description: Ind3 L-iPSC replicate A


title: HDFC, serum Repeat 4 4_4

description: HDFC, serum


title: Ind2_F-iPSC

description: Ind2 Fibroblast-derived iPSC


title: Ind1_L-iPSC_repC

description: Ind1 L-iPSC replicate C


title: Ind3_Fibroblast

description: Ind3 source Fibroblast

source_name: Fibroblast


title: Ind4_LCL

description: Ind4 source LCL

source_name: LCL


title: Ind3_F-iPSC

description: Ind3 Fibroblast-derived iPSC


title: HDFC, no serum Repeat 3 2_3

description: HDFC, no serum


title: Gelatin, no serum Repeat 3 1_3

description: Gelatin, no serum


title: Ind2_Fibroblast

description: Ind2 source Fibroblast


title: HDFC, no serum Repeat 4 2_4

description: HDFC, no serum


title: Ind3_LCL

description: Ind3 source LCL


title: HDFC, serum Repeat 2 4_2

description: HDFC, serum


title: HDFC, serum Repeat 3 4_3

description: HDFC, serum


title: Ind2_L-iPSC_repA

description: Ind2 L-iPSC replicate A


title: Ind1_Fibroblast

description: Ind1 source Fibroblast


title: Gelatin, serum Repeat 2 3_2

description: Gelatin, serum


title: Ind4_Fibroblast

description: Ind4 source Fibroblast


title: Gelatin, no serum Repeat 4 1_4

description: Gelatin, no serum


title: Ind4_L-iPSC_repC

description: Ind4 L-iPSC replicate C


title: Gelatin, no serum Repeat 2 1_2

description: Gelatin, no serum


title: Ind1_L-iPSC_repA

description: Ind1 L-iPSC replicate A


title: Ind4_L-iPSC_repA

description: Ind4 L-iPSC replicate A


title: HDFC, serum Repeat 1 4_1

description: HDFC, serum


title: HDFC, no serum Repeat 2 2_2

description: HDFC, no serum


title: Ind2_LCL

description: Ind2 source LCL


title: Ind2_L-iPSC_repB

description: Ind2 L-iPSC replicate B


title: HDFC, no serum Repeat 1 2_1

description: HDFC, no serum


title: Ind3_L-iPSC_repB

description: Ind3 L-iPSC replicate B


title: Gelatin, no serum Repeat 1 1_1

description: Gelatin, no serum


title: Gelatin, serum Repeat 3 3_3

description: Gelatin, serum


title: TGCT7

type: SRA

city: Stockholm

first: Deniz

middle: Mahmut

last: Ozata

address: CCK R8:04

department: Oncology-pathology

country: Sweden

institute: Karolinska University Hospital, Karolinska Institutet

library_source: transcriptomic

data_processing:
We first aligned all reads to human mature miRNA sequences from miRBase release version 16, using the CLC Genomics Workbench 4.5.1 (www.clcbio.com).
The mapped reads were counted for each miRNA in individual samples, and the unaligned reads were further analyzed for identification of novel miRNAs.
These reads were initially filtered out other known structural RNAs (including tRNAs, rRNAs snRNAs, snoRNAs, piRNAs, and repetitive sequences), followed by mapping to human genome (hg19) using Bowtie 1.0.0 release
Genome_build: hg19

source_name: Testicular germ cell tumor

extract_protocol:
mirVana miRNA isolation kit (Applied Biosystems/ Ambion, Austin, TX) was used to extract small RNA for cloning
small RNAs were ligated with adenylated 3’-adaptor oligonucleotide [/5rApp/CTGTAGGCACCATCAAT/3ddC; IDT Inc., Coralville, IA, USA] and purified on a 12% denaturing polyacrylamide gel. Second ligation reaction was performed with 5’-adaptor oligonucleotide [5'-ACGCTCTTCCGATCTv-3' (uppercase, DNA; v = barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT)], followed by gel purification. The double ligated product was converted to cDNA using the reverse transcription enzyme SuperScript II (Invitrogen) and the reverse primer [5'-ATTGATGGTGCCTACAG-3'], and then PCR amplified for 16-20 cycles using a forward primer 5'-GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5'-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG- 3'.

value: Seminoma


title: TGCT8


title: TGCT6


title: TGCT5

value: Mixed germ cell


title: Ind1_F-iPSC

description: Ind1 Fibroblast-derived iPSC


title: Ind1_LCL

description: Ind1 source LCL


title: Ind2_L-iPSC_repC

description: Ind2 L-iPSC replicate C


title: TGCT9


title: TGCT2


title: TGCT4


title: TGCT3

value: Embryonal Carcinoma


title: NT2

source_name: Normal Testis

value: Normal


title: TGCT1


title: NT1


title: Gelatin, serum Repeat 1 3_1

description: Gelatin, serum


title: Reference single cell (Sample25)

source_name: embryoid body (EBs), mouse embryo

value: CPC,CM,SMC,FB,EDC and ESC


title: B6-ChrY^SJL_female_CD4+ T cells, rep1

city: Burlington

first: Laure

last: Case

address: 89 Beaumont Ave

institute: University of Vermont

hyb_protocol: After purification and fragmentation, biotinylated-cDNA targets were hybridized to the Mouse Gene 1.0 ST Arrays oligonucleotide arrays for 16 hours at 45oC. Hybridized arrays were washed and stained with streptavidin-phycoerythrin followed by sequential incubations with biotin-coupled polyclonal anti-streptavidin antibody and streptavidin phycoerythrin as a fluorescent amplification step.

scan_protocol: After staining, arrays were scanned (3000-7G Scanner, Affymetrix Inc., Santa Clara, CA) and data collected for statistical analysis.

data_processing:
Raw GeneChip data (one DAT file for each chip) includes a collection of images, one for each probe and chip.  Each image was summarized by Affymetrix GCOS software using one probe intensity (in CEL files, one per chip).sample.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na32.mm9.transcript.csv
Information from multiple probes was combined to obtain a single measure of expression for each probe set and sample.  Probe-level intensities were calculated using the Robust Multichip Average (RMA) algorithm, including background-correction, normalization (quantile), and summarization (median polish), for each probe set and sample, as is implemented in Partek Genomic Suites, version 6.6 (Copyright © 2009, Partek Inc., St. Louis, MO, USA).

label: Biotin

source_name: B6-ChrY^SJL_CD4+ T cells

label_protocol: Oligonucleotide microarray analysis of RNA expression levels was performed in the Vermont Genetics Network Microarray Facility using the Affymetrix GeneChip Platform (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s protocols. In brief, the Nugen Ovation system v.2 with SPIA® RNA amplification was employed to convert 50ng of total RNA to cDNA. This isothermal RNA amplification system produces 5-12 ug of anti-sense cDNA targets that is followed by several steps to produce sense strand cDNA to be fragmented, biotinylated and hybridized to the genechip.

extract_protocol: Three biological replicates were pooled from the axillary, brachial, and inguinal lymph nodes from 5 mice for each replicate. Cells were washed with PBS/1%FCS, pelleted at 300g for 5 min at 4C. A working stock of Live/Dead-775 dye (Invitrogen L10119) was made by adding 1ul of reconstituted dye to 1ml PBS and cells were resuspended in 100ul of working stock per 1x106 cells. Cells were incubated for 30 minutes on ice in the dark. Cells were washed with cold PBS/1%FCS, pelleted, and resuspended in 100ul of an antibody mixture containing 1ug/ml PerCp-Cy5.5 anti-mouse TCRβ chain and 1ug/ml Alexa Flour® 488 anti-mouse CD4 antibodies in PBS/1%FCS. Cells were incubated on ice in the dark for 30 minutes then washed with cold PBS/1%FCS, pelleted, and resuspended at a concentration of 10x10^6 cells per 1ml of PBS/10%FCS. Cells were filtered through 50um nylon mesh and sorted using BD FACSAria to collect ~3x10^6 CD4+ T cells per sample. RNA was isolated using the Qiagen RNeasy® Plus Mini Kit following the manufacturer’s instructions (Qiagen, Valencia, CA).

tag: strain background

tag: genotype/variation

value: ChrY^SJL

value: females from mixed sex litters

value: 8 weeks

value: Lymph nodes

value: CD4+TCRB+ cells, naive


title: B6 uninfected

city: Bar Harbor

first: Joanne

last: Berghout

state: ME

address: 600 Main St

department: Mouse Genome Informatics

institute: The Jackson Laboratory

description: B6 d0 rep1-3; 3 replicates of 'B6 uninfected'; PGS816-818

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
data were log2 transformed and median normalized using GeneSifter by GeoSpiza
normalized data were exported from GeneSifter using internal export tools. Data are presented as mean, standard error of the mean, and quality for each comparison group.

source_name: B6 uninfected

label_protocol: standard Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent in accordance with the prescribed protocol provided with the kit. RNAeasy columns were used to further purify samples. RNA auality control was performed by gel electrophoresis and nanodrop spectral analysis. Agilent bioanalyzer was also used prior to chip hybridization

treatment_protocol: Infected experimental mice were injected i.p. with 10^6 Plasmodium berghei ANKA parasites one week before tissue harvest. Uninfected animals were simply collected from the animal facility at the same point in time.

value: 8-10 weeks

tag: mice group

value: cerebral malaria susceptible

value: wild type

tag: infected with

value: none (uninfected)

value: total brain


title: B6-ChrY^SJL_female_CD4+ T cells, rep2


title: BXH2 P. berghei d7

description: BXH2 d7 rep1-4; 4 replicates of 'BXH2 d7'; PGS822, PGS828-830

source_name: BXH2 P. berghei d7

value: cerebral malaria resistant

value: carrying a severe hypomorphic Irf8-R294C allel

value: 10^6 Plasmodium berghei d7


title: B6_female_CD4+ T cells, rep2

source_name: B6_CD4+ T cells


title: B6-ChrY^SJL_female_CD4+ T cells, rep3


title: B6_female_CD4+ T cells, rep1


title: B6_female_CD4+ T cells, rep3


title: B6 P. berghei d7

description: B6 d7 rep1-2; 2 replicates of 'B6 P. berghei d7'; PGS823, PGS824

source_name: B6 P. berghei d7


title: B6, sperm, rep2

hyb_protocol: Each sample was hybridized to a GeneChip® miRNA 2.0 Array (Affymetrix, Santa Clara, CA, USA) at 48°C and 60 rpm for 16 hours then washed and stained on Fluidics Station 450 (Fluidics script FS450_0003) and finally scanned on a GeneChip® Scanner 3000-7G (Affymetrix).

data_processing:
Raw GeneChip data (one DAT file for each chip) includes a collection of images, one for each probe and chip.  Each image was summarized by Affymetrix GCOS software using one probe intensity (in CEL files, one per chip).sample.
miRNA-2_0_v2.pgf
miRNA-2_0.annotations.20101222.csv
Information from multiple probes was combined to obtain a single measure of expression for each probe set and sample.  Probe-level intensities were calculated using the Robust Multichip Average (RMA) algorithm, including background-correction, normalization (quantile), and summarization (median polish), for each probe set and sample, as is implemented in Partek Genomic Suites®, version 6.6 (Copyright © 2009, Partek Inc., St. Louis, MO, USA).

source_name: epidydimal sperm

label_protocol: Total RNA containing small RNA was labeled using the Flashtag RNA labeling kit (Genisphere, Hatfield, PA, USA) and performed in the Vermont Genetics Network Microarray Facility according to the manufacturer's instructions. Briefly, for each sample, 500ng of total RNA were subjected to a tailing reaction (2.5 mM MnCl2, ATP, Poly A Polymerase - incubation for 15 minutes at 37°) followed by ligation of the biotinylated signal molecule to the target RNA sample (1× Flash Tag ligation mix biotin, T4 DNA ligase - incubation for 30 minutes at 25oC) and addition of HSR stop solution.

extract_protocol: Epidydimal sperm was collected using the double swim-out method. The large pieces of tissue were removed using forceps, and the remaining media was filtered through 150 uM mesh and centrifuged. Sperm were treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X-100) and miRNA was isolated using the mirVana miRNA isolation method for enrichment of small RNAs

value: Male

value: epidydimus


title: B6-ChrY^SJL, sperm, rep2


title: B6-ChrY^SJL, sperm, rep3


title: B6-ChrY^SJL, sperm, rep1


title: B6-ChrY^RF, sperm, rep2


title: B6-ChrY^RF, sperm, rep3


title: BXH2 uninfected

description: BXH2 d0 rep1-3;3 replicates of 'BXH2 uninfected'; PGS819-821

source_name: BXH2 uninfected


title: B6-ChrY^RF, sperm, rep1


title: B6, sperm, rep3


title: B6, sperm, rep1


title: KYSE410 treated B2 rep2

city: Beijing

first: Yang

last: Xu

address: No.17 Panjiayuan Nanli, Chaoyang district

country: China

institute: Cancer Hospital

description: Gene expression data from KYSE410 treated with YM155 for 6 hrs.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

source_name: KYSE410 treated with YM155 for 6 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: KYSE410 cells were clutured in RPMI medium with 10% fetal bovin serum (FBS) and antibiotics

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

treatment_protocol: KYSE410 cells were treated with 10mM of cisplatin for 12 hrs or left untreated

value: 20 nM of YM155 for 6 hrs


title: seasonal allergic rhinitis patient 7

city: Tsukuba

first: Emiko

last: Noguchi

address: 1-1-1 Tennoudai

institute: University of Tsukuba

description: SAMPLE 12

data_processing: We performed normexp-by-control background correction, quantile normalization, and log2 transformation on the raw data using the neqc command of Illumina

source_name: nasal epithelial cells

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit

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.

tag: individual

value: seasonal allergic rhinitis patient

value: nasal epithelial cells


title: KYSE410 treated B1 rep1

source_name: KYSE410 treated with  YM155 for 6 hrs


title: seasonal allergic rhinitis patient 3

description: SAMPLE 8

tag: cell type


title: KYSE410 untreated rep2

description: Gene expression data from KYSE410 untreated.

source_name: KYSE410 untreated

value: Untreated


title: seasonal allergic rhinitis patient 6

description: SAMPLE 11


title: seasonal allergic rhinitis patient 2

description: SAMPLE 7


title: non-allergic control subject 5

description: SAMPLE 5

value: non-allergic control subject


title: seasonal allergic rhinitis patient 4

description: SAMPLE 9


title: non-allergic control subject 3

description: SAMPLE 3


title: seasonal allergic rhinitis patient 1

description: SAMPLE 6


title: non-allergic control subject 2

description: SAMPLE 2


title: non-allergic control subject 1

description: SAMPLE 1


title: KYSE410 untreated rep1


title: seasonal allergic rhinitis patient 5

description: SAMPLE 10


title: non-allergic control subject 4

description: SAMPLE 4


title: post-Tx biopsy 42, biopsy pair 1172-42, PBx group (control)

status: Public on Jan 15 2015

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

description: microRNA expression data from post-TX biopsy, protocol biopsy (PBx) without pathology

hyb_protocol: The complementary RNA hybridization cocktail was incubated overnight at 48°C while rotating in a hybridization oven. After 16 hours of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 7G.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA.

source_name: kidney allograft biopsy

label_protocol: Total RNA (1µg per sample) was labeled using the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit and hybridized to the arrays as described by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Kidney tissue in RNAlater, stored at -80°C. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: kidney

tag: biopsy type


title: post-Tx biopsy 07, biopsy pair 1073-07, AKI group

description: microRNA expression data from post-TX biopsy, acute tubular necrosis (ATN)


title: post-Tx biopsy 41, biopsy pair 1171-41, PBx group (control)

value: post-TX biopsy, protocol biopsy (PBx) without pathology


title: post-Tx biopsy 09, biopsy pair 1084-09, AKI group

value: post-TX biopsy, acute tubular necrosis (ATN)


title: post-Tx biopsy 39, biopsy pair 1162-39, AKI group


title: post-Tx biopsy 38, biopsy pair 1163-38, PBx group (control)


title: PBBA2_mRNA

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression analysis was performed for peripheral blood B cells using Affymetrix Human Gene 1.0 ST arrays

hyb_protocol: Products were hybridized to Affymetrix Human Gene 1.0 ST arrays according to the manufacturer’s protocol

data_processing: Gene expression levels were determined using the Affymetrix Expression Console software (v1.2.0.20) with exon-level RMA analysis and default settings

source_name: CD19+ B cells

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin kit

extract_protocol: RNA was purified using Qiagen RNeasy Kits according to the manufacturer’s protocol.

value: Activated (IL4, anti-CD40, IgM, and IgD) peripheral blood

tag: tumor

tag: Sex

value: male

tag: previously treated for nhl

value: peripheral blood B cells


title: PBBA1_mRNA


title: post-Tx biopsy 35, biopsy pair 1156-35, PBx group (control)


title: PBBA3_mRNA

value: female


title: post-Tx biopsy 43, biopsy pair 1174-43, AKI group


title: FL15_mRNA

description: Gene expression analysis was performed for FL using Affymetrix Human Gene 1.0 ST arrays

value: LN

value: no

value: follicular lymphoma


title: post-Tx biopsy 33, biopsy pair 1160-33, PBx group (control)


title: post-Tx biopsy 32, biopsy pair 1159-32, PBx group (control)


title: post-Tx biopsy 34, biopsy pair 1161-34, PBx group (control)


title: FL13_mRNA


title: FL10_mRNA


title: FL14_mRNA


title: PBBA4_mRNA


title: FL16_mRNA


title: post-Tx biopsy 02, biopsy pair 1047-02, AKI group


title: post-Tx biopsy 30, biopsy pair 1140-30, PBx group (control)


title: post-Tx biopsy 29, biopsy pair 1141-29, AKI group


title: FL12_mRNA


title: FL9_mRNA


title: FL11_mRNA

value: yes


title: post-Tx biopsy 28, biopsy pair 1039-28, AKI group


title: post-Tx biopsy 25, biopsy pair 1135-25, AKI group


title: FL6_mRNA


title: FL7_mRNA


title: zero-hour biopsy 1172, biopsy pair 1172-42, PBx group (control)

description: microRNA expression data from zero-hour biopsy

value: zero-hour biopsy


title: post-Tx biopsy 24, biopsy pair 1134-24, PBx group (control)


title: zero-hour biopsy 1171, biopsy pair 1171-41, PBx group (control)


title: zero-hour biopsy 1163, biopsy pair 1163-38, PBx group (control)


title: zero-hour biopsy 1162, biopsy pair 1162-39, AKI group


title: post-Tx biopsy 27, biopsy pair 1133-27, PBx group (control)


title: FL5_mRNA


title: zero-hour biopsy 1161, biopsy pair 1161-34, PBx group (control)


title: FL1_mRNA


title: FL4_mRNA


title: zero-hour biopsy 1160, biopsy pair 1160-33, PBx group (control)


title: FL2_mRNA


title: FL8_mRNA


title: zero-hour biopsy 1174, biopsy pair 1174-43, AKI group


title: zero-hour biopsy 1156, biopsy pair 1156-35, PBx group (control)


title: zero-hour biopsy 1141, biopsy pair 1141-29, AKI group


title: zero-hour biopsy 1159, biopsy pair 1159-32, PBx group (control)


title: FL3_mRNA


title: zero-hour biopsy 1140, biopsy pair 1140-30, PBx group (control)


title: zero-hour biopsy 1134, biopsy pair 1134-24, PBx group (control)


title: zero-hour biopsy 1084, biopsy pair 1084-09, AKI group


title: Normal_25

city: Los Angeles

first: David

last: Wong

address: 10833 Le Conte Ave

department: Dentistry

institute: UCLA

description: Sample name: N26

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Affymetrix Expression Console

source_name: Saliva

label_protocol: Biotin

growth_protocol: Un-stimulated saliva collected from patients

extract_protocol: Total RNA was extracted by using Qiagen Rneasy kit

treatment_protocol: Saliva was spun down to collect cell-free saliva supernatant

tag: disease state

value: normal

tag: rna source

value: cell-free saliva supernatant


title: Normal_26

description: Sample name: N27


title: zero-hour biopsy 1133, biopsy pair 1133-27, PBx group (control)


title: Normal_27

description: Sample name: N28


title: zero-hour biopsy 1135, biopsy pair 1135-25, AKI group


title: zero-hour biopsy 1047, biopsy pair 1047-02, AKI group


title: Normal_22

description: Sample name: N23


title: Normal_28

description: Sample name: N29


title: Normal_21

description: Sample name: N22


title: zero-hour biopsy 1039, biopsy pair 1039-28, AKI group


title: Normal_24

description: Sample name: N25


title: Normal_23

description: Sample name: N24


title: Normal_30

description: Sample name: N31


title: post-Tx biopsy 09, biopsy pair 1084-09, AKI group

description: Gene expression data from post-TX biopsy, acute tubular necrosis (ATN)

hyb_protocol: cDNA were hybridized for 18 hr at 45C on GeneChip Human ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

label_protocol: Total RNA (200 ng per sample) was amplified and labeled using the Applause WT-Amp ST and Encore Biotin Module kit (NuGEN, San Carlos, CA)


title: Normal_20

description: Sample name: N21


title: Normal_19

description: Sample name: N20


title: Normal_18

description: Sample name: N19


title: Normal_29

description: Sample name: N30


title: Normal_31

description: Sample name: N32


title: zero-hour biopsy 1073, biopsy pair 1073-07, AKI group


title: Normal_10

description: Sample name: N11


title: post-Tx biopsy 43, biopsy pair 1174-43, AKI group


title: Normal_17

description: Sample name: N18


title: Normal_15

description: Sample name: N16


title: Normal_8

description: Sample name: N9


title: post-Tx biopsy 42, biopsy pair 1172-42, PBx group (control)

description: Gene expression data from post-TX biopsy, protocol biopsy (PBx) without pathology


title: post-Tx biopsy 32, biopsy pair 1159-32, PBx group (control)


title: post-Tx biopsy 39, biopsy pair 1162-39, AKI group


title: post-Tx biopsy 38, biopsy pair 1163-38, PBx group (control)


title: Normal_12

description: Sample name: N13


title: Normal_16

description: Sample name: N17


title: Normal_11

description: Sample name: N12


title: Normal_13

description: Sample name: N14


title: post-Tx biopsy 33, biopsy pair 1160-33, PBx group (control)


title: post-Tx biopsy 29, biopsy pair 1141-29, AKI group


title: post-Tx biopsy 34, biopsy pair 1161-34, PBx group (control)


title: post-Tx biopsy 07, biopsy pair 1073-07, AKI group


title: post-Tx biopsy 35, biopsy pair 1156-35, PBx group (control)


title: post-Tx biopsy 30, biopsy pair 1140-30, PBx group (control)


title: Normal_14

description: Sample name: N15_2


title: post-Tx biopsy 27, biopsy pair 1133-27, PBx group (control)


title: post-Tx biopsy 02, biopsy pair 1047-02, AKI group


title: post-Tx biopsy 41, biopsy pair 1171-41, PBx group (control)


title: post-Tx biopsy 28, biopsy pair 1039-28, AKI group


title: Normal_7

description: Sample name: N8


title: Normal_9

description: Sample name: N10


title: Normal_6

description: Sample name: N7


title: Normal_4

description: Sample name: N4


title: Normal_5

description: Sample name: N6


title: post-Tx biopsy 25, biopsy pair 1135-25, AKI group


title: Normal_3

description: Sample name: N3


title: zero-hour biopsy 1174, biopsy pair 1174-43, AKI group

description: Gene expression data from zero-hour biopsy


title: Gastric_Cancer_59

description: Sample name: P61

value: gastric cancer


title: post-Tx biopsy 24, biopsy pair 1134-24, PBx group (control)


title: Gastric_Cancer_61

description: Sample name: P63


title: Normal_2

description: Sample name: N2


title: zero-hour biopsy 1160, biopsy pair 1160-33, PBx group (control)


title: zero-hour biopsy 1171, biopsy pair 1171-41, PBx group (control)


title: Gastric_Cancer_62

description: Sample name: P65


title: zero-hour biopsy 1161, biopsy pair 1161-34, PBx group (control)


title: zero-hour biopsy 1172, biopsy pair 1172-42, PBx group (control)


title: Gastric_Cancer_63

description: Sample name: P66


title: Normal_1

description: Sample name: N1


title: Gastric_Cancer_56

description: Sample name: P58


title: Gastric_Cancer_58

description: Sample name: P60


title: zero-hour biopsy 1156, biopsy pair 1156-35, PBx group (control)


title: Gastric_Cancer_55

description: Sample name: P57


title: Gastric_Cancer_60

description: Sample name: P62


title: zero-hour biopsy 1163, biopsy pair 1163-38, PBx group (control)


title: zero-hour biopsy 1162, biopsy pair 1162-39, AKI group


title: zero-hour biopsy 1159, biopsy pair 1159-32, PBx group (control)


title: zero-hour biopsy 1135, biopsy pair 1135-25, AKI group


title: zero-hour biopsy 1134, biopsy pair 1134-24, PBx group (control)


title: zero-hour biopsy 1141, biopsy pair 1141-29, AKI group


title: zero-hour biopsy 1133, biopsy pair 1133-27, PBx group (control)


title: Gastric_Cancer_57

description: Sample name: P59


title: Gastric_Cancer_54

description: Sample name: P56


title: Gastric_Cancer_52

description: Sample name: P54


title: Gastric_Cancer_51

description: Sample name: P53


title: zero-hour biopsy 1140, biopsy pair 1140-30, PBx group (control)


title: Gastric_Cancer_53

description: Sample name: P55


title: zero-hour biopsy 1084, biopsy pair 1084-09, AKI group


title: Gastric_Cancer_50

description: Sample name: P52


title: Gastric_Cancer_48

description: Sample name: P50


title: Gastric_Cancer_49

description: Sample name: P51


title: zero-hour biopsy 1047, biopsy pair 1047-02, AKI group


title: Capitol-2N_D-rep3

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

description: Gene expression with standard N supply 4d after leaf detachment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented in 1x Agilent fragmentation buffer (Agilent Technologies catalog number 5188-5242)  and 2x Agilent blocking agent (Agilent Technologies catalog number 5188-5242) following the manufacturers instructions. Hybridization was performed in a Agilent hybridization oven (Agilent Technologies catalog number G2545-90002) at standard conditions as recommended by the manufacturer. Subsequently, microarrays were washed 1 minute with GE Wash Buffer 1 at ambient temperature and 1 minute with GE Wash buffer 2 (Agilent Technologies catalog number 5188-5327) at 37°C.

scan_protocol: Microarrays were scanned immediately after washing with an Agilent High-Resolution Scanner (G2505C) using default settings.

data_processing: The images were processed with the Agilent Feature Extraction software 10.1 using default settings  (protocol GE1_105_Dec08 (Read Only) and GridName US91803681_252963410002_S01_grid (from grid_file)). The resulting processed signals of all individual hybridizations were quantile-normalized using the ranked median quantiles according to Bolstad et al. (2003. Bioinformatics 19, 185-193).

organism: Brassica napus

source_name: B. napus Capitol - 2N_D-rep3

label_protocol: Cy3-labeled cRNA was synthesized with the Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies catalog number 5190-2305) according to the manufacturer's instructions.

growth_protocol: Seven days old seedlings were hydroponically pre-cultured for 28 days at optimal N supply in a continuously aerated nutrient solution composed of 2 mM N [9:1 ratio of Ca(NO3)2 and (NH4)2SO4], 500 µM K2S04, 250 µM KH2PO4, 325 µM MgSO4, 50 µM NaCl, 8 µM H3BO3, 0.4 µM MnSO4, 0.4 µM ZnSO4, 0.4 µM CuSO4, 0.1 µM MoNa2O4, 40 µM Fe-EDDHA and 10 µM C2H4N4.

extract_protocol: Total RNA was extracted from 500 mg frozen and ground tissue according to Verwoerd et al. (1989. Nucleic Acids Res. 17, 2362) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA was photometrically quantified with a NanoPhotometer (Implen, München, Germany) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Leaf senescence was induced by (i) N starvation (0.1 mM N as Ca(NO3)2 and 1 mM CaSO4), (ii) shading of leaf 3 (counted from bottom to top of the plant), and (iii) detaching leaf 3 and incubating it in deionized water.

tag: cultivar

value: Capitol

tag: nitrogen efficiency status

value: N inefficient

value: leaf number 3

tag: treatment

value: N standard, leaf detached


title: Gastric_Cancer_44

description: Sample name: P46


title: Gastric_Cancer_46

description: Sample name: P48


title: Gastric_Cancer_45

description: Sample name: P47


title: Capitol-2N_S-rep3

description: Gene expression with standard N supply after 4d leaf shading

source_name: B. napus Capitol - 2N_S-rep3

tag: tissue

value: N standard, leaf shaded


title: zero-hour biopsy 1073, biopsy pair 1073-07, AKI group

value: kidney


title: zero-hour biopsy 1039, biopsy pair 1039-28, AKI group


title: Gastric_Cancer_42

description: Sample name: P44


title: LMD_LH2

first: Akiko

last: Satoh

address: 660 S Euclid Avenue

institute: Washington University

description: laser microdissected samples

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse_v1 8x60K microarrays (Design ID-028005).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

source_name: Lateral hypothalamus, replicate 2

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol.  cDNAs were quantitated on a Nanodrop spectrophotometer.

extract_protocol: RNA was prepared using the PicoPure RNA Isolation kit (Arcturus, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

value: Lateral hypothalamus

tag: gender

tag: age

value: 3 mo


title: LMD_VMH2

description: laser microdissected samples

source_name: Ventromedial hypothalamus, replicate 2

value: Ventromedial hypothalamus

value: female


title: Capitol-2N-rep1

description: Gene expression in control leaves with standard N supply

source_name: B. napus Capitol - 2 mM N - rep1

value: N standard control


title: Capitol-2N_S-rep2

source_name: B. napus Capitol - 2N_S-rep2


title: LMD_LH1

description: laser microdissected samples

source_name: Lateral hypothalamus, replicate 1


title: Capitol-0.1N-rep3

description: Gene expression after 4d N starvation

source_name: B. napus Capitol - 0.1 mM N - rep3

value: N starvation


title: Capitol-2N_D-rep1

source_name: B. napus Capitol - 2N_D-rep1


title: Gastric_Cancer_43

description: Sample name: P45


title: Capitol-2N_S-rep1

source_name: B. napus Capitol - 2N_S-rep1


title: Capitol-2N-rep3

source_name: B. napus Capitol - 2 mM N - rep3


title: LMD_DMH2

description: laser microdissected samples

source_name: Dorsomedial hypothalamus, replicate2

value: Dorsomedial hypothalamus


title: Gastric_Cancer_41

description: Sample name: P43


title: Capitol-2N_D-rep2

source_name: B. napus Capitol - 2N_D-rep2


title: LMD_DMH1

description: laser microdissected samples

source_name: Dorsomedial hypothalamus, replicate1


title: Capitol-2N-rep2

source_name: B. napus Capitol - 2 mM N - rep2


title: Gastric_Cancer_47

description: Sample name: P49


title: Gastric_Cancer_40

description: Sample name: P42


title: LMD_VMH1

description: laser microdissected samples

source_name: Ventromedial hypothalamus, replicate 1


title: Capitol-0.1N-rep1

description: Gene expression after 4d N starvation

source_name: B. napus Capitol - 0.1 mM N - rep1


title: Apex-2N_D-rep2

source_name: B. napus Apex - 2N_D-rep2

value: Apex

value: N efficient


title: Gastric_Cancer_39

description: Sample name: P41

source_name: Saliva

value: cell-free saliva supernatant


title: Gastric_Cancer_37

description: Sample name: P38

value: gastric cancer


title: LMD_Arc1

description: laser microdissected samples

source_name: Arcuate nucleus, replicate 1

value: Arcuate nucleus


title: Apex-2N_D-rep3

source_name: B. napus Apex - 2N_D-rep3


title: Apex-2N_D-rep1

source_name: B. napus Apex - 2N_D-rep1


title: Gastric_Cancer_34

description: Sample name: P35


title: LMD_Arc2

description: laser microdissected samples

source_name: Arcuate nucleus, replicate 2


title: Capitol-0.1N-rep2

description: Gene expression after 4d N starvation

source_name: B. napus Capitol - 0.1 mM N - rep2

value: Capitol

value: N inefficient


title: Gastric_Cancer_38

description: Sample name: P40


title: Apex-0.1N-rep3

description: Gene expression after 4d N starvation

source_name: B. napus Apex - 0.1 mM N - rep3

value: leaf number 3


title: Apex-2N-rep1

source_name: B. napus Apex - 2 mM N - rep1


title: Apex-2N_S-rep2

source_name: B. napus Apex - 2N_S-rep2

value: N standard, leaf shaded


title: Apex-2N_S-rep1

source_name: B. napus Apex - 2N_S-rep1


title: Apex-2N-rep3

source_name: B. napus Apex - 2 mM N - rep3


title: Apex-0.1N-rep2

description: Gene expression after 4d N starvation

source_name: B. napus Apex - 0.1 mM N - rep2


title: Apex-2N_S-rep3

source_name: B. napus Apex - 2N_S-rep3


title: Apex-2N-rep2

source_name: B. napus Apex - 2 mM N - rep2


title: Gastric_Cancer_36

description: Sample name: P37


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, kdrl+ sort at 3 dpf, bio rep 3

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description: RNA amplified using NuGEN Ovation Pico WTA System V2

hyb_protocol: Hybridization Control Kit, and Hybridization, Wash, and Staining Kit from Ambion

scan_protocol: Genechip Scanner 3000 7G

data_processing: All ZebGene 1.0 ST arrays were processed using the BioConductor [1] package oligo [2]. Arrays were assessed for quality with arrayQualityMetrics [3] and normalized using the Robust Multichip Average (RMA [4]) method at the probe level, collapsing probes into core transcripts based on the pd.zebgene.1.0.db annotation package [5]. Batch correction was performed with the sva [6] package and the ComBat method [7]. Control probes and those with either mean log transformed intensity values of less than 2.5 or standard deviations  of less than 0.1 among all samples were removed. Probes were assigned to genes using Netaffx [8] annotations (ZebGene-1_0-st-v1.na33.3.zv9.transcript.csv); probes were not combined at the gene level, but were treated as independent assays. Differential expression statistics for pairwise and three-way (interaction terms) comparisons were generated by linear model for microarray data analysis (limma) [9] using empirical Bayes shinkage methods. Differentially expressed genes were assessed as those with least a log fold expression change of 1 and an FDR [10] based adjusted pvalue of less than 0.1.    [1] R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. H. Yang, and J. Zhang, “Bioconductor: open software development for computational biology and bioinformatics.,” Genome Biol., vol. 5, no. 10, p. R80, 2004.    [2] B. S. Carvalho and R. A. Irizarry, “A framework for oligonucleotide microarray preprocessing.,” Bioinformatics, vol. 26, no. 19, pp. 2363–2367, Oct. 2010.    [3] A. Kauffmann, R. Gentleman, and W. Huber, “arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.,” Bioinformatics, vol. 25, no. 3, pp. 415–416, Feb. 2009.  [4] B. M. Bolstad, R. A. Irizarry, M. Astrand, and T. P. Speed, “A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.,” Bioinformatics, vol. 19, no. 2, pp. 185–193, Jan. 2003.    [5] Benilton Carvalho. pd.zebgene.1.0.st: Platform Design Info for Affymetrix ZebGene-1_0-st. R package version 3.8.0.    [6] J. T. Leek, W. E. Johnson, H. S. Parker, A. E. Jaffe, and J. D. Storey, “The sva package for removing batch effects and other unwanted variation in high-throughput experiments.,” Bioinformatics, vol. 28, no. 6, pp. 882–883, Mar. 2012.    [7] W. E. Johnson, C. Li, and A. Rabinovic, “Adjusting batch effects in microarray expression data using empirical Bayes methods.,” Biostatistics, vol. 8, no. 1, pp. 118–127, Jan. 2007.    [8] G. Liu, A. E. Loraine, R. Shigeta, M. Cline, J. Cheng, V. Valmeekam, S. Sun, D. Kulp, and M. A. Siani-Rose, “NetAffx: Affymetrix probesets and annotations.,” Nucleic Acids Res., vol. 31, no. 1, pp. 82–86, Jan. 2003.    [9] G. K. Smyth, “Linear models and empirical bayes methods for assessing differential expression in microarray experiments.,” Stat Appl Genet Mol Biol, vol. 3, p. Article3, 2004.    [10] Y. Benjamini and Y. Hochberg, “Controlling the false discovery rate: a practical and powerful approach to multiple testing,” Journal of the Royal Statistical Society Series B …, 1995.

organism: Danio rerio

source_name: dissociated 3 dpf embryos, kdrl+ sort

label_protocol: total RNA was amplified and labeled using the NuGEN Ovation Pico WTA System V2 and Encore Biotin Module kits, respectively

growth_protocol: embryos were raised in E3 media at 28.5C

extract_protocol: embryos were dissociated using Roche liberase, cell populations were sorted directly in Trizol LS using an Aria cell sorter, Trizol extraction was performed as per the manufacturer's instructions, with the addition of Sigma GenElute LPA

treatment_protocol: pools of embryos were treated form 2-3 dpf in 75 uM Lycorine in 1% DMSO, or 1% DMSO alone

value: Lycorine

value: dissociated sorted embryos

value: kdrl+ sort, endothelial

tag: developmental stage

value: 3 dpf

value: AB

tag: transgenes


title: Apex-0.1N-rep1

description: Gene expression after 4d N starvation

source_name: B. napus Apex - 0.1 mM N - rep1


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, Runx+ sort at 3 dpf, bio rep 3

source_name: dissociated 3 dpf embryos, Runx+ sort

value: Runx+ sort, HSPC


title: Gastric_Cancer_33

description: Sample name: P34

source_name: Saliva


title: Gastric_Cancer_35

description: Sample name: P36


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, negative sort at 3 dpf, bio rep 3

source_name: dissociated 3 dpf embryos, negative sort

value: negative sort, all cell types


title: Gastric_Cancer_31

description: Sample name: P32_5


title: Gastric_Cancer_32

description: Sample name: P33_5


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, kdrl+ sort at 3 dpf, bio rep 2


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, Runx+ sort at 3 dpf, bio rep 2


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, kdrl+ sort at 3 dpf, bio rep 1


title: Gastric_Cancer_30

description: Sample name: P31


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, negative sort at 3 dpf, bio rep 2


title: SW620 Post-Selection-2

city: New York

first: Jia Min

last: Loo

address: 1230 York Avenue #342

institute: The Rockefeller University

description:
miRNA present after intrahepatic selection
Post-2

hyb_protocol: Genoexplorer miRNA arrays (human) were used for hybridization. One miRNA microarray chip were used for each sample. The hybrization was performed at 42 dgrees celcius for 16hrs, then stained by streptavidin-Cy5 dye. After washes, the arrays were dried and scanned.

scan_protocol: Arrays were scanned using Axon 400B. Raw data with signal intensity were analyzed by GenePix Software.

data_processing: Raw intensity values for each of the three probes for every miRNA or control were averaged and standard deviation was also calculated. Array background was calculated as the average of signal intensity of all negative controls and buffers, and a signal threshold was determined by array background + 2x background's standard deviation, for each array; only averaged miRNA intensities higher than the signal threshold were considered. Across individual samples, raw data was median normazlized.

source_name: SW620 Post-Intrahepatic Sample-2

label_protocol: Labeling was performed by Genosensor using in-house protocol.

growth_protocol: SW620 cells were routinely cultured in McCoy media supplemented with 10% FBS, glutamine, pyruvate, pen-strep and fungizone.

extract_protocol: Genomic DNA was extracted from reference samples and from liver nodule using Qiagen Dneasy Kit and lenti-viral derived miRNA were enriched by vector specific PCR and in vitro transcription according to manufacturer's protocol. RNA was cleaned up using Ambion's Mega Clear kit and sent to Genosensor for profiling.

treatment_protocol: SW620 cells were cultured in McCoy media and transduced with the Lenti-miR library (System Biosciences). A portion of cells were saved as reference samples. A separate portion was injected into the liver of immunodeficient mice to allow for in vivo selection. The resulting liver nodule was extracted after 3-5 weeks.

tag: cell line

tag: transduced with

value: Lenti-miR library

tag: injected into

value: liver of immunodeficient mice

tag: time point

value: after in vivo selection


title: Gastric_Cancer_28

description: Sample name: P29

value: cell-free saliva supernatant


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, negative sort at 3 dpf, bio rep 1

tag: cell type


title: Lycorine-treated Runx1+23:GFP;kdrl:DsRed2 embryos, Runx+ sort at 3 dpf, bio rep 1


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, negative sort at 3 dpf, bio rep 3

value: DMSO


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, kdrl+ sort at 3 dpf, bio rep 2


title: Gastric_Cancer_29

description: Sample name: P30

value: gastric cancer


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, Runx+ sort at 3 dpf, bio rep 3


title: Hippocampal neurons treated with cholesterol-rep1

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

hyb_protocol: Two microgams of each Cy3-cRNA were hybridized overnight at 65°C on Whole Rat Genome Microarray 4x44K (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Microarrays data were acquired on a ScanArray GX (Perkin Elmer, UK) with a resolution of 5 µm

data_processing: Raw data were obtained with Mapix 5.0.0 software (Innopsys, France). For each sample, raw data consisted of the Median Feature Intensity – Median Background Intensity (F-B) at wavelength 532nm.

source_name: primary hippocampal neurons

label_protocol: Hundred nanograms of each RNA were amplified by IVT and labeled with Cy3 using the Low Imput Quick Amp labeling kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNAs were obtained from primary hippocampal neurons treated or not with 1.4mM MbCD-cholesterol  using Nucleospin RNA II kit (Macherey Nagel, France) in accordance with the manufacturer’s protocol. The quality and quantity of each RNA preparation was assessed on the Agilent 2100 Bioanalyzer with RNA 6000 NanoChips (Agilent Technologies).

value: primary hippocampal neurons

value: treated with 1.4mM MbCD-cholesterol


title: Hippocampal neurons treated with cholesterol-rep3


title: Hippocampal neurons treated with cholesterol-rep4


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, Runx+ sort at 3 dpf, bio rep 2


title: Gastric_Cancer_27

description: Sample name: P28_5


title: Hippocampal neurons-control-rep4

value: without cholesterol


title: Hippocampal neurons treated with cholesterol-rep2


title: Hippocampal neurons-control-rep3


title: Gastric_Cancer_25

description: Sample name: P26


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, kdrl+ sort at 3 dpf, bio rep 1


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, negative sort at 3 dpf, bio rep 2


title: SW620 Pre-Selection-2

description:
miRNA present in reference sample
Pre-2

source_name: SW620 Pre-Injection Sample-2

value: before in vivo selection


title: SW620 Post-Selection-1

description:
miRNA present after intrahepatic selection
Post-1

source_name: SW620 Post-Intrahepatic Sample-1


title: Gastric_Cancer_26

description: Sample name: P27


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, Runx+ sort at 3 dpf, bio rep 1


title: SW620 Pre-Selection-1

description:
miRNA present in reference sample
Pre-1

source_name: SW620 Pre-Injection Sample-1


title: Arabidopsis_seedling_3 h S__Exp2

city: Potsdam-Golm

first: Rainer

last: Hoefgen

address: Am Mühlenberg 1

institute: Max-Planck Institute for Molecular Plant Physiology

description: 3 hours resupply rep2

hyb_protocol: ATH1 GeneChip hybridizations, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

scan_protocol: Washing, staining, and scanning, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

data_processing: Raw intensity values from the scanned ATH1 GeneChip were analyzed using RMAExpress.

organism: Arabidopsis thaliana

source_name: Arabidopsis, seedling, 3 h S (sulphate re-supply condition)

label_protocol: Preparation and biotin labeling of cRNA, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

growth_protocol: Arabidopsis seedlings (100-120 seeds) were grown in 30 ml of sterile liquid medium (250 mL Erlenmeyer glass flasks) on orbital shakers with constant, uniform fluorescent light (~50 µE in the flask) and temperature (22°C). Shaker speed was low (30 rpm) during the first three days, and then increased to 80 rpm.

extract_protocol: Frozen plant material (100-200 mg) was ground in liquid nitrogen in a pre-cooled mortar or homogenised using metal beads (Ø 5mm) in the MM200 homogenizer (Retsch). TRIzol reagent (Invitrogen) was then added and mixed well by vortexing. After 5 min incubation at room temperature the homogenate was centrifuged at 13,000 x g for 5 min at 4°C in pre-cooled centrifuge. The supernatant was removed to a fresh Eppendorf tube and 400 µL of chloroform was added and mixed by vortexing before incubation at RT for 5 min. After 10 min centrifugation at 13,000 x g, at 4°C, the aqueous phase (~1 mL) was transferred to a fresh Eppendorf tube. RNA was precipitated with 0.5 mL of isopropanol and 0.5 mL of HSS buffer (0.8 M sodium citrate and 1.2 M NaCl) per 1 mL of aqueous phase, overnight at -20°C. The precipitate was pelleted by centrifugation at 13,000 x g for 30 minutes at 4°C. The supernatant was removed and the pellet was washed twice with 1 mL 70% ethanol, air dried, and re-suspended in ca. 50 µL water (approx. 1 µg RNA/1 µL). RNA concentration, purity and integrity were determined by analysis with Bioanalyser (Agilent) according to the manufacturer’s instruction.

treatment_protocol: Arabidopsis seedlings were grown in 30 mL of sterile liquid full nutrition (FN) medium (3 mM sulphate) or 150 μM sulphate medium. Transferring pre-grown 7-days old seedlings to a sulphate depleted medium (0 μM sulphate) assured immediate and continued sulphate starvation during the next two days of plant cultivation. On day 9 subsets of the sulphate depleted cultures were supplied with sulphate (500 μM) and samples taken 30 min and 3 hours after re-supply.

value: seedling


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, negative sort at 3 dpf, bio rep 1

value: dissociated sorted embryos


title: Hippocampal neurons-control-rep2


title: Arabidopsis_seedling_-S__Exp2

description: sulphate starvation rep2

source_name: Arabidopsis, seedling, -S (sulphate starvation condition)


title: Gastric_Cancer_22

description: Sample name: P23


title: Gastric_Cancer_24

description: Sample name: P25


title: DMSO-treated Runx1+23:GFP;kdrl:DsRed2 embryos, kdrl+ sort at 3 dpf, bio rep 3

value: kdrl+ sort, endothelial


title: Arabidopsis_seedling_30 min S__Exp2

description: 30 min resupply rep2

source_name: Arabidopsis, seedling, 30 min S (sulphate re-supply condition)


title: Gastric_Cancer_23

description: Sample name: P24


title: Arabidopsis_seedling_FN__Exp2

description: Control rep2

source_name: Arabidopsis, seedling, FN (full nutrient condition)


title: Petunia_hybrida_cold_treatment_5d_rep1

city: wuhan

first: wei

last: zhang

institute: Huazhong Agricultural University

description: This sample is selfing line of Petunia hybrida. It is the first of three 5d cold treatment at 2°C biological replicates used in this experiment.

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

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

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

organism: Petunia x hybrida

source_name: Petunia hybrida selfing line_cold_5d

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

extract_protocol: Total RNA was extracted from both control and cold-treated samples with Trizol Reagent (Invitrogen,http://www.invitrogen.com). The RNA quality was checked on a 1.2% agarose gel using an RNase-free electrophoresis system.

tag: genotype

value: selfing line

tag: phenotype

value: normal


title: Arabidopsis_seedling_3 h S__Exp1

description: 3 hours resupply rep1


title: Hippocampal neurons-control-rep1


title: Petunia_hybrida_cold_treatment_5d_rep2

description: This sample is selfing line of Petunia hybrida. It is the second of three 5d cold treatment at 2°C biological replicates used in this experiment.


title: Gastric_Cancer_18

description: Sample name: P19

tag: disease state

tag: rna source


title: Petunia_hybrida_cold_treatment_5d_rep3

description: This sample is selfing line of Petunia hybrida. It is the third of three 5d cold treatment at 2°C biological replicates used in this experiment.

tag: cultivar


title: Gastric_Cancer_20

description: Sample name: P21


title: Gastric_Cancer_19

description: Sample name: P20


title: Gastric_Cancer_21

description: Sample name: P22