title: Data Slide254 Area4

city: Saskatoon

first: Fernanda

last: Dias

address: 52 Campus Dr

institute: University of Saskatchewan

hyb_protocol: Hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: This is a place holder for the Tecan scanning protocol.

data_processing: data was normalized with loess

source_name: Control

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol:
Oocyte collection and grading    Ovaries were collected from slaughterhouse at Calgary, Ab and were shipped to Saskatoon same day. Ovaries were washed with 1X normal saline and oocytes were aspirated from 2-5 mm follicles. Oocytes were held in oocyte holding media (5% CS in DPBS). Only first and second grade oocytes were collected.     In vitro maturation    Oocytes were incubated in maturation media [TCM-199+ 5% CS+ LH (5μg/ml) +FSH (0.5μg/ml)] for     22-24 hrs. in 5% CO2 incubator at 37˚C.     In vitro fertilization    Four of frozen straws (0.25 ml) were thawed and spermatozoa were processed. 1.5 ml of spermatozoa was layered on 4 ml of percol gradient and centrifuged at 2000 rpm for 20 mins. Spermatozoa were washed with sperm washing solution and centrifuged for 5 mins at 2000 rpm. 50 μl of spermatozoa was dissolved in 4.95 ml of 5% sodium chloride solution to calculate the sperm concentration on the cell counting chamber. Spermatozoa concentration was adjusted to 3 million cells per ml using sperm washing and sperm diluting solutions. 20 oocytes per 100μl of spermatozoa solution drop were incubated under mineral oil in 5% CO2 solution for 18-22 hrs.     In vitro Culture    The fertilized oocytes were transferred to culture media and incubated in 5% CO2, 5% O2 and 90% N2.    Collection of morula    The embryos were cultured in CR1aa for 6 days after fertilization and morula rate was recorded. Morula were collected and randomly distributed into 3 treatment groups: Control, Slow freezing and Vitrification.    Morulae in control group were further cultured for next 24 hrs.
The morulae collected were washed with DPBS+ 5% CS. The washed morulae were incubated in 1.5 M glycerol + 5 % CS in DPBS for 10 mins. These morulae were transferred to 0.25 ml straws (as shown). Following temperature treatments were given:    First cycle -7˚C 10 min    Ice seeding    Second cycle -7˚C 5 min    Third cycle Upto -35˚C @ 0.5˚C/min Directly plunge into Liq. N2        Embryos were stored in Liq. N2 for next 24 hrs. They were thawed in 0.7M sucrose and 5% CS solution for 10 mins. and washed in 5% CS and CR1aa and put in culture for 24 hrs. The expanded blastocysts were collected for RNA extraction in RNase free water and stored in Liq. N2.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: Cow ovaries were collected at a commercial abattoir and transported at 20-25C to Saskatoon within 12-18 h. Follicular fluid containing cumulus oocyte complexes (COCs) was aspirated from <4mm ovarian follicles. COCs were collected and washed in holding solution (HS). COC grading was done and only first and second grade oocytes were pooled. COCs were washed 3X in maturation media. They were matured in vitro for 22-24h. For in vitro fertilization (IVF), in vitro matured COCs were incubated with frozen-thawed semen from a high genetic healthy dairy bull for 18-22 h. The zygotes were washed and transferred to in vitro culture (IVC) for further development to morula stage embryos. On 6th day of IVC, compact morulas were collected. These were further randomly divided into three treatment groups; control, vitrification and slow freezing

tag: sample type

tag: developmental stage

tag: embryo quality score (iets codes)

value: not scored

tag: breed (cattle)

value: beef

tag: time of embryo collection

value: 7 dpf (days post-in vitro fertilization)

tag: blast staging method

value: Morphological

tag: number per pool

tag: in vitro production

value: Yes

tag: cryopreservation

tag: exogenous hormone ovarian stimulation

tag: reproductive status (cattle)

value: embryo

tag: treatment

value: Control

source_name: EmbryoSF

value: SF


title: Tumor_7631 (aCGH)

status: Public on Mar 31 2017

type: genomic

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

hyb_protocol: Hybridization probes were denatured, preannealed, and cohybridized to arrays pretreated with the Universal Microarray Hybridization Kit. Following hybridization, slides were washed at room temperature and dried by centrifugation.

scan_protocol: Images and raw signal intensities were acquired using an Agilent G2505B DNA microarray scanner and GenePix Pro 6.0.1.22 image analysis software

data_processing: Pin-based LOWESS normalized, spot intensities representing the tumor (cy3) and reference (cy5) channels were background-corrected by subtracting the median background from the median foreground signal intensities. BASE database used.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human breast tumor

label_protocol: Tumor and reference genomic DNA were differentially labeled using a random labeling kit with Cy3-dCTP and Cy5-dCTP, respectively

extract_protocol: Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification

tag: tissue

value: breast tumor

tag: 8p11-p12 amplification

value: Amplified

tag: age

tag: pt status

tag: lymph node status

tag: er status

value: neg

tag: pgr status

tag: her2 status

source_name: Normal female genomic DNA reference

tag: reference

value: Normal female genomic DNA


title: Tumor_7253 (aCGH)

value: pos


title: Tumor_7105 (aCGH)

value: Loss


title: July_11_2012_at_12:00_in_Toyama_DPS_53

type: RNA

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description:
raw data file: S254663310040_A4.txt
02_12_0076

hyb_protocol: 825ng of labelled cRNA were hybridized using Gene Expression Hybridization Kit following manufacturer's instructions at NIAS RGRC Open Laboratory.

scan_protocol: Scanned with Agilent G2505C.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Signal after background detrend, multiplicative detrend and dye normalization by Agilent Feature Extraction Software and 'quantile' nomalization using normalize.qspline in affy package in R.
Data were filtered for cross-hybridization and probe design mistake (resulting ~125K data rows).

molecule: total RNA

organism: Oryza sativa

source_name: rice, leaf

label_protocol: 200 ng of total RNA were reverse-transcribed and labelled using Low Input Quick Amp Labeling Kit following manufacturer's instructions. Labelled cRNA were purified with Qiagen RNeasy mini kit.

growth_protocol: The rice seedlings were transplanted on 2012/4/25, or 2012/5/18. The rice plants were grown in Toyama field.

extract_protocol: Total RNA was extracted using Promega Maxwell 16 Instrument following manufacturer's instructions.

treatment_protocol: No particular treatment. The plants were grown according to practical cultivation at the sites.

tag: variety

value: Koshihikari

tag: place

value: Toyama

tag: sampling date

tag: days from transplanting to sampling

value: leaf


title: Tumor_6915 (aCGH)


title: July_11_2012_at_10:00_in_Toyama_DPS_53

description:
raw data file: S254663310040_A2.txt
02_12_0070


title: July_11_2012_at_12:00_in_Toyama_DPS_76

description:
raw data file: S254663310040_A4.txt
02_12_0075


title: Tumor_6846 (aCGH)


title: Tumor_6522 (aCGH)


title: Data Slide254 Area1

country: Canada

organism: Bos taurus

tag: sample type

tag: developmental stage

tag: embryo quality score (iets codes)

value: not scored

tag: breed (cattle)

tag: time of embryo collection

tag: blast staging method

tag: number per pool

tag: in vitro production

tag: cryopreservation


title: Data Slide253 Area4

growth_protocol: Oocyte collection and grading    Ovaries were collected from slaughterhouse at Calgary, Ab and were shipped to Saskatoon same day. Ovaries were washed with 1X normal saline and oocytes were aspirated from 2-5 mm follicles. Oocytes were held in oocyte holding media (5% CS in DPBS). Only first and second grade oocytes were collected.     In vitro maturation    Oocytes were incubated in maturation media [TCM-199+ 5% CS+ LH (5μg/ml) +FSH (0.5μg/ml)] for     22-24 hrs. in 5% CO2 incubator at 37˚C.     In vitro fertilization    Four of frozen straws (0.25 ml) were thawed and spermatozoa were processed. 1.5 ml of spermatozoa was layered on 4 ml of percol gradient and centrifuged at 2000 rpm for 20 mins. Spermatozoa were washed with sperm washing solution and centrifuged for 5 mins at 2000 rpm. 50 μl of spermatozoa was dissolved in 4.95 ml of 5% sodium chloride solution to calculate the sperm concentration on the cell counting chamber. Spermatozoa concentration was adjusted to 3 million cells per ml using sperm washing and sperm diluting solutions. 20 oocytes per 100μl of spermatozoa solution drop were incubated under mineral oil in 5% CO2 solution for 18-22 hrs.     In vitro Culture    The fertilized oocytes were transferred to culture media and incubated in 5% CO2, 5% O2 and 90% N2.    Collection of morula    The embryos were cultured in CR1aa for 6 days after fertilization and morula rate was recorded. Morula were collected and randomly distributed into 3 treatment groups: Control, Slow freezing and Vitrification.    Morulae in control group were further cultured for next 24 hrs.     Vitrification    The morulae collected were washed with DPBS+5% CS. These were transferred and equilibrated in vitrification solution 1 (VS1) and incubated at room temperature for 5 mins. Approximately, 3-4 morulae were passed through 3 drops of vitrification solution 2 (VS2). These morulae were then put on cryotop to immediately plunge in liq. N2. The morulae were stored in Liq. N2 for 24 hrs. The vitrified morulae were warmed in warming solution for 5 mins. and washed with DPBS+5% CS. The morulae were put to culture for next 24 hrs in CR1aa media to develop into expanded blastocyst. These blastocysts were washed and stored in RNAse free water in Liq. N2 for further use in RNA extraction.

value: beef

tag: exogenous hormone ovarian stimulation

tag: reproductive status (cattle)

tag: tissue

tag: treatment

source_name: EmbryoVit

value: Vit


title: Data Slide253 Area3

value: 7 dpf (days post-in vitro fertilization)

value: Morphological


title: Tumor_6521 (aCGH)

tag: 8p11-p12 amplification

tag: age

tag: pt status

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: reference


title: Tumor_6039 (aCGH)


title: Data Slide254 Area2

tag: sample type

tag: developmental stage

tag: embryo quality score (iets codes)

tag: breed (cattle)

tag: time of embryo collection

value: Yes

value: embryo


title: Data Slide253 Area2

tag: blast staging method

tag: number per pool

tag: in vitro production

tag: cryopreservation

tag: exogenous hormone ovarian stimulation

value: Control


title: Data Slide254 Area3

tag: reproductive status (cattle)

tag: tissue

tag: treatment

value: SF


title: July_11_2012_at_08:00_in_Toyama_DPS_53

description:
raw data file: S254663310036_A4.txt
02_12_0064

tag: variety

tag: place

tag: sampling date

tag: days from transplanting to sampling


title: Data Slide253 Area1

tag: sample type


title: Tumor_4302 (aCGH)

value: breast tumor

tag: 8p11-p12 amplification

value: Gain

tag: age

tag: pt status

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: reference


title: July_11_2012_at_08:00_in_Toyama_DPS_76

description:
raw data file: S254663310036_A4.txt
02_12_0063


title: July_11_2012_at_10:00_in_Toyama_DPS_76

description:
raw data file: S254663310040_A2.txt
02_12_0069


title: S Fred1 Vitgreen3

scan_protocol: Tecan scanning protocol.

growth_protocol:
The morulae collected were washed with DPBS+ 5% CS. The washed morulae were incubated in 1.5 M glycerol + 5 % CS in DPBS for 10 mins. These morulae were transferred to 0.25 ml straws (as shown). Following temperature treatments were given:    First cycle -7˚C 10 min    Ice seeding    Second cycle -7˚C 5 min    Third cycle Upto -35˚C @ 0.5˚C/min Directly plunge into Liq. N2        Embryos were stored in Liq. N2 for next 24 hrs. They were thawed in 0.7M sucrose and 5% CS solution for 10 mins. and washed in 5% CS and CR1aa and put in culture for 24 hrs. The expanded blastocysts were collected for RNA extraction in RNase free water and stored in Liq. N2.
Oocyte collection and grading    Ovaries were collected from slaughterhouse at Calgary, Ab and were shipped to Saskatoon same day. Ovaries were washed with 1X normal saline and oocytes were aspirated from 2-5 mm follicles. Oocytes were held in oocyte holding media (5% CS in DPBS). Only first and second grade oocytes were collected.     In vitro maturation    Oocytes were incubated in maturation media [TCM-199+ 5% CS+ LH (5μg/ml) +FSH (0.5μg/ml)] for     22-24 hrs. in 5% CO2 incubator at 37˚C.     In vitro fertilization    Four of frozen straws (0.25 ml) were thawed and spermatozoa were processed. 1.5 ml of spermatozoa was layered on 4 ml of percol gradient and centrifuged at 2000 rpm for 20 mins. Spermatozoa were washed with sperm washing solution and centrifuged for 5 mins at 2000 rpm. 50 μl of spermatozoa was dissolved in 4.95 ml of 5% sodium chloride solution to calculate the sperm concentration on the cell counting chamber. Spermatozoa concentration was adjusted to 3 million cells per ml using sperm washing and sperm diluting solutions. 20 oocytes per 100μl of spermatozoa solution drop were incubated under mineral oil in 5% CO2 solution for 18-22 hrs.     In vitro Culture    The fertilized oocytes were transferred to culture media and incubated in 5% CO2, 5% O2 and 90% N2.    Collection of morula    The embryos were cultured in CR1aa for 6 days after fertilization and morula rate was recorded. Morula were collected and randomly distributed into 3 treatment groups: Control, Slow freezing and Vitrification.    Morulae in control group were further cultured for next 24 hrs.     Vitrification    The morulae collected were washed with DPBS+5% CS. These were transferred and equilibrated in vitrification solution 1 (VS1) and incubated at room temperature for 5 mins. Approximately, 3-4 morulae were passed through 3 drops of vitrification solution 2 (VS2). These morulae were then put on cryotop to immediately plunge in liq. N2. The morulae were stored in Liq. N2 for 24 hrs. The vitrified morulae were warmed in warming solution for 5 mins. and washed with DPBS+5% CS. The morulae were put to culture for next 24 hrs in CR1aa media to develop into expanded blastocyst. These blastocysts were washed and stored in RNAse free water in Liq. N2 for further use in RNA extraction.

extract_protocol:
Vitrification of morula was done as described by Prentice et al., 2011. Morulae were stored in liquid N2 for at least 24 h before warming. Slow freezing of morula was done as described by Carvalho et al., 1996. Vitrified morulae were transferred from cryotop to warming solution and incubated for 5 min at 37°C. Embryos were washed with HS and were put to culture for 24-48 h. Similarly, slow frozen 0.5 ml plastic straws containing embryos were thawed in air for 10s and in water bath for 1 min. The embryos were transferred to thawing solution and incubated for 5 min at 37°C. Embryos were washed with HS and were put to culture for 24-48 h. Recovered morulae from each treatment group were cultured for 24-48 h to expanded blastocyst stage and examined for quality. Blastocysts from each treatment group replicate, were collected in groups of 5-7 blastocysts in 50-100 μl (approx.) RNAse free water in RNase free cryo-tubes. These tubes were snap frozen by plunging into liquid N2. A total of eight biological replicates were conducted on separate dates (4; Microarray and 4; qRT-PCR).
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: Cow ovaries were collected at a commercial abattoir and transported at 20-25C to Saskatoon within 12-18 h. Follicular fluid containing cumulus oocyte complexes (COCs) was aspirated from <4mm ovarian follicles. COCs were collected and washed in holding solution (HS). COC grading was done and only first and second grade oocytes were pooled. COCs were washed 3X in maturation media. They were matured in vitro for 22-24h. For in vitro fertilization (IVF), in vitro matured COCs were incubated with frozen-thawed semen from a high genetic healthy dairy bull for 18-22 h. The zygotes were washed and transferred to in vitro culture (IVC) for further development to morula stage embryos. On 6th day of IVC, compact morulas were collected. These were further randomly divided into three treatment groups; control, vitrification and slow freezing.

tag: developmental stage

tag: embryo quality score (iets codes)

tag: breed (cattle)

tag: time of embryo collection

tag: blast staging method

tag: number per pool

tag: in vitro production

tag: cryopreservation


title: Tumor_4296 (aCGH)

tag: tissue

value: neg

value: Normal female genomic DNA


title: S Fred2 Vitgreen4

tag: sample type

tag: reproductive status (cattle)

tag: treatment


title: Tumor_5582 (aCGH)

tag: 8p11-p12 amplification

value: Amplified

tag: age

tag: pt status

tag: lymph node status

value: pos


title: S Fgreen3 Vitred1


title: July_11_2012_at_06:00_in_Toyama_DPS_53

description:
raw data file: S254663310036_A2.txt
02_12_0058

tag: variety

value: Koshihikari

tag: place

value: Toyama

tag: sampling date

tag: days from transplanting to sampling


title: July_11_2012_at_04:00_in_Toyama_DPS_76

description:
raw data file: S254663310035_A4.txt
02_12_0051

value: leaf


title: S Fgreen4 Vitred2

tag: developmental stage

tag: embryo quality score (iets codes)

value: not scored

tag: breed (cattle)

value: beef

tag: time of embryo collection


title: July_11_2012_at_04:00_in_Toyama_DPS_53

description:
raw data file: S254663310035_A4.txt
02_12_0052


title: July_11_2012_at_02:00_in_Toyama_DPS_76

description:
raw data file: S254663310035_A2.txt
02_12_0045


title: July_11_2012_at_00:00_in_Toyama_DPS_53

description:
raw data file: S254663310033_A4.txt
02_12_0040


title: July_11_2012_at_02:00_in_Toyama_DPS_53

description:
raw data file: S254663310035_A2.txt
02_12_0046


title: July_11_2012_at_00:00_in_Toyama_DPS_76

description:
raw data file: S254663310033_A4.txt
02_12_0039


title: Rescue_03

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

country: Germany

institute: University of Lübeck

description: Liver gene expression at ZT10 from Clock-D19 mutant mice with liver clock rescue on high-fat diet

hyb_protocol: 17 hours, 60 rpm, 45C

scan_protocol: GeneChip Scanner 3000

data_processing: Data were extracted from CEL files and normalized by RMA method using Expression Console (Affymetrix) software.

label: biotin

organism: Mus musculus

source_name: Liver at ZT10

label_protocol: Labelling was with GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mice were kept under 12h:12h light:dark conditions with 45% high-fat diet ad libitum for 5 weeks (starting at 10 weeks of age) and killed at Zeitgeber time 10 (ZT10) by cervical dislocation and livers isolated and stored in RNAlater.

extract_protocol: Liver samples were homogenized using ceramic beads and total RNA isolated with TRIzol.

treatment_protocol: Rescue mice received 35 µg of WT-Clock expression plasmid (pLIVE vector; MIR 5420, Mirus Bio) by hydrodynamic tail vein injection at week 10.

value: Liver


title: Wildtype_02

description: Liver gene expression at ZT10 from wild-tpye (C57BL/6J) mice  on high-fat diet


title: Wildtype_01


title: Clock_03

description: Liver gene expression at ZT10 from Clock-D19 mutant mice  on high-fat diet


title: July_10_2012_at_22:00_in_Toyama_DPS_76

description:
raw data file: S254663310033_A2.txt
02_12_0033


title: Rescue_01


title: July_10_2012_at_22:00_in_Toyama_DPS_53

description:
raw data file: S254663310033_A2.txt
02_12_0034


title: Clock_02


title: July_10_2012_at_20:00_in_Toyama_DPS_53

description:
raw data file: S254663310023_A4.txt
02_12_0028


title: fibrotic mesenchymal stromal cell_rep3

city: New York

first: Lei

last: Ding

state: New York

country: USA

institute: Columbia University Medical Center

description: Fibrotic 3

hyb_protocol: About 3ug of input was used for hybridization

scan_protocol: GeneChip Scanner 3000 with Autoloader was used to obtain expression value.

data_processing: Expression values for all probes were normalized and determined using the robust multi-array (RMA) method via Affymetrix Expression Console.

source_name: mesenchymal stromal cells from Tpo virus infected Cxcl12-DsRed/+ mice

label_protocol: Total RNA from each replicate was amplified using NuGen Ovation Pico WTA System V2, converted to ST DNA using NuGen WT-Ovation Exon module and labelled using NuGen Encore Biotin Module according to manufacture's recommendation.

growth_protocol: Cxcl12-DsRed/+ mice were transplanted with Tpo-overexpressing or control retrovirus infected bone marrow cells. Myelofibrosis developed 2-3 months after the bone marrow transplantation.

extract_protocol: Trizol total RNA extraction according to manufacture's recommendation.

treatment_protocol: Bone marrow was digested with Collagenase IV and DnaseI for 20 minutes at 37 degree. Dissociated single cell suspension was incubated with CD45 and Ter119 antibody. About 5000 CD45/Ter119- Cxcl12-DsRed+ cells were directly sorted into Trizol using flow cytometry (double sort).

tag: strain

tag: protocol

value: transplanted with Tpo-overexpressing retrovirus infected bone marrow cells

tag: disease state

value: myelofibrosis

tag: cell type

value: mesenchymal stromal cells


title: fibrotic mesenchymal stromal cell_rep1

description: Fibrotic 1


title: July_10_2012_at_18:00_in_Toyama_DPS_76

description:
raw data file: S254663310023_A2.txt
02_12_0021

tag: tissue


title: Rescue_02


title: Clock_01


title: July_10_2012_at_16:00_in_Toyama_DPS_53

description:
raw data file: S254663310005_A4.txt
02_12_0016


title: control mesenchymal stromal cell_rep3

description: Control 3

source_name: mesenchymal stromal cells from control virus infected Cxcl12-DsRed/+ mice

value: transplanted with control retrovirus infected bone marrow cells

value: control


title: July_10_2012_at_12:00_in_Toyama_DPS_76

description:
raw data file: S254663310003_A4.txt
02_12_0003


title: July_10_2012_at_14:00_in_Toyama_DPS_53

description:
raw data file: S254663310005_A2.txt
02_12_0010


title: Wildtype_03


title: July_10_2012_at_16:00_in_Toyama_DPS_76

description:
raw data file: S254663310005_A4.txt
02_12_0015


title: July_10_2012_at_18:00_in_Toyama_DPS_53

description:
raw data file: S254663310023_A2.txt
02_12_0022


title: fibrotic mesenchymal stromal cell_rep2

description: Fibrotic 2


title: control mesenchymal stromal cell_rep2

description: Control 2


title: control mesenchymal stromal cell_rep1

description: Control 1


title: July_10_2012_at_12:00_in_Toyama_DPS_53

description:
raw data file: S254663310003_A4.txt
02_12_0004


title: July_10_2012_at_14:00_in_Toyama_DPS_76

description:
raw data file: S254663310005_A2.txt
02_12_0009


title: July_10_2012_at_20:00_in_Toyama_DPS_76

description:
raw data file: S254663310023_A4.txt
02_12_0027


title: SKOV3_cell_cFos_2

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

hyb_protocol: The samples were hybridized on Affymetrix Human Gene 1.0 ST Array for 16 h at 45°C.

scan_protocol: Arrays were washed to remove nonspecifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix) and then scanned on Gene- Chip Scanner 3000 7G system (Affymetrix).

data_processing:
CEL-files were jointly preprocessed in Affymetrix Expression Console (build 1.4.1.46) using RMA-sketch method.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: cFos-overexpressed SKOV3 ovarian cancer cells

label_protocol: The procedures for cDNA synthesis and labelling were carried out according to the Ambion WT Expression Kit (Life Technologies, Darmstadt, Germany) using 500 ng total RNA as starting material.

growth_protocol: The cells were cultivated in phenol red-free DMEM with 4.5 glucose/1, supplemented with10% FCS, 10 mg/ml insulin,L-glutamine, and antibiotics in 5% CO2, 37° C.

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

treatment_protocol:
Stable clones with c-Fos overexpression were generated performing transfections with the plasmid c-Fos-pIRES-P containing the full c-Fos cDNA cloned in the bicistronic vector pIRES-P.
xenograft mouse model: For injection into SCID mice, OVCAR8-NC and OVCAR8-c-Fos cells as well as SKOV3-NC and SKOV3-c-Fos were taken at concentration of 5 х 10^6 ml-1 in RPMI medium. A total of 200 μl of that suspension was injected into the peritoneal cavity of female mice (10 animals per group). Mice that showed strong signs of tumor progression (ascites, shaggy coat and loss of appetite) were sacrificed.

tag: cell line

tag: cell/tissue type

value: ovarian cancer cells

tag: genotype/variation

value: cFos-overexpressed


title: SKOV3_tumor_cFos_2

source_name: cFos-overexpressed SKOV3 primary tumor

value: primary tumor; intraperitoneal xenograft model

tag: host strain

value: SCID mice


title: SKOV3_cell_cFos_1


title: SKOV3_tumor_cFos_1


title: SKOV3_tumor_control_1

source_name: Control SKOV3 primary tumor

value: Control


title: SKOV3_tumor_cFos_3


title: oocyte in vivo,  biological rep2

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

description: Gene expression data from porcine oocytes before In vitro maturation

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Porcine Gene 1.1 ST Array Strip (48°C/20 h), washed and stained using the Affymetrix GeneAtlas Fluidics Station according to the manufacturer technical protocol

scan_protocol: The array strips were scanned employing Imaging Station of the GeneAtlas System.

data_processing: Obtained cell files were submied to bioconductor and R programing lenguage. Each CEL file was merged with a description file.  In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

label: Biotin

organism: Sus scrofa

source_name: pubertal crossbred Landrace gilt

label_protocol: Biotin labeling and fragmentation were performed by Affymetrix GeneChip® WT Terminal Labeling and Hybridization (Affymetrix).

growth_protocol: Ovaries and reproductive tracts were recovered at slaughter and transported to the laboratory at 38o C in 0.9% NaCl within 40 min. Cumulus-oocyte-complexes were selected under an inverted microscope, counted, and morphologically evaluated.

extract_protocol: Total RNA was extracted from samples using TRI Reagent (Sigma, St Louis, MO, USA) and RNeasy MinElute cleanup Kit (Qiagen, Hilden, Germany).  After extraction total RNA (100 ng) from each pooled sample was subjected to two round, sense cDNA amplification (Ambion® WT Expression Kit).

treatment_protocol: Cumulus-oocyte-complexes were cultured in 500 μl of standard porcine IVM culture medium TCM-199 (tissue culture medium) with Earle’s salts and L-glutamine, (Gibco BRL Life Technologies, Grand Island, NY, USA) supplemented with 2.2 mg/ml sodium bicarbonate (Nacalai Tesque, Inc., Kyoto, Japan), 0.1 mg/ml sodium pyruvate (Sigma-Aldrich, St. Louis, MO, USA), 10 mg/ml BSA (bovine serum albumin), (Sigma-Aldrich, St. Louis, MO, USA), 0.1 mg/ml cysteine (Sigma-Aldrich, St. Louis, MO, USA), 10% filtered porcine follicular fluid (v/v),  and gonadotropin supplements at final concentrations of 2.5 IU/ml hCG (Ayerst Laboratories, Inc., Philadelphia, PA, USA) and 2.5 IU/ml eCG (Intervet, Whitby, ON, Canada).  Wells were covered with a mineral oil overlay and cultured for 44 h at 38o C under 5% CO2.

value: oocyte

tag: breed

value: Landrace


title: SKOV3_cell_cFos_3


title: in vitro-maturated oocyte,  biological rep2

description: Gene expression data from In vitro-maturated porcine oocytes


title: SKOV3_cell_control_2

source_name: Control SKOV3 ovarian cancer cells


title: OVCAR8_tumor_cFos_3

source_name: cFos-overexpressed OVCAR8 primary tumor


title: in vitro-maturated oocyte,  biological rep3


title: oocyte in vivo,  biological rep3


title: SKOV3_tumor_control_2


title: SKOV3_cell_control_1


title: oocyte in vivo,  biological rep1


title: in vitro-maturated oocyte,  biological rep1


title: OVCAR8_tumor_cFos_2


title: OVCAR8_cell_cFos_2

source_name: cFos-overexpressed OVCAR8 ovarian cancer cells


title: OVCAR8_cell_cFos_3


title: OVCAR8_tumor_control_1

source_name: Control OVCAR8 primary tumor


title: OVCAR8_tumor_control_3


title: OVCAR8_cell_control_2

source_name: Control OVCAR8 ovarian cancer cells


title: OVCAR8_tumor_control_2


title: OVCAR8_cell_cFos_1


title: OVCAR8_cell_control_1


title: OVCAR8_tumor_cFos_1


title: OVCAR8_cell_control_3


title: Brain_iAg_T3_rep4

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

institute: University of Victoria

hyb_protocol: MAGEX DNA array slides were briefly rinsed in a plastic coplin jar containing WB2 buffer (0.1x SSC, 0.1% (w/v) SDS) and subsequently incubated with 90 ml of PB1 buffer (5x SSC, 0.2% (w/v) BSA, and 0.2% (w/v) SDS) at 48°C for 45 min.  Each slide was dried by centrifugation in a 50 ml falcon tube for 3 min at 200x g. Dried Lifterslip CS/3 coverslips (Erie Scientific Company) prerinsed with dH2O and 100% ethanol were placed over each DNA array region and the preheated cDNA/UDR samples added to each array. MAGEX DNA array slides were placed in a slide rack and 300µl of dH2O was added to the humidity filter prior to chamber assembly. Hybridization was done for 18 h at 42°C in a Hybex Microsample Incubator (SciGene).  All buffers used in washing the microarry slides were prewarmed at 48°C prior to use. Following hybridization, coverslips were removed and each slide washed for 5 min with WB1 buffer (1x SSC and 0.1% (w/v) SDS). Two subsequent washes were performed with WB2 buffer followed by a wash with WB3 buffer (0.01x SSC and 0.1% (w/v) SDS). Slides were dried by centrifugation for 3 min at 200x g and stored in the dark in a Scienceware autodessicator.

scan_protocol: Scanning was done on a Packard Bioscience Scan Array Express Micro array scanner with the Cy3 PMT gain at 80% and Cy5 PMT gain at 70%. Laser strength was set at 90% for both channels. MAGEX 2008 microarray slides were scanned at 5 um resolution with an X=0 mm, Y=11.73 mm, W=22 mm, and H=52.38mm.  Spot intensity levels were obtained via ImaGene Version 9.0 (BioDiscovery Inc.) as per the manufacturer’s protocol using the UDR to align the spot grid.

data_processing: Data normalization involved use of the geometric means derived from spot values representing high quality gene signals obtained for each sample. This resulted in normalization factors between 1.00 to 1.95 (brain) or 1.00 to 4.36 (liver). An appropriate background signal was determined by evaluating the empty and buffer-only spot positions interspersed throughout each array. The universal floor value was set at 1 robust standard deviation greater than the highest median background signal across all arrays, helping to minimize false positives due to low signal intensities.The floor was 326 and 166 for brain and liver, respectively.

organism: Aquarana catesbeiana

source_name: Brain, iAg, T3

label_protocol: The DecaLabel DNA Labelling Kit (Fermentas) was used to incorporate Cy3-dCTP (GE Healthcare Bio-Sciences Corp.) into cDNA according to manufacturer’s specifications. To aid in microarray data collection, a universal DNA reference (UDR) containing amplicons representative of all gene sequences present on the MAGEX microarray was similarly prepared with Cy5-dCTP (GE Healthcare Bio-Sciences Corp.). Labelled DNA was purified with the GeneJET PCR Purification Kit, and sufficient fluorophore incorporation was determined with the Nanodrop UV-Vis spectrophotometer (ND-1000, Thermo Scientific). Labelled DNA was precipitated with sequential addition of 20 μg glycogen (ThermoFisher Scientific), 5 µl of 3 M sodium acetate (pH 5.2), and 150 µl of chilled 100% ethanol. Samples were incubated at -20°C for a minimum of 60 min followed by centrifugation at 13,000 x g at 4°C for 20 min. The DNA pellet was washed once with 300 µl 75% ethanol and air dried for 10 min prior to addition of 7 µl (tadpole tissue samples) or 30 µl (UDR) dH2O, and stored at -20°C in 1.5 ml amber tubes. For hybridization, Cy5-labeled UDR (1 µl) was mixed with each Cy3-labeled cDNA (5.5 µl) and incubated at 95°C for 3 min followed by cooling on ice and a brief centrifugation to collect the denatured material. For each sample, a 33 µl hybridization solution was prepared that contained 5x SSC, 25% (v/v) deionized formamide, 0.02% (w/v) BSA, 1 µg A45 oligonucleotide, 0.1% (w/v) SDS, 5% (w/v) dextran, and 6.5 µl denatured labelled DNA and warmed briefly at 37°C prior to application onto the covered MAGEX DNA array.

growth_protocol: Animals used in the present study were treated and maintained in accordance with the guidelines of the Canadian Council on Animal Care and the Animal Care Committee guidelines of the University of Victoria. The exposures were carried out at the Pacific Environmental Environment Centre (PESC) in Vancouver, BC using locally wild-caught R. catesbeiana tadpoles ranging between Taylor-Kollros developmental stages IV and X. Animals were maintained in 35 L tanks filled with well water (WW) for the duration of the exposures. Water temperature was maintained at 20.41 ± 0.07°C with 84.2 ± 0.4% dissolved oxygen and a pH of 7.78 ± 0.01. The photoperiod was kept at 12 hrs for both light and dark periods. The exposure was a static renewal system and water + treatmentswere replaced every 2-6 d followed by tadpole feeding of algal pellets. Nitrogenous wastes were monitored and kept within non-toxic levels for ammonium (15 ± 5 μg/L), nitrite (13 ± 3 μg/L), and nitrate (71 ± 18μg/L).

extract_protocol: Total RNA was extracted from brain and liver tissues using TRIzol reagent (Invitrogen) according to manufacturer’s protocol. Each sample was homogenized at 20 Hz for 6 min in 700 µl TRIzol using a 3 mm tungsten-carbide bead and a Retsch MM301 mixer mill. RNA pellets were resuspended in 100 µl (liver) or 40 µl (brain) diethyl pyrocarbonate-treated water, quantified by spectrophotometry, and stored at -80°C. Each total RNA sample was used to prepare amplified cDNA with the SMARTer PCR cDNA Synthesis Kit as per manufacturer’s protocol (Clontech Laboratories Inc.) with subsequent cDNA purification using the GeneJET PCR Purification Kit (Fermentas). All cDNA was stored at -20°C.

treatment_protocol: The exposure setup was modified from the Organization for Economic Co-operation and Development (OECD) Amphibian Metamorphosis Assay (AMA) guidelines (2009). Twenty four tadpoles were immersed for 6 d in WW, nAg (6 µg/L nominal Ag; Vive Nano, Toronto, ON), or iAg (6 µg/L nominal Ag; AgNO3, Fisher Scientific).  On experimental day 4, half the tadpoles in each immersion condition (n=12) received a 0.1% (0.01 ml/g body weight) intraperitoneal injection of TH (10 nM 3,3′,5-triiodo-L-thyronine; Sigma- Aldrich) prepared in 100 nM NaOH, while the remaining half were injected with vehicle alone. At 48 h post-injection (experimental day 6), animals were euthanized in 0.1% (w/v) tricaine methanesulfonate (MS-222; Syndel Laboratories Ltd, Vancouver, BC) buffered with 25 mM NaHCO3 and brain and liver tissues collected and immediately preserved in RNAlater (Qiagen) at 4°C followed by long term storage at -20°C.

value: brain

tag: treatment

value: iAg (6 µg/L nominal Ag; AgNO3, Fisher Scientific) with vehicle


title: Brain_iAg_T3_rep6


title: Brain_iAg_T3_rep5


title: Brain_iAg_T3_rep3


title: Brain_iAg_T3_rep2


title: Brain_iAg_T3_rep1


title: Brain_iAg_NaOH_rep5

source_name: Brain, iAg, NaOH

value: iAg (6 µg/L nominal Ag; AgNO3, Fisher Scientific) prepared in 100 nM NaOH


title: Brain_iAg_NaOH_rep6


title: MEKi-121493-pretx

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: Agilent Quick-Amp labeling Kit

extract_protocol: Total RNA isolated by stratagene

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label: Qiagen Rneasy Kit

extract_protocol: total RNA

tag: sample

value: Breast tumor


title: MEKi-121463-pretx


title: Brain_iAg_NaOH_rep4


title: MEKi-120161-pretx


title: MEKi-120202-posttx


title: MEKi-120651-posttx


title: SKOV3_cell_control_3


title: MEKi-121566-posttx


title: MEKi-120468-pretx


title: MEKi-120545-pretx


title: Brain_iAg_NaOH_rep3


title: KD2-2

city: Los Angeles

first: Ranjani

last: Lakshminarasimhan

state: California

address: 1441 Eastlake ave NOR7336

department: Urology

institute: University of Southern California

description:
10002121022_L
rep2

hyb_protocol: Standard

scan_protocol: Standard

data_processing: Quantile normalization and fold-change calculated using the lumi and limma packages in R

source_name: iEEC16 cells transfected with shARID1A

label_protocol: Standard labeling performed in SanfordBurnham, LaJolla,CA

extract_protocol: Total RNA was extracted with TRIZOL and cleaned up using DirectZOL (Zymo) kit according to manufacture's protocol.

value: iEEC16 cells

value: endometriosis

tag: arid1a status

value: knockdown


title: KD1-2

description:
8473515010_H
rep2


title: KD1-1

description:
8473515010_G
rep1


title: KD2-1

description:
10002121022_K
rep1


title: Brain_iAg_NaOH_rep2


title: Brain_iAg_NaOH_rep1


title: MEKi-130017-posttx


title: MEKi-120513-posttx


title: Brain_nAg_T3_rep3

source_name: Brain, nAg, T3

value: nAg (6 µg/L nominal Ag; Vive Nano, Toronto, ON) with vehicle


title: Brain_nAg_T3_rep4


title: SCR-1

description:
8473515010_E
rep1

source_name: iEEC16 cells transfected with shSCR

value: control


title: Brain_nAg_T3_rep6


title: Brain_nAg_T3_rep2


title: Brain_nAg_T3_rep1


title: Brain_nAg_NaOH_rep4

source_name: Brain, nAg, NaOH

value: nAg (6 µg/L nominal Ag; Vive Nano, Toronto, ON) prepared in 100 nM NaOH


title: Brain_nAg_NaOH_rep5


title: Brain_nAg_T3_rep5


title: Brain_nAg_NaOH_rep6


title: Brain_nAg_NaOH_rep3


title: Brain_nAg_NaOH_rep1


title: Brain_nAg_NaOH_rep2


title: Brain_T3_rep2

source_name: Brain, T3

value: vehicle


title: Brain_T3_rep5


title: Brain_T3_rep4


title: Brain_T3_rep6


title: Brain_NaOH_rep6

source_name: Brain, NaOH

value: 100 nM NaOH


title: Brain_T3_rep1


title: SCR-2

description:
8473515010_F
rep2


title: Denver_002

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on Xenopus Genome 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

organism: Xenopus laevis

source_name: preoptic area/hypothalamus/pituitary

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5)

extract_protocol: RNA extraction with Trizol followed by Qiagen total RNA extraction columns

value: 0.6% saline


title: Denver_004

value: recombinant X. laevis leptin (rxLeptin; 20 ng/g BW)


title: Denver_006


title: Denver_005


title: Brain_NaOH_rep4


title: Brain_T3_rep3


title: TCRabCD8ab.hr0.2

city: London

first: Lucie

last: Abeler-Dörner

address: Great Maze Pond

department: Immunobiology

country: United Kingdom

institute: King's College London

description:
replicate 2
4655469008_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R.

source_name: TCRαβ CD8αβ IEL, unstimulated

label_protocol: Standard Illumina biotin labelling protocol

growth_protocol:
Intestinal intraepithelial lymphocytes (IEL) were extracted from murine gut by DTT treatment and purified using a percoll gradient.
They were stimulated with plate-bound anti-CD3 (1 μg/ml) and a cytokine cocktail (IL-2,3,4,15) for 48 hours, then maintained on Il-2 alone for 14 days.

extract_protocol: RNA was extracted using a Qiagen RNA extraction kit. The RNA was amplified using an Ambion Illumina TotalPrep RNA Amplification Kit.

treatment_protocol: IEL were sorted into TCRαβ CD8αβ and TCRγδ CD8αα subsets and restimulated on plate-bound anti-CD3 (1 μg/ml) for 24 hours.

value: intestinal intraepithelial lymphocytes


title: TCRabCD8ab.hr24.2

description:
replicate 2
4655469008_F

source_name: TCRαβ CD8αβ IEL, anti-CD3, 24h


title: Denver_001


title: TCRcdCD8aa.hr24.2

description:
replicate 2
4655469009_B

source_name: TCRαα CD8αα IEL, anti-CD3, 24h


title: Denver_003


title: TCRcdCD8aa.hr0.1

description:
replicate 1
4655469008_C

source_name: TCRαα CD8αα IEL, unstimulated


title: TCRcdCD8aa.hr24.1

description:
replicate 1
4655469008_D


title: TCRcdCD8aa.hr0.2

description:
replicate 2
4655469009_A


title: TCRabCD8ab.hr0.1

description:
replicate 1
4655469008_A


title: Brain_NaOH_rep2


title: Brain_NaOH_rep5


title: Liver_iAg_T3_rep6

source_name: Liver, iAg, T3

value: liver


title: Brain_NaOH_rep1

value: brain


title: Brain_NaOH_rep3


title: Liver_iAg_T3_rep5

value: iAg (6 µg/L nominal Ag; AgNO3, Fisher Scientific) with vehicle


title: Liver_iAg_T3_rep4


title: Liver_iAg_T3_rep2


title: Liver_iAg_T3_rep3


title: Liver_iAg_T3_rep1


title: SKOV3_tumor_control_3

source_name: Control SKOV3 primary tumor

value: primary tumor; intraperitoneal xenograft model

value: Control

value: SCID mice


title: Liver_iAg_NaOH_rep6

source_name: Liver, iAg, NaOH

value: iAg (6 µg/L nominal Ag; AgNO3, Fisher Scientific) prepared in 100 nM NaOH


title: Liver_iAg_NaOH_rep5


title: Liver_iAg_NaOH_rep4


title: Liver_iAg_NaOH_rep3


title: hCTB (4') cultured 3h

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

state: CA

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

description: Sample processing and hybridization was performed by the UCSF Gladstone Institute (Winn et al., 2007)

hyb_protocol: Labeled cRNA was purified with an RNeasy column (QIAGEN). Quality was evaluated by using the Agilent Bioanalyzer 2100 system. cRNA was fragmented at 94 C for 35 min.

scan_protocol: Hybridized with 15ug of cRNA and then washed, stained, and imaged at the Gladstone Genomics Core Facility by using standard Affymetrix protocols.

data_processing: Affymetrix CEL files were processed using the Affymetrix Expression Console and Transcriptome Analysis Console (TAC) software packages. Raw values were normalized via the Robust Multi-array Average (RMA) algorithm.

molecule: polyA RNA

source_name: primary villous cytotrophoblast (2nd trimester)

label_protocol: Hybridization and labeling was accomplished by using the protocol devised by the UCSF Gladstone Genomics Core Facility. Double-stranded cDNAs were generated from total RNA samples by using SuperScript II reverse transcriptase (Invitrogen) and a T7-oligo primer (QIAGEN). Biotin-labeled cRNA was synthesized by in vitro transcription using an Enzo Bioassay RNA labeling kit (Enzo Diagnostics,

growth_protocol: As described with minor modifications (Hunkapiller and Fisher, 2008), cytotrophoblasts (CTBs) were isolated from 2nd trimester human placentas (GW14-21 wks). CTBs were cultured at a density of 500,000 CTBs/well in 1.5 ml medium containing DME/H-21, 2% Nutridoma (Roche), 1% sodium pyruvate (Sigma), 1% Hepes buffer (Invitrogen), 1% glutamate plus (Atlanta Biologicals), and 1% penicillin/streptomycin (Invitrogen) on Matrigel substrate.

extract_protocol: Immediately following CTB isolation (0 h) or after 3, 15, or 39 h in culture, RTL Lysis Buffer (Qiagen) was added to either the cell pellet or culture dish well. The lysate was collected and stored at -80oC. We isolated and purified RNA using the RNeasy Micro Kit (Qiagen). The RNA concentration and quality were estimated (Absorbance 260nm/280nm = 1.9 - 2.1) by using a Nanodrop spectrometer (Thermo Scientific) and the Agilent RNA 6000 Nano LabChip Kit and Bioanalyzer 2100 system (RIN > 9).

treatment_protocol: Cells were incubated at 37oC in 5% CO2/ 95% air.

value: villous cytotrophoblast

tag: gestational age

value: 20+21wk (pooled)

tag: culture time


title: hCTB (4) cultured 0h


title: hCTB (4) cultured 39h


title: Liver_iAg_NaOH_rep2


title: hCTB (4) cultured 15h


title: hCTB (3) cultured 15h


title: hCTB (3) cultured 39h


title: hCTB (3) cultured 3h


title: TCRabCD8ab.hr24.1

description:
replicate 1
4655469008_B


title: hCTB (2) cultured 39h

value: 19+14wk (pooled)


title: hCTB (2) cultured 3h


title: Liver_iAg_NaOH_rep1


title: hCTB (3) cultured 0h


title: hCTB (1) cultured 39h


title: hCTB (2) cultured 0h


title: hCTB (1) cultured 15h


title: hCTB (2) cultured 15h


title: V583 tyrosine (test) compared to V583 (reference) Replicate 3

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

description:
Technical replicate 1 of 1.
V583 tyr vs. V583. rep3

hyb_protocol: Three hundred ng of DyLight 550- and three hundred ng of DyLight 650-labelled cDNA were mixed and hybridized for 17 h at 60°C in the E. faecalis V583 DNA microarray using the In situ Hybridization Kit Plus, the Hybridization Gasket Slide and the Agilent G2534A Microarray Hybridization Chamber (Agilent Technologies). Slides were washed using the washing buffers indicated by the manufacturer.

scan_protocol: Microarrays were scanned using a GenePix 4200A Microarray Scanner (Molecular Devices, Sunnyvale, CA)

data_processing: Slide images were analyzed using GenePix Pro v.6.0 software. Background subtraction and LOWESS (locally weighted scatterplot smoothing) normalization were done using the standard routines provided by GENOME2D software available at http://server.molgenrug.nl/index.php/analysis-pipeline.

label: DyLigth 550

organism: Enterococcus faecalis

source_name: V583 with 15 mM tyrosine

label_protocol: Total cDNA was synthesized from 20 µg of RNA using the SuperScript® III Reverse Transcriptase kit (Life Technologies, Bleiswijk, Netherlands). The cDNA was purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nager, Landsmeer, The Netherlands) following the manufacturer instructions. Twenty µg of the purified cDNA was immediately labeled with DyLight 550 or DyLight 650 using the DyLight® Amine-Reactive Dyes kit (Thermo Scientific) as the manufacturer indicated. Quality and quantity of cDNA and DyLight 550 and DyLight 650 labelling were checked on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

growth_protocol: E. faecalis V583 cultures were grown in 30 mL of M17 culture medium (Oxoid, UK) supplemented with 0.5% glucose (w/v) (GM17) and 5 mM agmatine (Sigma-Aldrich, Barcelona, Spain) and in presence or abscense of 15 mM tyrosine (Sigma-Aldrich) for 7 h at 37°C without aereation. After a centrifugation at 16,000 x g for 1 min at 4˚C, the supernatants were discarded and cell pellets were frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Cell pellets were resuspended in 400 µl of TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) and 50 µl of 10% SDS, 500 µl of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich), 500 mg of glass beads (75–150 µm) (Sigma-Aldrich), and 175 µl of Macaloid suspension (Bentone MA, Rheox Inc., Scotland, United Kingdom) were added. Cells were mechanically disrupted in a bead beater at 4˚C with two cycles of 60 s. During the shaking intervals the cells were kept on ice for 1 min. The samples were then centrifuged at 16,000 x g for 1 min at 4˚C. The upper phase was transferred to fresh tubes containing 500 µl chloroform: isoamyl alcohol (24:1) and centrifuged for 5 min at 4˚C. Total RNA was isolated with the High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany) following the instructions provided by the manufacturer. The concentration and quality of the RNA was determined on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

treatment_protocol: Presence or absence of 15 mM tyrosine in the culture medium

tag: cultured with

value: 15 mM tyrosine

label: DyLigth 650

source_name: V583 without 15 mM tyrosine

value: none (no tryrosine)


title: hCTB (1) cultured 0h


title: Liver_nAg_T3_rep5

source_name: Liver, nAg, T3

value: nAg (6 µg/L nominal Ag; Vive Nano, Toronto, ON) with vehicle


title: Liver_nAg_T3_rep4


title: Liver_nAg_T3_rep3


title: Liver_nAg_T3_rep1


title: Liver_nAg_T3_rep6


title: V583 tyrosine (test) compared to V583 (reference) Replicate 2

description:
Biological replicate 2 of 2.
V583 tyr vs. V583. rep2

tag: strain


title: Liver_nAg_T3_rep2


title: V583 tyrosine (test) compared to V583 (reference) Replicate 1

description:
Biological replicate 1 of 2.
V583 tyr vs. V583. rep1


title: KO_untreat_biological rep2

city: Uchinada

first: Chieko

last: Hashizume

address: 1-1 Daigaku

department: Medicine

institute: Kanazawa Medical University

description:
KO-UN2
Gene expression data from SMS2 KO mouse colon epithelial cells.

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Clariom™ S Mouse Array by GeneChip® Hybridization Oven 645 according to the protocols recommended by the manufacturer (Affymetrix, Inc).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix, Inc).

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software (Affymetrix, Inc).

label: DLR (Biotin-11-dXTP Analog)

source_name: Mouse colon epithelial cells, KO, untreated

label_protocol: DLR-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip® WT PLUS Reagent Kit (Affymetrix), according to manufacturer's instructions.

growth_protocol: Mice were fed ad libitum.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: 3.5% DSS in drinking water during 2 days.

tag: strain/background

value: SMS2 KO

value: Colon epithelial cells


title: KO_DSS_biological rep2

description:
KO-DSS2
Gene expression data from SMS2 KO mouse colon epithelial cells after 2-days DSS treatment.

source_name: Mouse colon epithelial cells, KO, DSS treatment for 2 days

value: 3.5% DSS in drinking water during 2 days


title: Liver_nAg_NaOH_rep6

source_name: Liver, nAg, NaOH

value: nAg (6 µg/L nominal Ag; Vive Nano, Toronto, ON) prepared in 100 nM NaOH


title: hCTB (1) cultured 3h


title: HONE1 Negative control, biological rep 1

city: Hong Kong

first: Wei

last: Gao

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

description: HONE1 was established from a poorly differentiated nasopharyngeal carcinoma

hyb_protocol: Following fragmentation, RNA were hybridized for 16 hr at 45 °C on Human Genome U133 Plus 2.0 with a rotation speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HONE1 transfected with negative control siRNA

label_protocol: Biotinylated RNA was prepared according to the standard Affymetrix protocol from 200 ng total RNA using GeneChip® 3’ IVT Express Kit.

growth_protocol: NPC cell line HONE1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 200 Unit/ml penicillin G sodium, 200 μg/ml streptomycin sulfate, and 0.5 μg/ml amphotericin B. Cells were incubated at 37°C in a humidified incubator with 5% CO2.

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

treatment_protocol: Cells were transfected with ebv-miR-BART7 mimic or negative control siRNA by Hiperfect transfection reagent. Cell irradiation was carried out by Gammacell® 3000 Elan system.

value: Nasopharyngeal carcinoma cell line

tag: transfection

value: negative control siRNA


title: Liver_nAg_NaOH_rep5

value: liver


title: Liver_nAg_NaOH_rep4


title: HONE1 Negative control, biological rep 2

tag: cell type


title: HONE1 ebv-miR-BART7, biological rep 2

source_name: HONE1 transfected with ebv-miR-BART7 mimic

value: ebv-miR-BART7 mimic


title: HONE1 ebv-miR-BART7, biological rep 1


title: sh_ZNF521_3

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from THP-1 cells treated with short harpin vector to silecing ZNF521

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng of Total RNA.

growth_protocol: No growth protocol

extract_protocol: RNA was isolated from THP-1 cultured cells treated with an shScram or shZNF521 using Trizol in 3 independent experiments after sorting of GFP-postive transduced cells

treatment_protocol: No treatment protocol

value: MLL-AF9-rearranged acute myeloid leukemia cell line

tag: transfected with

value: Lentiviral shRNA vector against ZNF521 (shZNF521)


title: KO_DSS_biological rep1

description:
KO-DSS1
Gene expression data from SMS2 KO mouse colon epithelial cells after 2-days DSS treatment.


title: WT_untreat_biological rep1

description:
WT-UN1
Gene expression data from WT mouse colon epithelial cells.

source_name: Mouse colon epithelial cells, WT, untreated

value: wild-type


title: Liver_nAg_NaOH_rep3

tag: tissue


title: Liver_nAg_NaOH_rep2


title: sh_ZNF521_2

tag: cell line


title: KO_untreat_biological rep1

description:
KO-UN1
Gene expression data from SMS2 KO mouse colon epithelial cells.

tag: genotype/variation


title: shScram_3

description: Gene expression data from THP-1 cells treated with scramble vector

value: control scrambled shRNA (shScram)


title: Liver_nAg_NaOH_rep1


title: WT_DSS_biological rep2

description:
WT-DSS2
Gene expression data from WT mouse colon epithelial cells after 2-days DSS treatment.

source_name: Mouse colon epithelial cells, WT, DSS treatment for 2 days


title: WT_untreat_biological rep2

description:
WT-UN2
Gene expression data from WT mouse colon epithelial cells.


title: Liver_T3_rep5

source_name: Liver, T3

value: vehicle


title: Liver_T3_rep6


title: Liver_T3_rep4


title: shScram_2


title: WT_DSS_biological rep1

description:
WT-DSS1
Gene expression data from WT mouse colon epithelial cells after 2-days DSS treatment.


title: Liver_T3_rep3


title: sh_ZNF521_1


title: Liver_T3_rep2


title: WT mature green (MG)

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

description: WT-MG

hyb_protocol: performed by Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

organism: Solanum lycopersicum

source_name: pericarp_WT mature green fruits

growth_protocol: Seeds were surface-sterilized for 1 min in 70% ethanol and then in sterilisation solution (20% sodium hypochlorite) for 20 min. After sterilization, the seeds were sown on half-strength MS medium (Murashige and Skoog, 1962), supplemented with 1% (w/v) sucrose and solidified with 0.7% (w/v) phytoagar and appropriate antibiotics. After imbibition, the seeds were stratified at 4°C for 3 days. The seeds were germinated at 22°C under a 16-h day (140 µmol m-2 s-1) / 8-h night regime. The two-week-old Arabidopsis seedlings were carefully transplanted into the soil and grown under long day growth conditions in the green house. Fruits at the indicated developmental stages were harvested for transcriptome analysis.

extract_protocol: Trizol RNA extraction method (Ambion)

tag: variety

value: v. money maker

value: WT

tag: fruit stage

value: mature green

value: pericarp


title: Liver_T3_rep1

tag: treatment


title: AtJUB1-OX mature green (MG)

description: OX-MG

scan_protocol: performed by Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

source_name: pericarp_AtJUB1-OX mature green fruits


title: WT breaker+7 (B+7)

source_name: pericarp_WT Breaker+7 fruits

label_protocol: performed by Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

value: Breaker+7 days


title: AtJUB1-OX breaker+7 (B+7)

source_name: pericarp_AtJUB1-OX Breaker+7 fruits


title: Liver_NaOH_rep5

source_name: Liver, NaOH

value: 100 nM NaOH


title: Liver_NaOH_rep6


title: shScram_1


title: Liver_NaOH_rep2


title: Liver_NaOH_rep3


title: Liver_NaOH_rep4


title: Liver_NaOH_rep1


title: H3K79me2 IP from MEF

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Department of Regenerative Biology

institute: University of Wisconsin

description: MEFs

hyb_protocol: Hybridization was performed according to manufacurer's protocol

scan_protocol: Scanning was performed according to manufacturer's protocol

data_processing: Data analysis was performed according to Agilent Chip analytics software

source_name: IP  DNA

label_protocol: Labeling was performed according to manufacturer's protocol

growth_protocol: MEFs were cultured in standard mouse embryonic fibroblast media. iPSCs and pre-iPSCs were cultured in FBS containing mouse embryonic stem cell media on a  feeder layer of irradiated MEFs. iPSCs and pre-iPSCs were derived from MEFs by the viral transduction of Oct4, Sox2, c-Myc and Klf4

extract_protocol: Formaldehyde crosslinked genomic DNA was immunoprecipitated with antibody as indicated and purified for IP DNA, or directly processed for input DNA.

value: MEFs

source_name: input DNA


title: H3K79me2 IP from pre-iPSC

description: 1A2 cell line

value: pre-iPSCs derived from MEFs


title: H3K79me2 IP from iPSC

description: 2D4 cell line

value: iPSC derived from MEFs


title: Glycerol + vs glycerol -, sample B

city: Grenoble

first: Valeria

last: Villanova

address: 14 avenue Albert 1er de Belgique

department: LPCV

country: France

institute: CEA

description: B - Biological replicate 2 of 3, dye swap of A

hyb_protocol: For each hybridization, 300 ng of cRNA from reference cells was mixed with 300 ng of cRNA from the glycerol-treated cells. Three biologically independent experiments were performed for each condition. The cRNA mixture was fragmented and hybridized on 8x60K P. tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) following the Agilent protocol.

scan_protocol: The microarray sides were scanned twice at 2 µm resolution on an Agilent laser scanner (G2505 CA). The resulting images were processed using Agilent Feature Extraction software v11.5.

data_processing: Microarray normalization was performed by global lowess using Goulphar (Lemoine et al, 2006). For each gene, the Cy5/Cy3 ratios corresponding to the different probes were averaged.

organism: Phaeodactylum tricornutum

source_name: cell culture

label_protocol: 200 ng of total RNA was reverse transcribed, amplified and labelled with Cy3-CTP or Cy5-CTP using the Low Input Quick Amp Labelling Kit, Two-Color (Agilent, 5190-2306).

growth_protocol: Phaeodactylum tricornutum (Pt1, CCAP 1055/3) was grown in a chamber at 20°C, 60 µE m-2 s-1 irradiance with a 12-h-light / 12-h-dark photoperiod and shaking at 100 rpm in artificial seawater ESAW (Abida et al., 2015).

extract_protocol: 108 total cells were centrifugated, washed with PBS and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol following manufacturer's instructions, with a further purification by ammonium acetate precipitation as described in Huysman et al., 2013. The recovered RNA was processed with the RNA cleanup protocol of the RNeasy Mini Kit (Qiagen, 74106) performing the in-column DNAse treatment. The eluted RNA was then quantified using a spectrophotometer and its integrity checked on 2% agar gel.

treatment_protocol: 0,5*106 cells/ml of Phaeodactylum were grown for 5 days in presence (glycerol-treated cells) and absence of glycerol (reference cells).

tag: nutrient

value: normal conditions

tag: time

value: 5 days

value: glycerol-treated


title: Glycerol + vs glycerol -, sample C

description: C - Biological replicate 3 of 3


title: Glycerol + vs glycerol -, sample A

description: A - Biological replicate 1 of 3


title: H3K9ac IP from iPSC

description: 2D4 cell line


title: H3K18ac IP from MEF

description: MEFs


title: Tumor_11378 (expr)

status: Public on Mar 30 2017

city: Gothenburg

first: Toshima

last: Parris

address: Medicinaregatan 1G, 6th floor

institute: University of Gothenburg

data_processing: The data were normalized using quantile normalization with BASE

source_name: Human breast tumor

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: breast tumor

tag: 8p11-p12 amplification

value: Amplified

tag: age

tag: pt status

tag: lymph node status

tag: er status

value: neg

tag: pgr status

tag: her2 status

value: pos


title: Tumor_11659 (expr)


title: Tumor_11821 (expr)


title: Tumor_11315 (expr)


title: Tumor_11633 (expr)


title: H3K18ac IP from pre-iPSC

description: 1A2 cell line

tag: cell type


title: Tumor_11372 (expr)


title: Tumor_10415 (expr)


title: H3K9ac IP from pre-iPSC

description: 1A2 cell line


title: Tumor_10408 (expr)


title: Tumor_10823 (expr)


title: Tumor_11314 (expr)


title: Tumor_11248 (expr)


title: H3K14ac IP from MEF

description: MEFs


title: H3K18ac IP from iPSC

description: 2D4 cell line


title: H3K9me3 IP from pre-iPSC

description: 1A2 cell line


title: Tumor_10400 (expr)


title: Tumor_10133 (expr)


title: Tumor_9534 (expr)

value: Gain


title: Tumor_11271 (expr)


title: H3K9me2 IP from pre-iPSC

description: 1A2 cell line


title: H3K9me2 IP from MEF

description: MEFs


title: Tumor_9632 (expr)

value: Loss


title: Tumor_10068 (expr)


title: H3K9ac IP from MEF

description: MEFs


title: H3K9me3 IP from MEF

description: MEFs


title: H3K14ac IP from iPSC

description: 2D4 cell line


title: H3K14ac IP from pre-iPSC

description: 1A2 cell line


title: Tumor_8652 (expr)


title: Tumor_8931 (expr)


title: Tumor_9494 (expr)


title: Tumor_9000 (expr)


title: H3K9me2 IP from iPSC

description: 2D4 cell line


title: Tumor_8842 (expr)


title: Tumor_8901 (expr)


title: Tumor_8800 (expr)


title: Tumor_8860 (expr)


title: Tumor_9533 (expr)


title: H3K9me3 IP from iPSC

description: 2D4 cell line


title: Tumor_8472 (expr)


title: Tumor_8629 (expr)


title: Tumor_8903 (expr)


title: Tumor_8360 (expr)


title: Tumor_8010 (expr)


title: Tumor_8341 (expr)


title: Tumor_8114 (expr)


title: Tumor_8827 (expr)


title: Tumor_8138 (expr)


title: Tumor_8083 (expr)


title: Tumor_8007 (expr)


title: Tumor_6915 (expr)


title: Tumor_7325 (expr)


title: Tumor_7807 (expr)


title: Tumor_7960 (expr)


title: Tumor_7682 (expr)


title: Tumor_7631 (expr)


title: Tumor_7105 (expr)


title: Tumor_6522 (expr)


title: Tumor_7253 (expr)


title: Tumor_6039 (expr)


title: Tumor_5582 (expr)


title: Tumor_6521 (expr)


title: 319-SH

city: Guangzhou

first: Nu

last: Zhang

state: Guangdong

address: NO.58, The Second Zhongshan Road，Yuexiu District

department: Neurosurgery

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: Gene expression data from human glioma cell LN-319 stable expression with sh-Circ-SHPRH

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: human glioma cells LN-319 stable expression with sh-Circ-SHPRH

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion)

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum , 10 U/ml penicillin-streptomycin  and incubated at 37℃ in a humid incubator containing 5% CO2.

extract_protocol: Cells were washed with PBS and extract with trizol.

treatment_protocol: Cells were infected with GFP expression lenti-virus or sh-Circ-SHPRH lentivirus for 48h and selected with puromycine for 72h.

value: glioma cells


title: IMR-90 ER:Ras_OIS

city: Chuo-ku, Kumamoto

first: Mitsuyoshi

last: Nakao

state: Kumamoto

address: 2-2-1 Honjo

department: Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics

institute: Kumamoto university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Expression Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: IMR-90 ER:Ras cells, 4-OHT treatment, 6 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: IMR-90 ER:Ras cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% (v/v) heat-inactivated fetal bovine serum.

extract_protocol: Total cellular RNA was isolated from cells with RNeasy kit (Qiagen).

treatment_protocol: To induce OIS, IMR-90 ER:Ras cells were treated with 100 nM 4-OHT for 6 days. RS cells were prepared by repeated passage for 10 weeks.

value: IMR90 ER:Ras

value: 4-OHT for 6 days


title: IMR-90 ER:Ras_RS

source_name: IMR-90 ER:Ras cells, repeated passage, 10 weeks

value: repeated passage for 10 weeks


title: Tumor_4302 (expr)

department: Department of Oncology


title: Tumor_4296 (expr)


title: 251-GFP

description: Gene expression data from human glioma cell U215 stable expression with GFP

source_name: human glioma cells U251 stable expression with GFP


title: IMR-90_Ctrl siRNA_24 h

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Expression Array.

source_name: IMR-90 cells, Ctrl siRNA, 24 h

growth_protocol: IMR-90 cells were cultured in Dulbecco's modified Eagle's medium F12 supplemented with 10% (v/v) heat-inactivated fetal bovine serum.

treatment_protocol: Specific siRNAs were introduced to the cells using RNAiMAX reagent (Invitrogen) for 24 h.

tag: sirna


title: IMR-90_SETD8-2 siRNA_24 h

source_name: IMR-90 cells, SETD8-2 siRNA, 24 h


title: IMR-90 ER:Ras_Growing

source_name: IMR-90 ER:Ras cells, no treatment


title: IMR-90_SETD8-1 siRNA_24 h

source_name: IMR-90 cells, SETD8-1 siRNA, 24 h


title: 251-SH

description: Gene expression data from human glioma cell U251 stable expression with sh-Circ-SHPRH

source_name: human glioma cells U251 stable expression with sh-Circ-SHPRH


title: 319-GFP

description: Gene expression data from human glioma cell LN-319 stable expression with GFP

source_name: human glioma cells LN-319 stable expression with GFP


title: Tumor_6846 (expr)

tag: tissue


title: Tumor_8828 (expr)


title: GCs_advanced age_patient 2

city: Wuhan

first: Jing

last: Cheng

state: Hubei

address: Jiefang Avenue 1095

department: Obstetrics and Gynecology

institute: Tongji Hospital

description:
tissue: ovary; gender: female; sample type: ovarian granulosa cells from a 43-year-old woman; clinical pregnancy outcomes: failed
circular RNA

hyb_protocol: Each labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar) according to the Arraystar’s standard protocols. Briefly, 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed and fixed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package.   After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: ovarian granulosa cells from women with age ≥ 38 years old

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The sample preparation and microarray hybridization were performed according to the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

value: ovary


title: GCs_advanced age_patient 3

description:
tissue: ovary; gender: female; sample type: ovarian granulosa cells from a 41-year-old woman; clinical pregnancy outcomes: failed
circular RNA


title: GCs_young age_patient 3

description:
tissue: ovary; gender: female; sample type: ovarian granulosa cells from a 23-year-old woman; clinical pregnancy outcomes: success
circular RNA

source_name: ovarian granulosa cells from women with age ≤ 30 years old


title: GCs_young age_patient 2

description:
tissue: ovary; gender: female; sample type: ovarian granulosa cells from a 24-year-old woman; clinical pregnancy outcomes: success
circular RNA


title: GCs_advanced age_patient 1

description:
tissue: ovary; gender: female; sample type: ovarian granulosa cells from a 40-year-old woman; clinical pregnancy outcomes: failed
circular RNA


title: GCs_young age_patient 1

value: ovarian granulosa cells from a 24-year-old woman


title: Ppara KO mouse #5

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

description: Transcriptomic liver of Ppara kO mouse

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC)

data_processing: RMA and Quantile Normalization  with median polish using Partek. The data obtained are log2-transformed

source_name: C57Bl/6 adult mouse

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a relative humidity of 36%–80%, and 12-hour light/12-hour dark cycles. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol: RNA was extracted using Trizol and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies)

value: liver

tag: background strain

tag: gender

value: female

tag: developmental stage

value: adult - 12-14 weeks

tag: genotype

value: Ppara KO


title: Ppara KO mouse #3

description: Transcriptomic liver of Ppara kO mouse


title: Ppara KO mouse #6

description: Transcriptomic liver of Ppara kO mouse


title: Ppara KO mouse #2

description: Transcriptomic liver of Ppara kO mouse


title: WT mouse #5

description: Transcriptomic liver of WT mouse

value: WT


title: WT mouse #2

description: Transcriptomic liver of WT mouse


title: Ppara KO mouse #4

description: Transcriptomic liver of Ppara kO mouse


title: Ppara KO mouse #1

description: Transcriptomic liver of Ppara kO mouse


title: WT mouse #6

description: Transcriptomic liver of WT mouse


title: WT mouse #4

description: Transcriptomic liver of WT mouse


title: MPH GW4064 #3

description: Transcriptomic MPH

data_processing: RMA and Quantile Normalization with median polish using Partek. The data obtained are log2-transformed.

source_name: C57Bl6 adult male mouse

treatment_protocol: Mouse primary hepatocytes were prepared as described in (Bantubungi et al.  2014). Hepatocytes were grown in serum free William's medium and treated for 4h with GW4064 (2µM) or DSMO.

value: primary hepatocytes

value: adult

tag: Sex

value: male

tag: strain

value: wild type


title: WT mouse #3

description: Transcriptomic liver of WT mouse


title: MPH GW4064 #1

description: Transcriptomic MPH


title: WT mouse #1

description: Transcriptomic liver of WT mouse


title: MPH DMSO #1

description: Transcriptomic MPH


title: DF PN2-DF E17

city: Beijing

first: Ping

last: Dang

address: Anxiang bei li

institute: 306 hospital

description: whole embryo

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: mouse dental follicle tissues at E17 and PN2

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. L

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

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

value: DF PN3

source_name: mouse dental follicle and papilla tissues at E17

value: DF E17


title: MPH DMSO #2

description: Transcriptomic MPH


title: DF E17-P E17

description: whole embryo

source_name: P E17

value: P E17


title: Treated [gene-level]

city: Memphis

first: Marcy

middle: Cain

last: Purnell

state: TN

address: 4055 N. Park Loop

department: Loewenberg College of Nursing

institute: University of Memphis

hyb_protocol: Samples were hybridized together on the probe array controls onto the Human Genome U133 Plus 20 Gene Chip Array (Affymetrix)

scan_protocol: Array was washed and stained using Affymetrix fluidics station 450, scanned on Affymetrix GCS3000 7G scanner

data_processing: The data were normalized by Robust Multichip Averaging (RMA) using Affymetrix expression console in order to transform all arrays to a common distribution of intensities by removing technical variations from noisy data before analysis to quantile normalize 2 or more distributions to each other, both treated and control groups were set to the average (arithmetial mean) of both distributions, therefore the highest value in all cases becomes the mean of the highest values etc., data were then analyzed with Qiagen's Ingenuity Pathway Analyses.

source_name: Human breast carcinoma

label_protocol: Samples were fragmented and labeled with Affymetrix WT terminal labeling kit

growth_protocol: 10,000 Cells were plated in triplicate in 6-well plates. The cells were grown for 24 hours in standard growth media (DMEM with 10% FBS).  Then the treated media was made by diluting a 10X DMEM with 9 parts of a hypotonic saline solution that was exposed to the dc DEP EMF from the BEFE unit for 30 minutes and 1 part 10X DMEM.  The control media was made by diluting the 10X media with a hypotonic saline solution that was not exposed to the dc DEP EMF from the BEFE unit.  The cells were grown in the treated/control media for 3 days and then analyzed with the Affymetrix 2.0 Human Genome Microarray. We looked at the changes in gene expression between the treated and control groups.

extract_protocol: Rneasy Mini-kit was used for RNA extraction; Qiagen; RNA integrity was tested with Agilent 2100 Bioanalyzer and a RIN number of 10 for all 5 biological replicates of both the treated and control groups were found. cDNA was made using the Ambion WT amplification kit.

tag: cell line


title: Control [gene-level]


title: MPH GW4064 #2

description: Transcriptomic MPH


title: P PN2-P E17

description: whole embryo

source_name: mouse dental papilla tissues at E17 and PN2

value: P PN2


title: MPH DMSO #3

description: Transcriptomic MPH


title: DF PN2-P PN2

description: whole embryo

source_name: mouse dental follicle and papilla tissues at PN2

value: DF PN2


title: migratory LC_medium 344 23

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

institute: University of Southampton

hyb_protocol: Affymetrix Gene Atlas standard protocol, 200 ng RNA

scan_protocol: Affymetrix Gene Atlas

data_processing: Bioconductor, RMA normalisation

growth_protocol: 48h ex vivo culture of human epidermal biposies

extract_protocol: microRNeasy, Qiagen, UK

treatment_protocol: LC migrated during incubation

tag: treatment

value: control


title: migratory LC_inhibitor 344 PI3KR 24

label_protocol: Affymetrix Gene Atlas standard protocol, 200 ng RNA

value: inhibitor


title: migratory LC_medium 345 25


title: flag leaves UD-2_greenhouse care_rep2

city: Lincoln

first: Pamela

middle: A.

last: Pena

state: NE

address: 1901 Vine St

department: Agronomy

institute: University of Nebraska-Lincoln

description:
gene expression from CB037 carrying ZmDof1 pPTN1034-NN569-3-5-1 (UD-2) flag leaves, greenhouse conditions, at anthesis
UD-2_rep2

hyb_protocol: After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, according to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChip image acquisition and data processing was obtained using Affymetrix GCS 3000 7G scanner; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using R  3.1.1 with Bioconductor 2.4. Arrays were normalised via RMA and transgenic event pPTN1034-NN569-3-5-1 (UD-2) was compared to the control CB037 (WT) via the limma package.  Storey and Tibshirani adjusted p-values were used as significance measurement.

organism: Triticum aestivum

source_name: flag leaves UD-2_greenhouse care

label_protocol: Biotinylated cRNA were prepared following the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CB037 and transgenic pPTN1034-NN569-3-5-1 (UD-2) plants were grown side by side under greenhouse conditions (10/14 h photoperiod and day/night temperatures of 29°C/24°C ) until anthesis in pots with normal watering and fertilizer conditions.

extract_protocol: Total RNA was isolated from flag leaves using TRIzol ® reagent (Invitrogen cat. # 10296-028) following the manufacturer’s protocol.

tag: genotype/variation

value: flag leaves pooled from three plants (UD-2-4, UD-2-5, UD-2-6)

tag: Stage

value: Anthesis


title: flag leaves UD-2_greenhouse care_rep1

description:
gene expression from CB037 carrying ZmDof1 pPTN1034-NN569-3-5-1 (UD-2) flag leaves, greenhouse conditions, at anthesis
UD-2_rep1

value: flag leaves pooled from three plants (UD-2-1, UD-2-2, UD-2-3)


title: migratory LC_inhibitor 345 PI3KR 26


title: brainstem ppi untested C57BL10/J biological replicate 2

city: Toronto

first: James

middle: Nicholas

last: Samsom

state: Ontario

address: 544, 155 Dalhousie Street

department: Pharmacology

institute: University of Toronto

description: pooled tissue from 3 mice

hyb_protocol: as per the User Manual: GenChip 3' IVT Express kit: EukGE-WS2v4 of Toronto Centre for Applied Genomics standard hybridization protocol

scan_protocol: as per the User Manual: GenChip 3' IVT Express kit: using Affymetrix Genechip Scanner 3000 as per standard protocol used by Toronto Centre for Applied Genomics

data_processing: The raw array data was investigated for distributional and spatial homogeneity. No artifacts or outliers were detected. The data were loaded into R (v2.6.1) using the affy package (v1.16.0) of the BioConductor open-source project, and pre-processed using the GCRMA variant of the RMA algorithm implemented in the gcrma package (v2.10.0) of BioConductor. Transcriptome-wide correlation analysis between PPI and mRNA relied on Spearman’s rho and linear modelling analysis, simultaneously fitting 18 arrays per tissue to the model: y=b+(m)x(PPI), where y is GCRMA pre-processed signal intensity, b the expression level, PPI  levels for a given strain, and m is the slope. Probesets were annotated using Affymetrix NetAffx (v27)21 and FDR-adjusted p-value (q-value)(Storey and Tibshirani, 2003) using the limma software package (v.2.12.0) and followed by a Bayesian moderation of standard error (Smyth, 2004); correlations and q-values were calculated and candidate genes selected on the combined q-values from the three brain regions: -log|q(Hippocampus) x q(Striatum) x q(Brainstem)|.

source_name: brainstem, untested

label_protocol: as per the User Manual: GenChip 3' IVT Express kit: Enzo IVT kit as per Toronto Centre for Applied Genomics standard labeling protocol

growth_protocol: Six mouse strains were used: C3H/HeJ; BALB/cJ; C57BLKS/J; C57BL/6J and C57L/J (JAX, Bar Harbor, ME, USA) spanning the range of PPI.19 PND40 mice were housed 6 per cage with a 12 hr light/dark cycle (0700-1900h), at 21±1°C , 50-60% humidity, food and water ad libitum.

extract_protocol: Mice were sacrificed on PND60. RNA was prepared as previously described dissected and snap frozen (-80°C) whole striatum, hippocampus, and brainstem using TRIzol® reagent. RNA quality was determined using the Agilent BioAnalyzer with no RIN <7.7, prepared for hyrbidization and hybridized and scanned at The Centre for Applied Genomics (TCAG) at SickKids, Toronto, Ontario, Canada.

treatment_protocol: PPI testing used 120dB (40ms) startle, prepulses of 75 or 80dB (20ms), 65dB background, prepulse-startle latency of 100ms, and inter-trial-time 15-30s. Scores were averaged across three sessions, PPI calculated as [(PA–PP)/(PA)] × 100, and the mean of 75dB and 80dB trials was used. 6 of 12 mice were tested per strain every other day for 5d at PND50.

value: brainstem


title: brainstem ppi tested C57BLKS/J biological replicate 1

description: pooled tissue from 3 mice

source_name: brainstem, tested


title: brainstem ppi tested C57L/J biological replicate 1

description: pooled tissue from 3 mice


title: brainstem ppi untested C57L/J biological replicate 2

description: pooled tissue from 3 mice


title: brainstem ppi untested C57BLKS/J biological replicate 2

description: pooled tissue from 3 mice


title: brainstem ppi tested C57BL6/J biological replicate 1

description: pooled tissue from 3 mice


title: flag leaves wildtype_greenhouse care_rep2

description:
gene expression from Triticum aestivum CB037 flag leaves, greenhouse conditions, at anthesis
WT_rep2

source_name: flag leaves wildtype_greenhouse care

value: flag leaves pooled from three plants (WT-4, WT-5, WT-6)


title: flag leaves wildtype_greenhouse care_rep1

description:
gene expression from Triticum aestivum CB037 flag leaves, greenhouse conditions, at anthesis
WT_rep1

value: flag leaves pooled from three plants (WT-1, WT-2, WT-3)


title: brainstem ppi untested C57BL6/J biological replicate 1

description: pooled tissue from 3 mice


title: brainstem ppi untested C57L/J biological replicate 1

description: pooled tissue from 3 mice


title: CRC organoid 7 knock-in KRT20-EGFP Low_1

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

institute: Keio University

hyb_protocol: standard Affymetrix procedures

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: The data was analyzed with RMA for normalization (R package affy v.1.48.0). The pre-processed data was median-centered.

source_name: CRC organoid 7 knock-in KRT20-EGFP Low

label_protocol: standard Affymetrix procedures

extract_protocol: Total RNA was extracted using Rneasy Plus Mini Kit according to the manufacturer's instructions.

tag: source subject id

value: Patient 19

value: Large intestine

value: KRT20-GFP knock-in colorectal tumor organoids


title: CRC organoid 12 knock-in KRT20-EGFP Low_1

source_name: CRC organoid 12 knock-in KRT20-EGFP Low

value: Patient 23


title: CRC organoid 12 knock-in KRT20-EGFP High_1


title: brainstem ppi untested C57BL10/J biological replicate 1

description: pooled tissue from 3 mice

value: male


title: striatum ppi untested C57BL6/J biological replicate 2

description: pooled tissue from 3 mice

source_name: striatum, untested

value: striatum


title: brainstem ppi untested C57BLKS/J biological replicate 1

description: pooled tissue from 3 mice


title: brainstem ppi untested C57BL6/J biological replicate 2

description: pooled tissue from 3 mice


title: brainstem ppi tested BalbC/J biological replicate 1

description: pooled tissue from 3 mice

value: BalbC/J


title: brainstem ppi untested BalbC/J biological replicate 1

description: pooled tissue from 3 mice


title: brainstem ppi untested C3H HeJ biological replicate 1

description: pooled tissue from 3 mice

value: C3H HeJ


title: brainstem ppi tested C3H HeJ biological replicate 1

description: pooled tissue from 3 mice


title: brainstem ppi untested C3H HeJ biological replicate 2

description: pooled tissue from 3 mice


title: brainstem ppi untested BalbC/J biological replicate 2

description: pooled tissue from 3 mice


title: brainstem ppi tested C57BL10/J biological replicate 1

description: pooled tissue from 3 mice


title: CRC organoid 28 knock-in LGR5-EGFP High_1

source_name: CRC organoid 28 knock-in LGR5-EGFP High

value: Patient 39

value: LGR5-GFP knock-in colorectal tumor organoids


title: CRC organoid 7 knock-in KRT20-EGFP High_1

source_name: CRC organoid 7 knock-in KRT20-EGFP High


title: CRC organoid 12 knock-in LGR5-EGFP High_2

source_name: CRC organoid 12 knock-in LGR5-EGFP High


title: CRC organoid 28 knock-in LGR5-EGFP Low_1

source_name: CRC organoid 28 knock-in LGR5-EGFP Low


title: striatum ppi tested C57BL6/J biological replicate 1

description: pooled tissue from 3 mice

source_name: striatum, tested


title: CRC organoid 12 knock-in LGR5-EGFP Low_2

source_name: CRC organoid 12 knock-in LGR5-EGFP Low


title: striatum ppi untested C57L/J biological replicate 2

description: pooled tissue from 3 mice


title: CRC organoid 12 knock-in LGR5-EGFP Low_1


title: CRC organoid 12 knock-in LGR5-EGFP High_1


title: striatum ppi tested C57L/J biological replicate 1

description: pooled tissue from 3 mice


title: striatum ppi untested C57BL6/J biological replicate 1

description: pooled tissue from 3 mice


title: striatum ppi untested C57BLKS/J biological replicate 2

description: pooled tissue from 3 mice


title: striatum ppi untested C57BLKS/J biological replicate 1

description: pooled tissue from 3 mice


title: CRC organoid 7 knock-in LGR5-EGFP Low_2

source_name: CRC organoid 7 knock-in LGR5-EGFP Low


title: striatum ppi untested C57L/J biological replicate 1

description: pooled tissue from 3 mice


title: striatum ppi tested C57BLKS/J biological replicate 1

description: pooled tissue from 3 mice


title: striatum ppi untested BalbC/J biological replicate 2

description: pooled tissue from 3 mice


title: striatum ppi untested C57BL10/J biological replicate 2

description: pooled tissue from 3 mice


title: striatum ppi untested BalbC/J biological replicate 1

description: pooled tissue from 3 mice


title: striatum ppi untested C57BL10/J biological replicate 1

description: pooled tissue from 3 mice


title: CRC organoid 7 knock-in LGR5-EGFP Low_1


title: striatum ppi tested C3H HeJ biological replicate 1

description: pooled tissue from 3 mice


title: striatum ppi tested BalbC/J biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi tested C57L/J biological replicate 1

description: pooled tissue from 3 mice

source_name: hippocampus, tested

value: hippocampus


title: hippocampus ppi untested C57BL6/J biological replicate 2

description: pooled tissue from 3 mice

source_name: hippocampus, untested


title: striatum ppi untested C3H HeJ biological replicate 2

description: pooled tissue from 3 mice


title: hippocampus ppi untested C57L/J biological replicate 1

description: pooled tissue from 3 mice


title: striatum ppi untested C3H HeJ biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi tested C57BL6/J biological replicate 1

description: pooled tissue from 3 mice


title: CRC organoid 7 knock-in LGR5-EGFP High_1

source_name: CRC organoid 7 knock-in LGR5-EGFP High


title: hippocampus ppi untested C57L/J biological replicate 2

description: pooled tissue from 3 mice


title: CRC organoid 7 knock-in LGR5-EGFP High_2


title: hippocampus ppi untested C57BLKS/J biological replicate 2

description: pooled tissue from 3 mice


title: striatum ppi tested C57BL10/J biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi untested C57BL6/J biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi tested C57BLKS/J biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi untested C57BL10/J biological replicate 2

description: pooled tissue from 3 mice


title: hippocampus ppi untested C57BL10/J biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi tested C57BL10/J biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi untested C3H HeJ biological replicate 2

description: pooled tissue from 3 mice


title: hippocampus ppi untested BalbC/J biological replicate 2

description: pooled tissue from 3 mice


title: hippocampus ppi untested BalbC/J biological replicate 1

description: pooled tissue from 3 mice


title: hippocampus ppi untested C3H HeJ biological replicate 1

description: pooled tissue from 3 mice


title: G4-R

city: Changsha

first: zhang

last: fangliang

state: hunan

address: Changsha City Kaifu District

institute: Changsha University

description:
S04 G4-W-Cy5 Signal
raw data file:
02_CSU_121662-121207-Chu-G4R+G4W-430-530_Data.xls

hyb_protocol: Chip hybridizations were performed overnight on a μParaflo microfluidic chip using a microcirculation pump (Atactic Technologies). Based on mature miRNA sequences of zebrafish downloaded in miRBase Release 19.0 (http://microrna.sanger.ac.uk/), 246 probes were designed to detect S. chuatsi miRNAs on microarray chips. In addition, the arrays contained 95 probes complementary to the miRNA in S. chuatsi, positive control probes for zebrafish 5s rRNA, and negative controls for normalizing data with low-density signals. Sufficient RNA was extracted to hybridize in triplicatewith three biological repeats to ensure microarray reproducibility.

scan_protocol: Signals were detected using tag-specific Cy3 and Cy5 dyes. Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices, Sunnyvale, CA, USA) and digitized by Array-Pro image analysis software (Media Cybernetics, Bethesda, MD,  USA).

data_processing: The hybridization signals were detected and quantified, and data were analyzed by first subtracting the background.

organism: Siniperca chuatsi

source_name: Mandarin fish skeletal_red muscle

label_protocol: The assay started from 4 to 8µg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted from the white and red muscles of the Mandarin fish using Trizol reagent (Invitrogen, USA).  according to manufacturer's instructions.

value: Mandarin fish skeletal muscle

tag: tissue subtype

value: Red muscle


title: G5-W

description:
S05 G5-W-Cy3 Signal
raw data file:
03_CSU_121663-121207-Chu-G5W+G5R-445-525_Data.xls

source_name: Mandarin fish skeletal_white muscle

value: White muscle


title: Control [exon-level]

source_name: Human breast carcinoma


title: Treated [exon-level]


title: G1-W

description:
S01 G1-W-Cy3 Signal
raw data file:
01_CSU_121661-121207-Chu-G1W+G1R-425-510_Data.xls


title: G1-R

description:
S02 G1-R-Cy5 Signal
raw data file:
01_CSU_121661-121207-Chu-G1W+G1R-425-510_Data.xls


title: G5-R

description:
S06 G5-R-Cy5 Signal
raw data file:
03_CSU_121663-121207-Chu-G5W+G5R-445-525_Data.xls