title: iPSC_rep1

first: Min

last: Li

address: 1239 Siping Road, Yangpu District

institute: Tongji University

description: Gene expression data from 2nd iPS cells; iPS cells were maintained in ESM supplemented with 2i;

hyb_protocol: Hybridization, wash and Stain Kit(Affymetrix.Inc)

scan_protocol: GeneChip® Scanner 3000 7G 3000 (Affymetrix.Inc)

data_processing: The raw image files were processed by Bioconductor “Affy” and “vsn” package, the intensity of probes in arrays passed quality control were calculated and normalized for expression value.Gene expression value were calculated with RMA using alternative CDF: Brainarray MoGene10stv1_Mm_REFSEQ version 18.

source_name: the corresponding 2nd iPS cell line

label_protocol: WT Terminal Labeling Kit (Affymetrix.Inc)

growth_protocol: The 2nd mouse embyronic fibroblast were derived from E13.5 tetraploid complementated all-iPS embryos and cultured with Feeder Medium. On passages 4, MEFs were plated on gelatin-coated dishes at appropriate density and the culture medium was changed to ES Medium supplemented with 1µg/ml Doxcycline and 50µg/ml Vitamin C to induce iPS cells. After 15days of induction, majority of cells were reprogrammed into Oct4-GFP+ ES-like colonies and we withrew Doxcycline and Vc from the medium. 3days later, the remaining dox-indenpent iPS cells were collected as day18 sample. The 2nd iPS cell line was established and maintained in ES medium supplemented with 2i(Gsk3i+Meki) with/without feeder. Feeder Medium contains DMEM supplemented with 10% (v/v) fetal bovine serum and 1 mM L-glutamine; ES Medium contains DMEM supplemented with 15% (v/v) fetal bovine serum , 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock,1% penicillin/streptomycin stock,1% nucleosides stock and 1000 U/ml LIF.

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

tag: cell type

value: established iPS cell line

value: Oct4-GFP/ Rosa26-M2rtTA transgenic background


title: 12ppt-6hr-Rep3

status: Public on Dec 31 2015

type: RNA

city: Davis

first: Lisa

last: Komoroske

state: CA

address: One Shields Ave

department: Wildlife, fish and conservation biology

country: USA

institute: University of California, Davis

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >16.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

scan_protocol: Fluorescent images were scanned using an Axon GenePix 4000B Scanner and the analysis software GenePix Pro (Molecular Devices, LLC, Sunnyvale, CA). The images were quantified using Feature Extraction 11.5.1.1 (Agilent Technologies).

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 100 (~2 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

molecule: total RNA

organism: Hypomesus transpacificus

source_name: Gill, 12ppt-6hour exposure

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrometer.

growth_protocol: Delta smelt were  acclimatized to holding conditions at 2ppt for at least 2 weeks at the Center for Aquatic Biology and Aquaculture at the University of California, Davis.

extract_protocol: At each time point, fish were sacrificed by a lethal dose of MS-222, gills dissected and immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Gill samples were then homogenized using Qiagen's TissuelyserLT and Trizol reagent following manufacturer’s protocols. Samples purity was improved by using RNEasy columns and reagents prior to final elution in water. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Fish were placed in treatment vessels with flow through conditions the evening prior to experiments to acclimate, any mortalities were counted and removed prior to beginning the experiment. A subset of randomly selected fish were sampled at this time prior to beginning treatments as a control. Salinities were then ramped to targets over a period of 6 hours, and then held for the duration of the experiment (48hrs). Handling control treatments for each sampling time point were conducted by subjecting fish to the same conditions except they were held at the acclimation salinity of 2pptt.

tag: treatment

tag: time point

value: 6hour exposure


title: SS_hemibrain_5d_24h_rep4

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

description:
SS_hemibrain_5d_24h_rep4
US09493743_251486829525_1_2  -T5-138_5 DAY_24HR.txt

hyb_protocol: The slides were hybridized at 60ºC for 16 h

scan_protocol: Hybridized slides were scanned and recorded using a Agilent's Feature Extraction Software v 10.9  (Agilent Technology Inc.)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent's Feature Extraction Software V10.9 was used.

organism: Mus musculus

source_name: pooled whole mouse tissue cell line

label_protocol: RNA was reverse transcribed and labeled using Agilent's Mouse Chip Labeling and Detection Kit (Agilent Technologies, Inc.) following the manufacturer’s protocol.

extract_protocol: Total RNA extracted using Trizol from brain regions and organs and using PAXgene from blood following the manufacturers' instructions

treatment_protocol: C57B6 mice were exposed to SJL aggressor mice for periods of 5 days and 10days (6 hours each day) to induce anxiety/stress which parallels to PTSD in human. Organs, blood and brain regions were collected after 24 hours and 1.5 week of post 5 days social defeat period; and 24 hour and 6 weeks post 10 days social stress period.

tag: sample type

value: Strategen universal reference RNA (Cat. No. 740100)

tag: strain

value: social stress (SS)

value: after 24 hrs post 5 days social defeat period

tag: tissue

value: hemibrain


title: iPSC_rep2

city: Shanghai

country: China

label: biotin

tag: genotype


title: Reprogrammed_cells_at_day18_rep1

description: Gene expression data from reprogrammed cells at day 18；Dox and Vc were removed from the medium since day15

source_name: reprogrammed cells after 15days induction and 3days dox-withdrawl treatment

value: reprogrammed dox-independent cell

tag: day


title: Reprogramming_cells_at_day15_rep2

description: Gene expression data from reprogramming cells at day 15, 15 days after Dox induction; Vc was supplemented to enhance reprogramming efficiency.

source_name: reprogramming intermediate after 15days of induction

value: reprogramming intermediate


title: Reprogrammed_cells_at_day18_rep2


title: 12ppt-6hr-Rep2


title: SS_hemibrain_5d_24h_rep1

description:
SS_hemibrain_5d_24h_rep1
US09493743_251486829524_1_3  -T5-135_5 DAY_24HR.txt


title: SS_hemibrain_5d_1.5w_rep4

description:
SS_hemibrain_5d_1.5w_rep4
US09493743_251486829545_1_3  -T10-115 _5 DAY_1.5 WEEK.txt

value: after 1.5 wk post 5 days social defeat period


title: 12ppt-6hr-Rep4


title: SS_hemibrain_5d_24h_rep2

description:
SS_hemibrain_5d_24h_rep2
US09493743_251486829524_1_4 -T5-136_5 DAY_24HR.txt


title: 12ppt-6hr-Rep1


title: 12ppt-48hr-Rep3

source_name: Gill, 12ppt-48hour exposure

value: 48hour exposure


title: SS_hemibrain_5d_24h_rep3

description:
SS_hemibrain_5d_24h_rep3
US09493743_251486829525_1_1 -T5-137_5 DAY_24HR.txt


title: 12ppt-48hr-Rep2


title: 12ppt-48hr-Rep4


title: SMU1_KD_2 [probe-level]

city: Barcelona

first: Juan

last: Valcarcel

state: Barcelona

address: Dr Aiguader 88

department: Gene regulation stem cells and cancer

country: Spain

institute: CRG

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Affymetrix HJAY dataset analysis was performed by GenoSplice technology (www.genosplice.com). Raw data was processed using Expression Console to get the RMA intensities values of Affymetrix HJAY probesets. Additional analysis included the follwing. Data were normalized using quantile normalization. Background corrections were made with antigenomic probes and probes were selected according to their %GC, cross-hybridization status and potential overlap with repeat region as previously described [PMID:23321315, PMID:23284676]. Only probes targeting exons and exon-exon junctions annotated from FAST DB® transcripts (release fastdb_2012_2) were selected [PMID:16052034,PMID:17547750]. Only probes with a DABG Pvalue ≤ 0.05 in at least half of the arrays were considered for statistical analysis [PMID:23321315, PMID:23284676]. Only genes expressed in at least one compared condition were analyzed. To be considered to be expressed, the DABG Pvalue had to be ≤ 0.05 for at least half of the gene probes. We performed an unpaired Student’s t-test to compare gene intensities between two experimental conditions. Genes were considered significantly regulated when fold-change was ≥1.5 and Pvalue 0.05 (unadjusted P-value). Analysis at the splicing level was first performed taking into account only exon probes (EXON analysis) in order to potentially detect new alternative events that could be differentially regulated (i.e., without taking into account exon-exon junction probes). Analysis at the splicing level was also performed by taking into account exon-exon junction probes (SPLICING PATTERN analysis) using the FAST DB® splicing patterns annotation (i.e., for each gene, all possible splicing patterns were defined and analyzed. All types of alternative events can be analyzed: Alternative first exons, alternative terminal exons, cassette exon, mutually exclusive exons, alternative 5’ donor splice site, alternative 3’ acceptor splice sites and intron retention). EXON and SPLICING PATTERN analyses were performed using unpaired Student's t-test on the splicing-index as previously described [PMID:23321315, PMID:23284676]. Results were considered statistically significant for unadjusted P-values ≤ 0.05 and fold-changes ≥ 2.0 for EXON analysis and for unadjusted P-values ≤ 0.05 and fold-changes ≥ 1.5 for SPLICING PATTERN analysis. Gene Ontology (GO), KEGG and REACTOME analyses of differentially regulated genes were performed using DAVID [PMID:19131956].

label: Biotin

organism: Homo sapiens

source_name: HeLa cell SMU1 KD

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HeLa cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol: RNA from three biological replicates for control, IK or SMU1 knocked down HeLa cells was purified using Rneasy mini kit (Qiagen).

treatment_protocol: Knockdowns of IK or SMU1 in Hela cells were performed by forward transfection using the lipofectamine RNAiMAX protocol and siRNA pools for either control, IK or SMU1 genes (ON TARGET PLUS. Dharmacon).

tag: sirna sequence

tag: cell line

value: HeLa

value: SMU1 Knock-down


title: Reprogramming_cells_at_day11_rep2

description: Gene expression data from reprogramming cells at day 11, 11 days after Dox induction; Vc was supplemented to enhance reprogramming efficiency.

source_name: reprogramming intermediate after 11days of induction


title: SS_hemibrain_5d_1.5w_rep3

description:
SS_hemibrain_5d_1.5w_rep3
US09493743_251486829545_1_2  -T10-114 _5 DAY_1.5 WEEK.txt


title: SS_hemibrain_5d_1.5w_rep5

description:
SS_hemibrain_5d_1.5w_rep5
US09493743_251486829545_1_4  -T10-116 _5 DAY_1.5 WEEK.txt


title: IK_KD_3 [probe-level]

source_name: HeLa cell IK KD

value: IK Knock-down


title: SMU1_KD_3 [probe-level]


title: SS_hemibrain_5d_1.5w_rep2

description:
SS_hemibrain_5d_1.5w_rep2
US09493743_251486829545_1_1  -T10-113 _5 DAY_1.5 WEEK.txt


title: IK_KD_2 [probe-level]


title: Reprogramming_cells_at_day15_rep1


title: IK_KD_1 [probe-level]


title: CTRL_3 [probe-level]

source_name: HeLa cell control

value: control


title: 12ppt-48hr-Rep1


title: SS_hemibrain_10d_6w_rep5

description:
SS_hemibrain_10d_6w_rep5
US09493743_251486829526_1_4 -T10-64_10 DAY_6 WEEK.txt

value: after 6wks post 10 days social stress period


title: Reprogramming_cells_at_day3_rep2

description: Gene expression data from reprpgramming cells at day 3, 3 days after Dox induction; Vc was supplemented to enhance reprogramming efficiency.

source_name: reprogramming intermediate after 3days of induction


title: CTRL_2 [probe-level]


title: Reprogramming_cells_at_day11_rep1


title: CTRL_1 [probe-level]


title: Reprogramming_cells_at_day5_rep1

description: Gene expression data from reprogramming cells at day 5, 5 days after Dox induction; Vc was supplemented to enhance reprogramming efficiency.

source_name: reprogramming intermediate after 5days of induction


title: SS_hemibrain_10d_6w_rep4

description:
SS_hemibrain_10d_6w_rep4
US09493743_251486829526_1_3 -T10-63_10 DAY_6 WEEK.txt


title: 12ppt-24hr-Rep2

source_name: Gill, 12ppt-24hour exposure

value: 24hour exposure


title: Reprogramming_cells_at_day7_rep1

description: Gene expression data from reprogramming cells at day 7, 7 days after Dox induction; Vc was supplemented to enhance reprogramming efficiency.

source_name: reprogramming intermediate after 7days of induction


title: SS_hemibrain_10d_6w_rep2

description:
SS_hemibrain_10d_6w_rep2
US09493743_251486829524_1_2 -T10-60_10 DAY_6 WEEK.txt


title: 0ppt-6hr-Rep2

source_name: Gill, 0ppt-6hour exposure


title: Reprogramming_cells_at_day3_rep1


title: SS_hemibrain_10d_6w_rep3

description:
SS_hemibrain_10d_6w_rep3
US09493743_251486829526_1_2 -T10-59_10 DAY_6 WEEK.txt


title: 12ppt-24hr-Rep3


title: SS_hemibrain_10d_6w_rep1

description:
SS_hemibrain_10d_6w_rep1
US09493743_251486829524_1_1 -T10-57_10 DAY_6 WEEK.txt


title: 12ppt-24hr-Rep1


title: 0ppt-6hr-Rep4


title: SS_hemibrain_5d_1.5w_rep1

description:
SS_hemibrain_5d_1.5w_rep1
US09493743_251486828856_1_4  -T10-112_5 DAY_1.5 WEEK.txt


title: 0ppt-6hr-Rep3


title: Reprogramming_cells_at_day5_rep2


title: SMU1_KD_1 [probe-level]


title: Late Severe, X1068_2

city: Birmingham

first: S

middle: Louis

last: Bridges

state: Al

address: University Blvd

department: Rheumatology

institute: UAB

description:
X1068
PBMCs acquired from whole blood.

data_processing:
Non-normalized data represent median raw Ct values. Median of raw Ct values from three technical replicates for each of 60 samples.
Normalized data represent Delta Ct (dCt) values. dCt were obtained using housekeeping genes, excluding 18s.

label: FAM

source_name: PBMCs, late severe RA

label_protocol: Total RNA was reverse-transcribed into cDNA with High-Capacity cDNA Reverse Transcription Kit (Life Tech).

extract_protocol: Total RNA from whole blood was obtained from PAXgene Blood RNA Tubes (Qiagen) using PAXgene Blood RNA Kit (Qiagen), including treatment with RNase-free DNase Set (Qiagen) to eliminate genomic DNA.

value: peripheral blood mononuclear cells (PBMCs)

tag: disease status

value: late severe rheumatoid arthritis

tag: population

value: African-American


title: Reprogramming_cells_at_day7_rep2

value: Oct4-GFP/ Rosa26-M2rtTA transgenic background


title: Late Severe, X2022_2

description:
X2022
PBMCs acquired from whole blood.


title: Late Severe, X5025_2

description:
X5025
PBMCs acquired from whole blood.


title: Reprogramming_cells_at_day1_rep2

description: Gene expression data from reprogramming cells at day 1, 1 day after Dox induction; Vc was supplemented to enhance reprogramming efficiency.

source_name: reprogramming intermediate after 24hour of induction


title: SS_hemibrain_10d_24h_rep4

description:
SS_hemibrain_10d_24h_rep4
US09493743_251486828856_1_2  -T10-110_10 DAY_24HR.txt

value: Strategen universal reference RNA (Cat. No. 740100)

value: social stress (SS)

value: after 24 hrs post 10 days social stress period


title: Late Severe, X5015_2

description:
X5015
PBMCs acquired from whole blood.


title: 2ndMEF_at_day0_rep2

description: Gene expression data from 2nd MEFs at day 0, before Dox induction

source_name: 2nd mouse embryonic fibroblasts prior to induction

value: primary mouse embryonic fibroblast isolated from E13.5 tetraploid blastocyst complementation embryo,P4


title: Late Severe, X2039_2

description:
X2039
PBMCs acquired from whole blood.


title: 0ppt-48hr-Rep2

source_name: Gill, 0ppt-48hour exposure


title: 0ppt-48hr-Rep4


title: SS_blood_5d_24h_rep4

description:
SS_blood_5d_24h_rep4
US09493743_251486829496_1_4 -T5-138 _5 DAY_24HR.txt

source_name: pooled whole mouse tissue cell line

value: after 24 hrs post 5 days social defeat period

value: blood


title: Reprogramming_cells_at_day1_rep1

value: reprogramming intermediate


title: SS_blood_5d_24h_rep2

description:
SS_blood_5d_24h_rep2
US09493743_251486829496_1_2 -T5-136_5 DAY_24HR.txt


title: SS_blood_5d_24h_rep5

description:
SS_blood_5d_24h_rep5
US09493743_251486829537_1_2 -T10-105_5 DAY_24HR.txt


title: 0ppt-48hr-Rep5

value: 48hour exposure


title: 2ndMEF_at_day0_rep1


title: SS_hemibrain_10d_24h_rep1

description:
SS_hemibrain_10d_24h_rep1
US09493743_251486828855_1_3  -T10-107_10 DAY_24HR.txt

value: hemibrain


title: Late Severe, X4201_2

description:
X4201
PBMCs acquired from whole blood.


title: SS_hemibrain_10d_24h_rep5

description:
SS_hemibrain_10d_24h_rep5
US09493743_251486828856_1_3  -T10-111_10 DAY_24HR.txt


title: SS_hemibrain_10d_24h_rep2

description:
SS_hemibrain_10d_24h_rep2
US09493743_251486828855_1_4  -T10-108_10 DAY_24HR.txt


title: SS_blood_5d_24h_rep1

description:
SS_blood_5d_24h_rep1
US09493743_251486829496_1_1 -T5-135_5 DAY_24HR.txt


title: SS_hemibrain_10d_24h_rep3

description:
SS_hemibrain_10d_24h_rep3
US09493743_251486828856_1_1 -T10-109_10 DAY_24HR.txt


title: Late Severe, X2042_2

description:
X2042
PBMCs acquired from whole blood.


title: 0ppt-48hr-Rep1


title: 0ppt-24hr-Rep7

source_name: Gill, 0ppt-24hour exposure


title: 0ppt-24hr-Rep2


title: 0ppt-24hr-Rep1


title: 0ppt-24hr-Rep6


title: SS_blood_5d_24h_rep3

description:
SS_blood_5d_24h_rep3
US09493743_251486829496_1_3 -T5-137_5 DAY_24HR.txt


title: SS_blood_5d_1.5w_rep5

description:
SS_blood_5d_1.5w_rep5
US09493743_251486829654_1_2 -T10-114_5 DAY_1.5 WEEK.txt

value: after 1.5 wk post 5 days social defeat period


title: Late Severe, X2022

description:
X2022
PBMCs acquired from whole blood.

label: SYBR Green


title: Late Severe, X1126_2

description:
X1126
PBMCs acquired from whole blood.


title: Late Severe, X1122_2

description:
X1122
PBMCs acquired from whole blood.


title: Late Severe, X5025

description:
X5025
PBMCs acquired from whole blood.


title: Late Severe, X1068

description:
X1068
PBMCs acquired from whole blood.


title: Late Severe, X4201

description:
X4201
PBMCs acquired from whole blood.


title: Late Severe, X5015

description:
X5015
PBMCs acquired from whole blood.


title: Late Severe, X4187_2

description:
X4187
PBMCs acquired from whole blood.


title: Late Mild, X2051_2

description:
X2051
PBMCs acquired from whole blood.

source_name: PBMCs, late mild RA

value: late mild rheumatoid arthritis


title: Late Mild, X1177_2

description:
X1177
PBMCs acquired from whole blood.


title: Late Severe, X2042

description:
X2042
PBMCs acquired from whole blood.


title: Late Severe, X2039

description:
X2039
PBMCs acquired from whole blood.


title: Late Severe, X1126

description:
X1126
PBMCs acquired from whole blood.


title: Late Mild, X1003_2

description:
X1003
PBMCs acquired from whole blood.


title: Late Mild, X4083_2

description:
X4083
PBMCs acquired from whole blood.


title: Late Mild, X3012_2

description:
X3012
PBMCs acquired from whole blood.


title: Late Severe, X1122

description:
X1122
PBMCs acquired from whole blood.


title: Late Severe, X4187

description:
X4187
PBMCs acquired from whole blood.


title: Late Mild, X2033_2

description:
X2033
PBMCs acquired from whole blood.


title: 0ppt-6hr-Rep1

value: 6hour exposure


title: Late Mild, X2051

description:
X2051
PBMCs acquired from whole blood.


title: SS_blood_5d_1.5w_rep3

description:
SS_blood_5d_1.5w_rep3
US09493743_251486829539_1_3 -T10-112_5 DAY_1.5 WEEK.txt


title: SS_blood_5d_1.5w_rep1

description:
SS_blood_5d_1.5w_rep1
US09493743_251486829497_1_1 -T10-116 _5 DAY_1.5 WEEK.txt


title: SS_blood_5d_1.5w_rep4

description:
SS_blood_5d_1.5w_rep4
US09493743_251486829539_1_4 -T10-113_5 DAY_1.5 WEEK.txt


title: SS_blood_5d_1.5w_rep2

description:
SS_blood_5d_1.5w_rep2
US09493743_251486829536_1_1 -T10-115 _5 DAY_1.5 WEEK.txt


title: SS_blood_10d_6w_rep1

description:
SS_blood_10d_6w_rep1
US09493743_251486829498_1_3 -T10-57 _10 DAY_6 WEEK.txt

value: after 6wks post 10 days social stress period


title: SS_blood_10d_6w_rep4

description:
SS_blood_10d_6w_rep4
US09493743_251486829535_1_2 -T10-63_10 DAY_6 WEEK.txt


title: SS_blood_10d_6w_rep3

description:
SS_blood_10d_6w_rep3
US09493743_251486829535_1_1 -T10-60_10 DAY_6 WEEK.txt


title: SS_blood_10d_6w_rep5

description:
SS_blood_10d_6w_rep5
US09493743_251486829535_1_3 -T10-64_10 DAY_6 WEEK.txt


title: SS_blood_10d_6w_rep2

description:
SS_blood_10d_6w_rep2
US09493743_251486829526_1_1 -T10-59_10 DAY_6 WEEK.txt


title: Late Mild, X1177

description:
X1177
PBMCs acquired from whole blood.

value: peripheral blood mononuclear cells (PBMCs)


title: Late Mild, X1085_2

description:
X1085
PBMCs acquired from whole blood.


title: Late Mild, X4167_2

description:
X4167
PBMCs acquired from whole blood.


title: SS_blood_10d_24h_rep5

description:
SS_blood_10d_24h_rep5
US09493743_251486829539_1_2 -T10-111_10 DAY_24HR.txt


title: Late Mild, X1003

description:
X1003
PBMCs acquired from whole blood.


title: Late Mild, X4179_2

description:
X4179
PBMCs acquired from whole blood.


title: Late Mild, X2033

description:
X2033
PBMCs acquired from whole blood.


title: Early Severe, X4186_2

description:
X4186
PBMCs acquired from whole blood.

source_name: PBMCs, early severe RA

value: early severe rheumatoid arthritis


title: Early Severe, X4174_2

description:
X4174
PBMCs acquired from whole blood.

value: African-American


title: Late Mild, X3040

description:
X3040
PBMCs acquired from whole blood.


title: SS_blood_10d_24h_rep2

description:
SS_blood_10d_24h_rep2
US09493743_251486829537_1_3 -T10-107_10 DAY_24HR.txt


title: SS_blood_10d_24h_rep3

description:
SS_blood_10d_24h_rep3
US09493743_251486829537_1_4 -T10-108_10 DAY_24HR.txt


title: Late Mild, X3040_2

description:
X3040
PBMCs acquired from whole blood.


title: Late Mild, X3012

description:
X3012
PBMCs acquired from whole blood.


title: Late Mild, X4167

description:
X4167
PBMCs acquired from whole blood.


title: Early Severe, X1055_2

description:
X1055
PBMCs acquired from whole blood.


title: C_spleen_5d_24h_rep5

description:
C_spleen_5d_24h_rep5
US09493743_251486832510_1_4 - C5-131 5day 24hrs control.txt

value: control (C)

value: spleen


title: Late Mild, X4179

description:
X4179
PBMCs acquired from whole blood.


title: SS_blood_10d_24h_rep4

description:
SS_blood_10d_24h_rep4
US09493743_251486829539_1_1 -T10-109_10 DAY_24HR.txt

value: Strategen universal reference RNA (Cat. No. 740100)

value: social stress (SS)


title: Late Mild, X4083

description:
X4083
PBMCs acquired from whole blood.


title: C_spleen_5d_24h_rep3

description:
C_spleen_5d_24h_rep3
US09493743_251486832510_1_2 - C5-129 5day 24hrs control.txt


title: Early Severe, X4170

description:
X4170
PBMCs acquired from whole blood.


title: Early Severe, X4170_2

description:
X4170
PBMCs acquired from whole blood.


title: SS_blood_10d_24h_rep1

description:
SS_blood_10d_24h_rep1
US09493743_251486829535_1_4 -T10-110_10 DAY_24HR.txt

value: after 24 hrs post 10 days social stress period


title: Early Severe, X4174

description:
X4174
PBMCs acquired from whole blood.


title: Early Severe, X4164_2

description:
X4164
PBMCs acquired from whole blood.


title: Early Severe, X1153_2

description:
X1153
PBMCs acquired from whole blood.


title: C_spleen_5d_24h_rep1

description:
C_spleen_5d_24h_rep1
US09493743_251486832284_1_4 - C5-127 5day 24hrs control.txt


title: C_spleen_5d_24h_rep4

description:
C_spleen_5d_24h_rep4
US09493743_251486832510_1_3 - C5-130 5day 24hrs control.txt


title: Early Severe, X4186

description:
X4186
PBMCs acquired from whole blood.


title: Early Severe, X4032_2

description:
X4032
PBMCs acquired from whole blood.


title: Early Severe, X4032

description:
X4032
PBMCs acquired from whole blood.


title: Early Severe, X3022_2

description:
X3022
PBMCs acquired from whole blood.


title: Early Severe, X4084_2

description:
X4084
PBMCs acquired from whole blood.


title: Early Mild, X1112_2

description:
X1112
PBMCs acquired from whole blood.

source_name: PBMCs, early mild RA

value: early mild rheumatoid arthritis


title: Early Severe, X1055

description:
X1055
PBMCs acquired from whole blood.


title: Early Mild, X4027_2

description:
X4027
PBMCs acquired from whole blood.


title: C_spleen_5d_24h_rep2

description:
C_spleen_5d_24h_rep2
US09493743_251486832510_1_1 - C5-128 5day 24hrs control.txt


title: C_spleen_5d_1.5w-rep5

description:
C_spleen_5d_1.5w-rep5
US09493743_251486832351_1_4 - C5-134 5day 1.5wk control.txt


title: C_spleen_5d_1.5w-rep4

description:
C_spleen_5d_1.5w-rep4
US09493743_251486832351_1_3 - C5-133 5day 1.5wk control.txt


title: Early Severe, X4164

description:
X4164
PBMCs acquired from whole blood.


title: Early Severe, X1153

description:
X1153
PBMCs acquired from whole blood.


title: C_spleen_5d_1.5w-rep3

description:
C_spleen_5d_1.5w-rep3
US09493743_251486832351_1_2 - C5-132 5day 1.5wk control.txt


title: C_spleen_5d_1.5w-rep1

description:
C_spleen_5d_1.5w-rep1
US09493743_251486832305_1_1 - HC-125 5day 1.5wk control.txt


title: Early Severe, X3022

description:
X3022
PBMCs acquired from whole blood.


title: Early Mild, X1180_2

description:
X1180
PBMCs acquired from whole blood.


title: Early Severe, X2025

description:
X2025
PBMCs acquired from whole blood.


title: C_spleen_10d_6w_rep5

description:
C_spleen_10d_6w_rep5
US09493743_251486832281_1_1 -  C10-50 10day 6wk control.txt


title: Early Severe, X2025_2

description:
X2025
PBMCs acquired from whole blood.


title: Late Mild, X1085

description:
X1085
PBMCs acquired from whole blood.


title: Early Severe, X4084

description:
X4084
PBMCs acquired from whole blood.


title: Early Mild, X1165_2

description:
X1165
PBMCs acquired from whole blood.


title: Early Mild, X4197_2

description:
X4197
PBMCs acquired from whole blood.


title: Early Mild, X1112

description:
X1112
PBMCs acquired from whole blood.


title: Early Mild, X4136_2

description:
X4136
PBMCs acquired from whole blood.


title: Early Mild, X5001_2

description:
X5001
PBMCs acquired from whole blood.


title: Early Mild, X1180

description:
X1180
PBMCs acquired from whole blood.


title: Early Mild, X4027

description:
X4027
PBMCs acquired from whole blood.


title: Early Mild, X1071_2

description:
X1071
PBMCs acquired from whole blood.


title: C_spleen_10d_6w_rep3

description:
C_spleen_10d_6w_rep3
US09493743_251486832280_1_3 -  C10-48 10day 6wk control.txt


title: C_spleen_10d_6w_rep4

description:
C_spleen_10d_6w_rep4
US09493743_251486832280_1_4 -  C10-49 10day 6wk control.txt


title: Early Mild, X4197

description:
X4197
PBMCs acquired from whole blood.


title: Early Mild, X3017_2

description:
X3017
PBMCs acquired from whole blood.


title: Early Mild, X4080_2

description:
X4080
PBMCs acquired from whole blood.


title: Control, X2504_2

description:
X2504
PBMCs acquired from whole blood.

source_name: PBMCs, control

value: no rheumatoid arthritis


title: Early Mild, X1165

description:
X1165
PBMCs acquired from whole blood.


title: C_spleen_5d_1.5w-rep2

description:
C_spleen_5d_1.5w-rep2
US09493743_251486832305_1_2 - HC-126 5day 1.5wk control.txt


title: Early Mild, X5001

description:
X5001
PBMCs acquired from whole blood.


title: C_spleen_10d_6w_rep2

description:
C_spleen_10d_6w_rep2
US09493743_251486832280_1_2 -  C10-47 10day 6wk control.txt


title: Control, X7071_2

description:
X7071
PBMCs acquired from whole blood.


title: C_spleen_10d_24h_rep4

description:
C_spleen_10d_24h_rep4
US09493743_251486832504_1_3 -  C10-94 10day 24hr control rerun.txt


title: Early Mild, X4136

description:
X4136
PBMCs acquired from whole blood.


title: C_spleen_10d_6w_rep1

description:
C_spleen_10d_6w_rep1
US09493743_251486832280_1_1 -  C10-46 10day 6wk control.txt


title: Control, X5514_2

description:
X5514
PBMCs acquired from whole blood.


title: Early Mild, X1071

description:
X1071
PBMCs acquired from whole blood.


title: Control, X5505_2

description:
X5505
PBMCs acquired from whole blood.


title: Early Mild, X3017

description:
X3017
PBMCs acquired from whole blood.


title: Control, X7069_2

description:
X7069
PBMCs acquired from whole blood.


title: C_spleen_10d_24h_rep5

description:
C_spleen_10d_24h_rep5
US09493743_251486832504_1_4 -  C10-97 10day 24hr control rerun.txt


title: C_spleen_10d_24h_rep3

description:
C_spleen_10d_24h_rep3
US09493743_251486832504_1_2 -  C10-93 10day 24hr control rerun.txt


title: Early Mild, X4080

description:
X4080
PBMCs acquired from whole blood.


title: C_spleen_10d_24h_rep1

description:
C_spleen_10d_24h_rep1
US09493743_251486832282_1_3 -  C10-95 10day 24hrs control.txt


title: C_spleen_10d_24h_rep2

description:
C_spleen_10d_24h_rep2
US09493743_251486832282_1_4 -  C10-96 10day 24hrs control.txt


title: C_hemibrain_5d_24h_rep3

description:
C_hemibrain_5d_24h_rep3
US09493743_251486829542_1_4 -C5-130_5 DAY_24HR CONTROL.txt


title: Control, X7054_2

description:
X7054
PBMCs acquired from whole blood.


title: C_hemibrain_5d_24h_rep2

description:
C_hemibrain_5d_24h_rep2
US09493743_251486829542_1_3 -C5-129_5 DAY_24HR CONTROL.txt


title: Control, X1503_2

description:
X1503
PBMCs acquired from whole blood.


title: Control, X2504

description:
X2504
PBMCs acquired from whole blood.


title: C_hemibrain_5d_24h_rep4

description:
C_hemibrain_5d_24h_rep4
US09493743_251486829543_1_1 -C5-131_5 DAY_24HR CONTROL.txt


title: Control, X7071

description:
X7071
PBMCs acquired from whole blood.


title: C_hemibrain_5d_24h_rep1

description:
C_hemibrain_5d_24h_rep1
US09493743_251486829542_1_2 -C5-127_5 DAY_24HR CONTROL.txt


title: Control, X2501_2

description:
X2501
PBMCs acquired from whole blood.


title: Control, X5505

description:
X5505
PBMCs acquired from whole blood.


title: Control, X7072_2

description:
X7072
PBMCs acquired from whole blood.


title: Control, X7069

description:
X7069
PBMCs acquired from whole blood.


title: Control, X5514

description:
X5514
PBMCs acquired from whole blood.


title: Control, X7054

description:
X7054
PBMCs acquired from whole blood.


title: Control, X7015_2

description:
X7015
PBMCs acquired from whole blood.


title: Control, X1539_2

description:
X1539
PBMCs acquired from whole blood.


title: C_hemibrain_5d_1.5w_rep5

description:
C_hemibrain_5d_1.5w_rep5
US09493743_251486829544_1_2 -HC10-126 _5 DAY_1.5 WEEK HOME CAGE CONTROL.txt


title: C_hemibrain_5d_1.5w_rep2

description:
C_hemibrain_5d_1.5w_rep2
US09493743_251486829543_1_3 -C5-133_5 DAY_1.5 WEEK CONTROL.txt


title: C_hemibrain_5d_1.5w_rep4

description:
C_hemibrain_5d_1.5w_rep4
US09493743_251486829544_1_1 -HC10-125_5 DAY_1.5 WEEK HOME CAGE CONTROL.txt


title: C_hemibrain_5d_1.5w_rep1

description:
C_hemibrain_5d_1.5w_rep1
US09493743_251486829543_1_2 -C5-132_5 DAY_1.5 WEEK CONTROL.txt


title: C_hemibrain_5d_1.5w_rep3

description:
C_hemibrain_5d_1.5w_rep3
US09493743_251486829543_1_4 -C5-134_5 DAY_1.5 WEEK CONTROL.txt


title: Control, X1519

description:
X1519
PBMCs acquired from whole blood.


title: C_hemibrain_10d_6w_rep4

description:
C_hemibrain_10d_6w_rep4
US09493743_251486829540_1_4 -C10-49 _10 DAY_6 WEEK CONTROL.txt


title: C_hemibrain_10d_6w_rep5

description:
C_hemibrain_10d_6w_rep5
US09493743_251486829541_1_1 -C10-50 _10 DAY_6 WEEK CONTROL.txt


title: Control, X3509_2

description:
X3509
PBMCs acquired from whole blood.


title: Control, X1519_2

description:
X1519
PBMCs acquired from whole blood.


title: Control, X7028_2

description:
X7028
PBMCs acquired from whole blood.


title: Control, X1503

description:
X1503
PBMCs acquired from whole blood.


title: Control, X7011_2

description:
X7011
PBMCs acquired from whole blood.


title: Control, X2501

description:
X2501
PBMCs acquired from whole blood.


title: Control, X1523_2

description:
X1523
PBMCs acquired from whole blood.


title: Control, X7072

description:
X7072
PBMCs acquired from whole blood.


title: Control, X7015

description:
X7015
PBMCs acquired from whole blood.


title: C_hemibrain_10d_6w_rep2

description:
C_hemibrain_10d_6w_rep2
US09493743_251486829540_1_2  -C10-47 _10 DAY_6 WEEK CONTROL.txt


title: C_hemibrain_10d_6w_rep1

description:
C_hemibrain_10d_6w_rep1
US09493743_251486829540_1_1 -C10-46 _10 DAY_6 WEEK CONTROL.txt


title: Control, X1539

description:
X1539
PBMCs acquired from whole blood.


title: Control, X3509

description:
X3509
PBMCs acquired from whole blood.


title: C_hemibrain_10d_6w_rep3

description:
C_hemibrain_10d_6w_rep3
US09493743_251486829540_1_3 -C10-48 _10 DAY_6 WEEK CONTROL.txt


title: Control, X2532_2

description:
X2532
PBMCs acquired from whole blood.


title: Control, X1517_2

description:
X1517
PBMCs acquired from whole blood.


title: C_hemibrain_10d_24h_rep4

description:
C_hemibrain_10d_24h_rep4
US09493743_251486829541_1_4 -C10-95 _10 DAY_24HR CONTROL.txt


title: Control, X7008_2

description:
X7008
PBMCs acquired from whole blood.


title: C_hemibrain_10d_24h_rep5

description:
C_hemibrain_10d_24h_rep5
US09493743_251486829542_1_1 -C10-97 _10 DAY_24HR CONTROL.txt


title: Control, X7011

description:
X7011
PBMCs acquired from whole blood.


title: Control, X1523

description:
X1523
PBMCs acquired from whole blood.


title: Control, X7028

description:
X7028
PBMCs acquired from whole blood.


title: Control, X7151_2

description:
X7151
PBMCs acquired from whole blood.


title: Control, X7008

description:
X7008
PBMCs acquired from whole blood.


title: Control, X7151

description:
X7151
PBMCs acquired from whole blood.


title: Control, X2532

description:
X2532
PBMCs acquired from whole blood.


title: Control, X1517

description:
X1517
PBMCs acquired from whole blood.


title: C_hemibrain_10d_24h_rep1

description:
C_hemibrain_10d_24h_rep1
US09493743_251486828855_1_1 - C10-96_10 DAY_24HR CONTROL.txt


title: C_hemibrain_10d_24h_rep3

description:
C_hemibrain_10d_24h_rep3
US09493743_251486829541_1_3 -C10-94 _10 DAY_24HR CONTROL.txt


title: Patient 5

city: Lianyungang

first: Leilei

last: Wang

state: Jiangsu

address: No.10 Cangwu road

institute: Lianyungang maternal and child health hospital

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
To identify differentially expressed miRNAs with statistical significance, we performed a Volcano Plot filtering between the two groups from the experiment. The threshold we used to screen Up or Down regulated miRNAs is Fold Change>=2.0 and P-value<=0.05.

label: Hy3TM fluorescent label

source_name: recurrent miscarriage_chorionic villi

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Chorionic villi tissues were collected from cases. the criteria for early RM were three or more consecutive times of pregnancy loss, and pregnancy losses until a maximum of 12 weeks. Abnormal embryonic chromosomes were firstly excluded by karyotyping screening in the two groups. Then，other genomic confounding influences in embryonic chromosomes were excluded by array-comparative genomic hybridization (array-CGH). The two groups were matched for age, nulliparous times and gestational weeks. The average times of pregnancy loss was 3.8 (3~6) in RM group, which was zero in control group.

tag: subject status

value: recurrent miscarriage

value: chorionic villi

tag: molecule subtype

value: miRNA


title: 3A cytotrophoblast H2O2

city: Cairo

first: Mai

last: Tolba

state: Non-US/Non-Canadian

address: Abbasya

department: Pharmacology and Toxicology

country: Egypt

institute: Faculty of Pharmacy, Ain Shams University

data_processing: Data was generated automatically by the miScript miRNA PCR Array Data Analysis Webportal tool from SA Biosciences.  Data was normalized using 5 housekeeping genes

source_name: Placental 3A cytotrophoblast

label_protocol: cDNA was generated using the Qiagen miScript II RT kit.  Real-time PCR was performed using the Qiagen miRnome V16 PCR kit and appropriate SYBR green reagents

growth_protocol: Cells were maintained in a T-75 flask in a humified incubator at 37°C and 5% CO2

extract_protocol: MicroRNA was extracted using the Qiagen miRNEasy kit and trizol reagent

treatment_protocol: 70%-80% confluent cells were exposed to 25 uM H2O2 (5% of the IC50) for 4 hours

value: Exposed

value: Placenta


title: Patient 4


title: STD 017

type: genomic

city: Tianjin

first: Boyang

last: Cao

address: #23 HongDa Street

institute: Nankai Univ

hyb_protocol: All labeled PCR products were precipitated using 100% cold ethanol, centrifuged at 13,000 g for 10 min, washed with 75% ethanol, and dried at room temperature. The dried, labeled DNA was diluted in 16 µL of hybridization buffer ({25% formamide, 0.1% sodium dodecyl sulfate, 6x SSPE (1x SSPE contains 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA, pH 7.7)},  and hybridized with the prepared microarray at 50°C for 1.5 h. After hybridization, the slide was washed with solution A (1× SSC and 0.1% SDS) for 3 min, solution B (0.05× SSC) for 3 min, and solution C (95% ethanol) for 1.5 min.

scan_protocol: The microarray was dried under a gentle air stream and scanned with a laser beam of 532 nm using the GenePix biochip scanner 4100A (Axon Instruments, CA, USA) set to the following parameters: photomultiplier tube gain, 600, and pixel size, 5 µm.

data_processing: The signal-to-noise ratio (SNR) was calculated for each spot using the built-in software, GenePix Pro 6.0, with the threshold set at 3.0. A signal was considered positive when all the probes to a respective target gene generated hybridization signals above the SNR threshold.

molecule: genomic DNA

organism: human papillomavirus 33

source_name: HPV

label_protocol: To label the PCR products, 10 µL of the PCR products generated from the first run and the reverse primer and 0.3 µL of 25 nM Cy3-dUTP were added to the PCR mixture, and PCR was carried out using the same PCR conditions described for the first step.

extract_protocol: DNA was extracted from pure cultures using bacterial genomic DNA purification kit (Tiangen Biotech Co., Ltd., Beijing, China).

tag: source

value: HPV type 33


title: 3A cytotrophoblast mock

value: Unexposed


title: Patient 3


title: Normal case 5

source_name: normal chorionic villi

value: normal, control


title: Patient 2


title: C_hemibrain_10d_24h_rep2

description:
C_hemibrain_10d_24h_rep2
US09493743_251486829541_1_2  -C10-93 _10 DAY_24HR CONTROL.txt

value: hemibrain


title: Normal case 4


title: C_blood_5d_24h_rep3

description:
C_blood_5d_24h_rep3
US09493743_251486829494_1_3 -C5-129_5 DAY_24HR CONTROL.txt

value: blood


title: C_blood_5d_24h_rep4

description:
C_blood_5d_24h_rep4
US09493743_251486829494_1_4 -C5-130_5 DAY_24HR CONTROL.txt

value: control (C)


title: C_blood_5d_1.5w_rep5

description:
C_blood_5d_1.5w_rep5
US09493743_251486829537_1_1 -HC10-125_5 DAY_1.5 WEEK HOME CAGE CONTROL.txt


title: C_blood_10d_6w_rep4

description:
C_blood_10d_6w_rep4
US09493743_251486829498_1_1 -C10-50 _10 DAY_6 WEEK CONTROL.txt


title: C_blood_5d_24h_rep2

description:
C_blood_5d_24h_rep2
US09493743_251486829494_1_2 -C5-128_5 DAY_24HR CONTROL.txt


title: C_blood_5d_24h_rep5

description:
C_blood_5d_24h_rep5
US09493743_251486829495_1_1 -C5-131_5 DAY_24HR CONTROL.txt


title: Normal case 3


title: C_blood_5d_1.5w_rep2

description:
C_blood_5d_1.5w_rep2
US09493743_251486829495_1_3 -C5-133 _5 DAY_1.5 WEEK CONTROL.txt


title: STD 013

organism: human papillomavirus 39

value: HPV type 39


title: Patient 1


title: STD 016

organism: Mycoplasmoides genitalium

source_name: mycoplasma

value: Mycoplasma genitalium


title: C_blood_5d_1.5w_rep4

description:
C_blood_5d_1.5w_rep4
US09493743_251486829498_1_2 -HC10-126 _5 DAY_1.5 WEEK HOME CAGE CONTROL.txt

value: Strategen universal reference RNA (Cat. No. 740100)


title: STD 012

organism: human papillomavirus 35

value: HPV type 35


title: C_blood_10d_6w_rep3

description:
C_blood_10d_6w_rep3
US09493743_251486829497_1_4 -C10-47 _10 DAY_6 WEEK CONTROL.txt


title: C_blood_5d_1.5w_rep1

description:
C_blood_5d_1.5w_rep1
US09493743_251486829495_1_2 -C5-132 _5 DAY_1.5 WEEK CONTROL.txt


title: C_blood_5d_1.5w_rep3

description:
C_blood_5d_1.5w_rep3
US09493743_251486829495_1_4 -C5-134 _5 DAY_1.5 WEEK CONTROL.txt


title: C_blood_5d_24h_rep1

description:
C_blood_5d_24h_rep1
US09493743_251486829494_1_1 -C5-127_5 DAY_24HR CONTROL.txt


title: Normal case 2


title: STD 015

organism: human papillomavirus 58

value: HPV type 58


title: STD 014

organism: Alphapapillomavirus 13

value: HPV type 54


title: STD 011

organism: human papillomavirus 31

value: HPV type 31


title: Normal case 1

source_name: normal_chorionic villi

value: chorionic villi


title: STD 010

organism: human papillomavirus 18

value: HPV type 18


title: STD 009

organism: Human papillomavirus 16

value: HPV type 16


title: STD 008

organism: human papillomavirus 11

value: HPV type 11


title: C_blood_10d_6w_rep1

description:
C_blood_10d_6w_rep1
US09493743_251486829497_1_2 -C10-46 _10 DAY_6 WEEK CONTROL.txt


title: STD 007

organism: Human papillomavirus type 6

value: HPV type 6


title: C_blood_10d_6w_rep2

description:
C_blood_10d_6w_rep2
US09493743_251486829497_1_3 -C10-49 _10 DAY_6 WEEK CONTROL.txt


title: C_blood_10d_24h_rep2

description:
C_blood_10d_24h_rep2
US09493743_251486829536_1_3 -C10-95_10 DAY_24HR CONTROL.txt


title: STD 006

organism: Human alphaherpesvirus 2

source_name: HSV

value: HSV type 2


title: STD 004

organism: Chlamydia trachomatis

source_name: chlamydia

value: Chlamydia trachomatis


title: STD 005

organism: Human alphaherpesvirus 1

value: HSV type 1


title: C_blood_10d_24h_rep4

description:
C_blood_10d_24h_rep4
US09493743_251486829654_1_3 -C10-93_10 DAY_24HR CONTROL.txt

value: blood


title: STD 003

organism: Metamycoplasma hominis

value: Mycoplasma hominis


title: DAtfA NaCl

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

description: samples were taken at 0.5h

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom 4x44K array (design number 031140) for 17 hours at 65°Cand 10 rpm in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (FE SW 11.1) using one color scan setting for 1x44k array slides (Extended Dynamic Range, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: Agilent's Feature Extraction software (version 11.1) was used to obtaien prenormalised data. Prenormalised microarray data (median foreground, median background) was background corrected using the normexp+offset method suggested by Ritchie et al. (2007) followed by quantile normalization between arrays (Bolstad et al, 2003) as in Smyth (2005).

organism: Aspergillus nidulans

source_name: submerged culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling 6.5 version kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini spin column purification (QIAGEN). The quality of labeled cRNA was evaluated on the Agilent Bioanalyser 2100 and quantified using an ND-1000 NanoDrop spectrophotometer.

growth_protocol: A. nidulans strains THS30.3 TNJ 92.4 (pyrG89; pyroA4; delta-atfA::AfupyroA; veA+; AfuPyrG+) as DatfA strain and THS30.3 (pyrG89; pyroA+; veA+; AfupyrG+) as control were grown in shake flasks (500 ml) containing 100 ml Barratt’s minimal nitrate broth. Cultures were inoculated with 100 million conidia and were incubated at 37 ºC, 220 rpm for 16 h. Three cultures of the control strain were mixed and than divided into three equal parts. In case of the atfA strain, nine 16 h cultures were mixed, pellets were let think down and 600 ml supernatant was removed. The resulted 300 ml suspension (containing the total mycelia of the original nine cultures was divided into three equal parts. This way the starting dry cell masses (DCMs) were always between 4-5 g/l in case of both strains. Cultures were treated and were further incubated at 37 ºC, 220 rpm for 0.5 h.

extract_protocol: Total RNA was isolated from lyophilized mycelia following the instructions of Chomczynski (1993) (Trisol method). RNA samples from three parallel experiments were pooled in 1:1:1 ratios.

treatment_protocol: Cultures were treated with 0.12 mM MSB, 5 and 75 mM H2O2, 0.8 mM tBOOH, 1.8 mM diamide, 0.6 M NaCl or were kept untreated.

tag: stressor

value: 0.6 M NaCl


title: C_blood_10d_24h_rep3

description:
C_blood_10d_24h_rep3
US09493743_251486829536_1_4 -C10-97_10 DAY_24HR CONTROL.txt

organism: Mus musculus

value: control (C)


title: S.suis_hBMEC contact_3 h_rep4

city: Beijing

first: Huaijie

last: Hao

state: Beijing

address: NO. 20, Dongda Street, Fengtai District

institute: Institute of Microbiology and Epidemiology, Academy of Millitary Medicine Sciences

description:
4-Cy5_reference+Cy3_test_3h
technical replicate 2 of biologica replicate 2

hyb_protocol: Before hybridization, the microarray slides were prehybridized by incubation with 50 microliter of prehybridization buffer (5×buffer, 0.1% bovine serum albumin, and 0.1% sodium dodecyl sulfate (SDS)) at 42℃ for at least 2 h. After washing twice in water for 1 min and once in 95% ethanol for 1 min, the slides were dried with hot air. Dual-fluorescence-labeled probes were resuspended in hybridization solution (50% deionized formamide, 5×saline sodium citrate buffer (SSC), 0.1% SDS, 5×Denhardt’s solution, and 0.5 microgram/microliter of sheared salmon sperm DNA) and denatured at 98℃ for 7 min before applying to the microarray slides covered with a glass slip. Hybridization was carried out in a moisture chamber at 42℃ for 18-20 h. Then, the following washes were performed sequentially: 1× SSC with 0.06%   SDS for 2 min, 0.06×SSC for 2 min, and in ethanol for 1 min.

scan_protocol: Scanned using a GenePix personal 4100A microarray scanner

data_processing: The scan images were processed and data were further analyzed by uisng GenePix Pro 5.0 software combined with microsoft Excel software. Spots were analyzed by adaptive quantitation, and local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels of less than twofold of background intesity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods.

organism: Streptococcus suis 05ZYH33

source_name: S.suis serotype 2 strain 05ZYH33

label_protocol: At each growth condition, two total RNA samples were extracted from two indepent bacterial culture (biological replicates), respectively. And each RNA sample was used to synthesize two cDNA samples using Superscript III reverse transcriptase (Life technologies), random N6 primers and aminoallyl-dUTP. Then, each cDNA sample was individually chemically reacted with a monofunctional N-hydroxysuccinimidl (NHS) ester of either Cy3 or Cy5 (GE healthcare) (technical replicates).

growth_protocol: S.suis strain 05ZYH33 were inoculated and grown in THB medium to mid-log phase (OD600=0.4). After washed with PBS, S.suis strain 05ZY were resuspended in RPMI 1640 plus 10% FBS medium without antibiotics. Aliquots of bacteria were added to hBMEC monolayers cultured in 6-well plates and plates were centrifuged at 800 g for 5 min to make bacteria contact with hBMEC. Other aliquots of bacteria were added to 6-well plates without cells as control.

extract_protocol: S.suis strain 05ZY and hBMEC were collected with a cell scaper and immediately mixed with 2 volumes of RNAprotect Bacteria reagents (Qiagen). hBMEC cells were eliminated using RLT lysis buffer (Qiagen) that caused immediate and complete lysis of hBMEC cells but did not affect S.suis strain 05ZY. Total RNA of S.suis strain were extracted using MasterPure RNA purification kit without removing of contaminated DNA according to the manufacturer's instructions.

treatment_protocol: The bacteria were incubated with hBMEC cell monolayers for further 3 hour.

tag: growth condition

value: RPMI 1640, 10% FBS medium without antibiotics, 3 h

value: contact with hBMEC in RPMI 1640, 10% FBS medium without antibotics, 3 h


title: DAtfA tBOOH

description: samples were taken at 0.5h

value: 0.8 mM tert-butyl hydroperoxide


title: S.suis_hBMEC contact_3 h_rep3

description:
3-Cy3_reference+Cy5_test_3h
technical replicate 1 of biologica replicate 2


title: DAtfA MSB

description: samples were taken at 0.5h

value: 0.12 mM menadione sodium bisulfite


title: control NaCl

description: samples were taken at 0.5h


title: DAtfA low H2O2

description: samples were taken at 0.5h

value: 5 mM H2O2


title: DAtfA high H2O2

description: samples were taken at 0.5h

value: 75 mM H2O2


title: DAtfA diamide

description: samples were taken at 0.5h

value: 1.8 mM diamide


title: S.suis_hBMEC contact_3 h_rep1

description:
1-Cy3_reference+Cy5_test_3h
technical replicate 1 of biologica replicate 1


title: S.suis_hBMEC contact_1 h_rep4

description:
4-Cy5_reference+Cy3_test_1h
technical replicate 2 of biologica replicate 2

treatment_protocol: The bacteria were incubated with hBMEC cell monolayers for further 1 hour.

value: RPMI 1640, 10% FBS medium without antibiotics, 1 h

value: contact with hBMEC in RPMI 1640, 10% FBS medium without antibotics, 1 h


title: STD 002

organism: Ureaplasma

source_name: Ureaplasma

value: Ureaplasma


title: control diamide

description: samples were taken at 0.5h


title: S.suis_hBMEC contact_3 h_rep2

description:
2-Cy5_reference+Cy3_test_3h
technical replicate 2 of biologica replicate 1


title: C_blood_10d_24h_rep1

description:
C_blood_10d_24h_rep1
US09493743_251486829525_1_3 -C10-94_10 DAY_24HR CONTROL.txt

source_name: pooled whole mouse tissue cell line

value: Strategen universal reference RNA (Cat. No. 740100)


title: S.suis_hBMEC contact_1 h_rep2

description:
2-Cy5_reference+Cy3_test_1h
technical replicate 2 of biologica replicate 1

value: RPMI 1640, 10% FBS medium, 1 h


title: STD 001

organism: Neisseria gonorrhoeae

source_name: bacteria

value: Neisseria gonorrhoeae


title: srp1

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: Δsrp1 vs WT

hyb_protocol: Labelled cDNA was hybridized according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

scan_protocol: Arrays were scanned on GenePix 4000B scanner and images were quantified GenePic Pro 6.1 software

data_processing: Background subtraction and lowess normalization was applied according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

organism: Schizosaccharomyces pombe

source_name: ΔSPBC11C11.08-KanR (Bioneer)

label_protocol: Total RNA was reverse transcribed and labelled according to (Inada, M & Pleiss, JA. 2010, PMID 20946806)

growth_protocol: Cells were innoculated at an OD~0.05 in 25mL YES media and collected by vacuum filtration at mid-log-phase growth (OD~0.5). Where listed in SAMPLES, cells were shifted to 37°C for 5 minutes prior to harvesting.

extract_protocol: Total RNA was isolated by Acid-phenol extraction followed by ethanol precipitation and resuspension in 50uL TE buffer

tag: genotype/variation

value: srp1 deletion strain

tag: temperature shift (y/n)

value: N

source_name: ED666 (Bioneer)

value: Wild-type reference


title: DAtfA untreated

description: samples were taken at 0.5h

value: untreated


title: control tBOOH

description: samples were taken at 0.5h


title: control low H2O2

description: samples were taken at 0.5h


title: control high H2O2

description: samples were taken at 0.5h


title: SPAC1952.06C

description: ΔSPAC1952.06C vs WT (cells chifted to 37 for 5minutes before harvesting)

source_name: ΔSPAC1952.06c-KanR (Bioneer)

value: SPAC1952.06C deletion strain

value: Y


title: C3H10T1/2 cells exposed to 0.01 uM  Cr(VI)

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

country: India

institute: Indian Institute of Toxicology Research

description: C3H10T1/2 cells,exposed to 0.01uM  Cr(VI)

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent-Whole Genome Mouse 4x44k (AMADID: 14868) . 1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX V 11 75th Percentile Normalization

source_name: C3H10T1/2 cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

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

treatment_protocol: C3H10t1/2 cell were seeded into 25 cm2 flask (3 flasks for each group) in DMEM . Exposure of hexavalent chromium at dose of 1um and 0.01um was initiated 24h after seeding 2000 cells/flask. After 48h cells were rinsed 3 times with phosphate buffered saline (PBS) and fresh medium was added. Medium was changed twice weekly till 15 days. After 15 days cells were trypsinized and divided into two sets for different experiments. One   set of control and Cr6+ treated cells was seeded for soft agar assay to check the anchorage independent growth and other set of control and Cr6+ treated cells was proceeded for RNA isolation for microarray experiments.

value: C3H10T1/2 cells

tag: treatment

value: 0.01 uM Cr(VI)


title: C3H10T1/2 cells exposed to 1 uM  Cr(VI)

description: C3H10T1/2 cells,exposed to 1uM  Cr(VI)

growth_protocol: C3H10t1/2 cell were seeded into 25 cm2 flask (3 flasks for each group) in  DMEM

value: 1 uM Cr(VI)


title: S.suis_hBMEC contact_1 h_rep3

description:
3-Cy3_reference+Cy5_test_1h
technical replicate 1 of biologica replicate 2


title: lymphoid tissue inducer precursor LTiP.3.88

status: Public on Dec 30 2015

city: New York

first: Herman

last: Gudjonson

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

institute: Memorial Sloan Kettering Cancer Center

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+

data_processing: Normalization was performed using the average of three housekeeping genes: Actb, Gapdh, Hprt. Cells not expressing detectable levels of all three housekeeping genes were removed from further downstream analysis, along with a group of mast cell precursor contaminants. For quantification purposes, genes that were not detected were given a –ΔCt value of -30, close to the minimum value detected.

source_name: fetal liver

label_protocol: PCR assays were performed using a custom panel of lymphoid development factors. Preamplified cDNA was obtained after reverse transcription (15’ at 40°C, 15’ at 50°C and 15’ at 60°C), and preamplification (22 cycles : 15’’ at 95°C, 4’ at 60°C), and diluted 1 : 5 in TE pH8 Buffer (Ambion). Sample mix was as follows : diluted cDNA (2.9 μl), Sample Loading Reagent (0.29 μl, Fluidigm), TaqmanUniversal PCR Master Mix (3.3μl, Applied Biosystem) or Solaris qPCR Low ROX Master Mix (3.3 μl, GE Dharmacon). Assay mix was as follows: Assay Loading Reagent (2.5μl, Fluidigm), Taqman (2.5μl, Applied Biosystem) or Solaris (2.5μl, GE Dharmacon). 48.48 or 96.96 dynamic array integrated fluidic circuit (IFC, Fluidigm) was primed with control line fluid, and the chip was loaded with assays (either Taqman or Solaris) and samples using an HX IFC controller (Fluidigm). The experiments were run on a BiomarkHD (Fluidigm) for amplification and detection (2’ at 50°C, 10’ for Taqman reagents or 15’ for Solaris reagents at 95°C, 40 cycles : 15’’ at 95°C, 60’’ at 60°C).

extract_protocol: CellsDirectTM One-Step qRT-PCR Kit (Life Technologies)

tag: cell type

value: lymphoid tissue inducer precursor

tag: activation agent

tag: time


title: lymphoid tissue inducer precursor LTiP.3.53

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.77

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.65

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.64

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.27

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.54

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.89

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.5

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.41

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.28

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.3

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: lymphoid tissue inducer precursor LTiP.3.40

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: control untreated

description: samples were taken at 0.5h

tag: strain


title: C3H10T1/2 cells

description: C3H10T1/2 cells


title: SPAC30D11.14C

description: ΔSPAC30D11.14C vs WT

source_name: ΔSPAC30D11.14c-KanR (Bioneer)

value: SPAC30D11.14C deletion strain


title: srrm1

description: Δsrrm1 vs WT

source_name: ΔSPCC825.05c-KanR (Bioneer)

value: srrm1 deletion strain


title: control MSB

description: samples were taken at 0.5h

value: 0.12 mM menadione sodium bisulfite


title: S.suis_hBMEC contact_1 h_rep1

description:
1-Cy3_reference+Cy5_test_1h
technical replicate 1 of biologica replicate 1

value: RPMI 1640, 10% FBS medium without antibiotics, 1 h

value: contact with hBMEC in RPMI 1640, 10% FBS medium without antibotics, 1 h


title: common innate lymphoid cell precursor ILCP.3.99

description: Lin- IL7Rα+α4β7+PLZF+

value: common innate lymphoid cell precursor


title: common innate lymphoid cell precursor ILCP.3.97

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.86

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.84

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.96

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.72

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.98

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.60

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.62

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.50

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.49

description: Lin- IL7Rα+α4β7+PLZF+


title: lymphoid tissue inducer precursor LTiP.3.16

description: Lin- IL7Rα+α4β7+PLZF-CXCR5+


title: common innate lymphoid cell precursor ILCP.3.268

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.269

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.38

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.37

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.36

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.277

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.282

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.278

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.266

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.279

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.267

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.265

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.26

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.254

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.255

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.256

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.253

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.25

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.257

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.241

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.242

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.243

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.281

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.244

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.245

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.234

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.24

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.233

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.231

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.230

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.219

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.218

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.217

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.220

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.210

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.222

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.205

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.206

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.2

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.197

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.185

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.207

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.193

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.195

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.196

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.209

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.184

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.183

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.221

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.182

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.172

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.181

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.173

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.171

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.157

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.159

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.158

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.161

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.169

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.147

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.14

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.145

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.149

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.138

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.124

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.112

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.110

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.111

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.11

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.109

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.121

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.13

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.12

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.133

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.101

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.100

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.91

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.79

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.78

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.77

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.135

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.134

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.75

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.80

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.3.122

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.74

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.66

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.67

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.7

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.8

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.64

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.55

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.6

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.54

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.61

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.49

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.62

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.52

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.53

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.73

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.50

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.5

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.44

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.68

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.38

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.39

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.4

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.31

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.37

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.30

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.32

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.3

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.26

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.28

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.27

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.63

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.29

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.76

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.192

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.19

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.180

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.41

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.20

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.42

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.16

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.18

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.156

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.168

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.13

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.119

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.131

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.144

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.132

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.107

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.108

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.1

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.25

description: Lin- IL7Rα+α4β7+PLZF+


title: common innate lymphoid cell precursor ILCP.2.2

description: Lin- IL7Rα+α4β7+PLZF+


title: α4β7+ lymphoid precursor aLP.3.81

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-

value: alpha4-beta7+ lymphoid precursor


title: common innate lymphoid cell precursor ILCP.2.43

description: Lin- IL7Rα+α4β7+PLZF+


title: α4β7+ lymphoid precursor aLP.3.93

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.92

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: common innate lymphoid cell precursor ILCP.2.17

description: Lin- IL7Rα+α4β7+PLZF+


title: α4β7+ lymphoid precursor aLP.3.9

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.94

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.82

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: common innate lymphoid cell precursor ILCP.2.15

description: Lin- IL7Rα+α4β7+PLZF+


title: α4β7+ lymphoid precursor aLP.3.70

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.8

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.69

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.56

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.68

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.46

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.44

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.57

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.58

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.80

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.32

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.34

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.284

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.285

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.286

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.31

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.275

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.274

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.276

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.283

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.7

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.263

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.260

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.271

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.273

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.272

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.262

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.250

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.249

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.248

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.261

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.247

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.237

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.227

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.238

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.225

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.226

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.22

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.223

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.216

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.215

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.211

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.214

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.212

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.21

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.201

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.202

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.204

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.177

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.187

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.199

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.178

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.20

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.192

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.19

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.188

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.189

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.190

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.168

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.164

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.166

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.155

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.154

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.167

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.144

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.152

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.151

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.143

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.141

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.142

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.139

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.130

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.127

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.128

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.163

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.129

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.118

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.117

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.116

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.106

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.107

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.115

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.104

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.105

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.178

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.177

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.190

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.132

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.188

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.173

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.170

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.176

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.169

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.171

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.164

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.165

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.162

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.3.103

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.161

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.189

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.158

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.160

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.159

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.154

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.157

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.150

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.153

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.152

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.149

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.142

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.148

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.146

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.145

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.147

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.166

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.141

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.129

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.130

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.135

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.128

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.136

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.138

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Sub-cultured colony 1E of SLA64

city: Durham

first: Thomas

middle: D

last: Petes

state: NC

address: 213 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

description: SLA64.1 E SC WG

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. Probes that were flagged by the software were deleted from the analysis.

data_processing:
The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes.
Excel processed data file contents: The sample names (column A) show the name of the strain and isolate, the color of the sector (R1=red, W1=white), whether the strain was a sectored colony (labeled either R1 or W1) or a sub-cultured colony (SC), and the type of microarray used in the analysis. WG indicates that a whole-genome array was used, with densely spaced oligonucleotides located on every chromosome. VA indicates that an array with densely-spaced oligonucleotides on the left arm of chromosome V, the right arm of VIII, and chromosomes I and III was used. Column B has most of the information more explicitly. Column C shows the name of the .gpr files for each strain. All of the other columns are self-explanatory. Column R has the Excel file used to depict the hybridization ratios for our analysis.

organism: Saccharomyces cerevisiae

source_name: Sub-cultured colony grown for two days at 30 degrees

label_protocol: The methods used to label DNA were described in the Supplementary Information of St, Charles et al. (2012) Genetics 190: 1267-1284. DNA isolated from the experimental samples was labeled with Cy5-dUTP, and DNA from the control strains (PG311 and JSC23) was labed with Cy3-dUTP.

growth_protocol: For analysis of sectored colonies, we grew cells on solid medium lacking arginine and containing 10 micrograms/ml adenine and 120 micrograms/ml of canavanine. Cells were grown for three days at 30 degrees. For sub-culturing experiments, cells were grown from a single cell to a colony on rich solid growth medium (YPD) at 30 degrees.

extract_protocol: We extracted DNA from cultures derived from single colonies by the procedure described in St. Charles et al. (2012) Genetics 190: 1267-1284.

treatment_protocol: For red/white sectored colonies, we re-streaked cells from the sectors and analyzed single colonies derived from either the red or white sectors. The sub-cultured strains were streaked from single colonies, and allowed to form new colonies through 10 cycles of sub-cloning.

tag: color of sector/colony

value: pink

value: 2 days growth at 30

source_name: JSC23 control strain

tag: colony color

value: Pink

tag: sample type

value: Control heterozygous strain


title: α4β7+ lymphoid precursor aLP.2.126

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.127

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Sub-cultured colony 1C of SLA64

description: SLA64.1 C SC WG


title: Sub-cultured colony 1B of SLA64

description: SLA64.1 B SC WG


title: α4β7+ lymphoid precursor aLP.2.125

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Sub-cultured colony 7E of MD555

description: MD555-7 E SC WG

source_name: PG311 control strain


title: α4β7+ lymphoid precursor aLP.2.122

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.123

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Sub-cultured colony 7C of MD555

description: MD555-7 C SC WG


title: α4β7+ lymphoid precursor aLP.2.140

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Sub-cultured colony 7D of MD555

description: MD555-7 D SC WG


title: Sub-cultured colony 7A of MD555

description: MD555-7 A SC WG


title: Sub-cultured colony 1D of SLA64

description: SLA64.1 D SC WG


title: α4β7+ lymphoid precursor aLP.2.117

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Red sector of colony 1-2 derived from SLA64

description: SLA64.1-2 R1 WG

source_name: Sector of colony grown for two days at 30 degrees C

value: red


title: α4β7+ lymphoid precursor aLP.2.116

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.118

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.115

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.113

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.112

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: White sector of colony 1-1 derived from SLA64

description: SLA64.1-1 W1 WG

value: white


title: White sector of colony 23.5 derived from MD556

description: MD556-23.5 W1 WG


title: Red sector of colony 1-1 derived from SLA64

description: SLA64.1-1 R1 WG


title: White sector of colony 23.4 derived from MD556

description: MD556-23.4 W1 WG


title: Sub-cultured colony 1A of SLA64

description: SLA64.1 A SC WG


title: α4β7+ lymphoid precursor aLP.2.105

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.106

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.102

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: α4β7+ lymphoid precursor aLP.2.103

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Red sector of colony 23.4 derived from MD556

description: MD556-23.4 R1 WG


title: Sub-cultured colony 7B of MD555

description: MD555-7 B SC WG


title: White sector of colony 22.2 derived from MD556

description: MD556-22.2 W1 WG


title: White sector of colony 1-2 derived from SLA64

description: SLA64.1-2 W1 WG


title: White sector of colony 18.2 derived from MD556

description: MD556-18.2 W1 WG


title: Red sector of colony 22.2 derived from MD556

description: MD556-22.2 R1 WG


title: α4β7+ lymphoid precursor aLP.2.101

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Red sector of colony 15.8 derived from MD556

description: MD556-15.8 R1 WG


title: White sector of colony 15.8 derived from MD556

description: MD556-15.8 W1 WG


title: Red sector of colony 18.2 derived from MD556

description: MD556-18.2 R1 WG


title: White sector of colony 15.7 derived from MD556

description: MD556-15.7 W1 WG


title: α4β7+ lymphoid precursor aLP.2.110

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Red sector of colony 23.5 derived from MD556

description: MD556-23.5 R1 WG


title: α4β7+ lymphoid precursor aLP.2.104

description: Lin- IL7Rα+α4β7+PLZF-CXCR5-


title: Red sector of colony 15.7 derived from MD556

description: MD556-15.7 R1 WG


title: Amur sturgeon Heart

city: Guangzhou

first: zhang

middle: xiu

last: juan

state: Guangdong province

address: NO.105, Xingang west road, Haizhu district

institute: Guangdong Entomological institute

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

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

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

organism: Acipenser schrenckii

source_name: Amur sturgeon Heart

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using miRNeasy Kit(Qiagen, 217004), following the manufacturer's recommended protocol.

tag: tissue

value: Heart


title: White sector of colony 15.6 derived from MD556

description: MD556-15.6 W1 WG