title: OS195_nitrate_3

description:
X195DN; OS195DN
The same reference sample was labeled Cy3 on all arrays


title: OS185_oxygen_2

status: Public on Dec 15 2017

type: RNA

city: Norman

first: Jie

last: Deng

state: OK

address: 101 David L Boren Blvd, SRTC 2022

country: USA

institute: University of  Oklahoma

description:
X185BO; OS185BO
The same reference sample was labeled Cy3 on all arrays

hyb_protocol: For each hybridization, 10 μl of labeled cDNA from OS185 or OS195 was mixed with an equal volume of labeled reference cDNA. Hybridization reaction was at 50 °C for 18 h.

scan_protocol: Arrays were and scanned using an Axon GenePix 4000B scanner. For each array, Cy3 and Cy5 signals were normalized to the arithmetic mean of ratios using the GenePix software.

data_processing: Features having fewer than 50% of pixels with signal more than two standard deviations above background in both channels were excluded in downstream analysis. Genes showing significantly different expression levels between pair-wise comparisons among the three growth conditions were identified using Significance Analysis of Microarrays (Tusher et al., 2001).

molecule: total RNA

organism: Shewanella baltica

label_protocol: Resuspend pellets in 4.5uL 100 mM Na2CO3.  Mix with 4.5 uL Cy5 or Cy3, Incubate at 25C for 1.5 hrs, Clean-up with Qiagen Min-Elute PCR purification kit

growth_protocol: Cells were grown aerobically in HEPES medium or anaerobically with supplementation of 5 mM sodium nitrate or 10 mM sodium at 22 °C.

extract_protocol: RNA was extracted from cell pellets using a Qiagen RNeasy kit, followed by reverse transcription with random primers at 25 °C for 10 min, 42 °C for 70 min, and 70 °C for 15 min (Invitrogen). Labeled cDNAs were purified with QiaQuick MinElute PCR purification columns and eluted in 12 μl of RNase‐free water (Qiagen).

treatment_protocol: Aerobic growth, or anerobic nitrate or thiosulfate respiring growth condition

tag: strain

tag: growth condition

value: aerobic condition

source_name: Total RNA from cells of four strains OS155, OS185, OS195 and OS223 grown under conditions of respiring fumarate, nitrate, thiosulfate and under aerobic condition.


title: PBL_D7#1

city: La Jolla

first: John

middle: Justin

last: Milner

state: CA

address: 9500 Gilman Dr. MC0377

institute: UCSD

description: Gene expression data from various CD8+ T cell subsets

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: Data was processed in GenePattern.

label: Biotin

organism: Mus musculus

source_name: D7 PBL P14

label_protocol: Affy GeneChip WT cDNA synthesis kit/cRNA cleanup kit

extract_protocol: RNA was extracted using Trizol per manufacturer's instruction.

treatment_protocol: Naïve P14s were transferred into recipent mice and then infected with LCMV. P14 CD8+ T cell subsets were sorted on D7 or D35 of infection.

tag: tissue

value: PBL

tag: time point

value: day 7


title: OS195_nitrate_2

description:
X195FN; OS195FN
The same reference sample was labeled Cy3 on all arrays

value: anaerobic  nitrate respiratory condition


title: OS185_oxygen_3

description:
X185DO; OS185DO
The same reference sample was labeled Cy3 on all arrays


title: OS195_oxygen_3

description:
X195AO; OS195AO
The same reference sample was labeled Cy3 on all arrays


title: Kid_D7#1

source_name: D7 Kidney P14

value: Kidney


title: OS185_oxygen_1

description:
X185CO; OS185CO
The same reference sample was labeled Cy3 on all arrays


title: PBL_D7#2


title: Sp_D7#1

source_name: D7 Spleen P14

value: Spleen


title: OS185_nitrate_3

description:
X185CN; OS185CN
The same reference sample was labeled Cy3 on all arrays


title: Kid_D7#3


title: IEL_D7#2

source_name: D7 IEL P14

value: Small Intestine Epithelium


title: OS185_thiosulfate_2

description:
X185DT2; OS185DT2
The same reference sample was labeled Cy3 on all arrays

value: anaerobic thiosulfate respiratory condition


title: OS185_thiosulfate_1

description:
X185CT; OS185CT
The same reference sample was labeled Cy3 on all arrays


title: OS185_nitrate_1

description:
X185AN; OS185AN
The same reference sample was labeled Cy3 on all arrays


title: IEL_D7#3


title: OS185_nitrate_2

description:
X185DN; OS185DN
The same reference sample was labeled Cy3 on all arrays


title: Kid_D7#2


title: OS195_thiosulfate_2

description:
X195AT; OS195AT
The same reference sample was labeled Cy3 on all arrays


title: OS195_thiosulfate_3

description:
X195DT2; OS195DT2
The same reference sample was labeled Cy3 on all arrays


title: IEL_D7#1


title: HF_with_deband_repl4

status: Public on Dec 14 2017

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description:
27988_HF_DB_20
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 4 wk, repl 4
Gene expression after surgical manipulatoin

hyb_protocol: Hybridization of the labeled cDNAs was done in Agilent 2x gene expession hybrization buffer, agilent 10x blocking reagent and kreatech Kreablock onto Agilent 4x44K V2 microarrays at 65oC for 20 min

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner.

data_processing: Gridding and analysis of images was performed using Agilent Feature Extraction V11.5.1.1.

label_protocol: T7-MessageAmp II amplification and Kreatech ULS labeling with Cy5

extract_protocol: RNA was extracted from flash-frozen cardiac left ventricle sections using an Ika Turrax homogenizer and Trizol as per the manufacturer's directions.

tag: treatment

value: heart left ventricle

tag: gender

value: female

tag: age

value: 11 wk


title: sham_surgeries_repl6

description:
27977_sham_6
heart after sham surgeries at 0 wk and 2 wk, harvest at 4 wk, repl 6
Gene expression after surgical manipulatoin


title: sham_surgeries_repl5

description:
27976_sham_5
heart after sham surgeries at 0 wk and 2 wk, harvest at 4 wk, repl 5
Gene expression after surgical manipulatoin


title: HF_with_sham_deband_repl1

description:
27978_HF_shDB_7
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 4 wk, repl 1
Gene expression after surgical manipulatoin


title: HF_with_deband_repl3

description:
27987_HF_DB_17
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 4 wk, repl 3
Gene expression after surgical manipulatoin


title: HF_with_deband_repl1

description:
27985_HF_DB_8
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 4 wk, repl 1
Gene expression after surgical manipulatoin


title: HF_with_deband_repl5

description:
27989_HF_DB_23
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 4 wk, repl 5
Gene expression after surgical manipulatoin


title: HF_with_sham_deband_repl5

description:
27982_HF_shDB_24
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 4 wk, repl 5
Gene expression after surgical manipulatoin


title: OS195_thiosulfate_1

description:
X195CT; OS195CT
The same reference sample was labeled Cy3 on all arrays


title: sham_surgeries_repl1

description:
27972_sham_1
heart after sham surgeries at 0 wk and 2 wk, harvest at 4 wk, repl 1
Gene expression after surgical manipulatoin


title: HF_with_deband_repl6

description:
27990_HF_DB_28
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 4 wk, repl 6
Gene expression after surgical manipulatoin


title: sham_surgeries_repl3

description:
27974_sham_3
heart after sham surgeries at 0 wk and 2 wk, harvest at 4 wk, repl 3
Gene expression after surgical manipulatoin


title: HF_with_sham_deband_repl6

description:
27983_HF_shDB_25
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 4 wk, repl 6
Gene expression after surgical manipulatoin


title: HF_with_sham_deband_repl7

description:
27984_HF_shDB_27
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 4 wk, repl 7
Gene expression after surgical manipulatoin


title: Sirpa_Pos_Mature_6

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

hyb_protocol: Equal amounts of labeled material were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays. Hybridizations were performed for 14 hours and the arrays were scanned using the Agilent microarray scanner in the UCSF Shared Microarray Core Facility.

scan_protocol: Arrays were scanned using an Agilent 2uM scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v10.5 software. The dataset was normalized using the quantile normalization method, and the one-way ANOVA model was used to estimate relevant statistics for the comparisons of interest. The R package (limma in bioconductor) was utilized for these procedures.

label_protocol: The RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits (using manufacturer's protocol).

extract_protocol: mRNA was isolated by using mRNA-easy kit (Qiagen).

treatment_protocol: We sorted four subsets of dendritic cells in mouse thymus based on their expression of Sirpa and their maturation status

value: thymus

tag: cell type

value: sorted dendritic cells

tag: maturation status

value: mature

tag: sirpa status


title: sham_surgeries_repl4

description:
27975_sham_4
heart after sham surgeries at 0 wk and 2 wk, harvest at 4 wk, repl 4
Gene expression after surgical manipulatoin


title: OS185_thiosulfate_3

description:
X185AT; OS185AT
The same reference sample was labeled Cy3 on all arrays


title: HF_with_sham_deband_repl4

description:
27981_HF_shDB_15
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 4 wk, repl 4
Gene expression after surgical manipulatoin


title: HF_with_deband_repl2

description:
27986_HF_DB_12
heart after TAC+MI at 0 wk and TAC removal at 2 wk, harvest at 4 wk, repl 2
Gene expression after surgical manipulatoin


title: HF_with_sham_deband_repl3

description:
27980_HF_shDB_10
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 4 wk, repl 3
Gene expression after surgical manipulatoin


title: sham_surgeries_repl2

description:
27973_sham_2
heart after sham surgeries at 0 wk and 2 wk, harvest at 4 wk, repl 2
Gene expression after surgical manipulatoin


title: HF_with_sham_deband_repl2

description:
27979_HF_shDB_9
heart after TAC+MI at 0 wk and sham surgery at 2 wk, harvest at 4 wk, repl 2
Gene expression after surgical manipulatoin


title: Sirpa_Pos_Immature_3

value: immature


title: Sirpa_Pos_Immature_5


title: Sirpa_Neg_Mature_2


title: Sirpa_Neg_Immature_4


title: embryonic stem cells, biological rep1

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

description: Gene expression data from human embryonic stem cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affy Gene Chip Scanner 3000 7G.

data_processing:
The probe level intensities were adjusted by quantile normalization and gene expression measures were summarized by the robust multi-array analysis (RMA) approach with Bioconductor software
Statistical analysis of gene expression data used the LIMMA package for R
Genes for further investigation were identified by adjusted P values ≤0.01 (controlling expected false-discovery rates to not more than 1%) and fold difference in mean expression ≥2.0 to compare PP cells with other cell samples.

label: biotin

organism: Homo sapiens

source_name: H1 embryonic stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured according to Bandi et al. J Cell Sci 2012; 125:1274.

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

treatment_protocol: Cells were not specifically treated.

value: H1 embryonic stem cells


title: primary culture, biological rep1

description:
Gene expression data from primary culture of fetal hepatocytes isolated from mid-gestation human livers
P0A

source_name: Cultured cells

growth_protocol: Cells were either freshly isolated or cultured according to Inada et al. J Cell Sci 2008; 121:1002-13.

value: Fetal liver

tag: cell culture

value: primary culture (P0)


title: primary culture, biological rep3

description:
Gene expression data from primary culture of fetal hepatocytes isolated from mid-gestation human livers
P0C


title: embryonic stem cells, biological rep3


title: sixth passage, biological rep1

description:
Gene expression data from the culture of fetal hepatocytes isolated from mid-gestation human livers after 6 passages
P6A

value: cultured for 6 passages


title: freshly isolated cells, biological rep2

description:
Gene expression data from fresh fetal hepatocytes isolated from mid-gestation human livers
PPB

source_name: Primary cells

value: freshly isolated cells


title: Sirpa_Neg_Immature_7


title: Sirpa_Pos_Mature_1


title: meso-endoderm cells, biological rep3

description: Gene expression data from spontaneously differentiated embryonic stem cells

source_name: Spontaneously differentiated embryonic stem cells

value: Spontaneously differentiated cells with meso-endoderm phenotype


title: F5

city: Beijing

first: Jian

last: Li

address: Dahua Road

country: China

institute: Beijing Hospital

description: Human liver biopsies from 5 patients with NAFLD and 5 healthy control subjects were performed with patient consent within the diagnostic workup of NAFLD

hyb_protocol: According to the Agilent lncRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Human liver biopsies

label_protocol: The lncRNAs were labeled using the Agilent human lncRNA+mRNA Array V4.0. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to lncRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: liver

value: Male

tag: disease state

value: NAFLD


title: Sirpa_Neg_Mature_8


title: sixth passage, biological rep3

description:
Gene expression data from the culture of fetal hepatocytes isolated from mid-gestation human livers after 6 passages
P6C


title: meso-endoderm cells, biological rep1


title: F3


title: meso-endoderm cells, biological rep2


title: F4


title: third passage, biological rep3

description:
Gene expression data from the culture of fetal hepatocytes isolated from mid-gestation human livers after 3 passages
P3C

value: cultured for 3 passages


title: third  passage, biological rep2

description:
Gene expression data from the culture of fetal hepatocytes isolated from mid-gestation human livers after 3 passages
P3B


title: primary culture, biological rep2

description:
Gene expression data from primary culture of fetal hepatocytes isolated from mid-gestation human livers
P0B


title: sixth  passage, biological rep2

description:
Gene expression data from the culture of fetal hepatocytes isolated from mid-gestation human livers after 6 passages
P6B


title: embryonic stem cells, biological rep2


title: chondrocyte cell line:  HC-402-05a, biological rep3

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from human chondrocyte cell line:  HC-402-05a

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized by the Affymetrix Human Gene 2.1 ST ArrayStrip (20 h, 48°C).

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

source_name: chondrocyte cell line:  HC-402-05a (Merck Millipore, Germany)

label_protocol: The entire procedure for preparing RNA for hybridization was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA). One-hundred ng of RNA was subjected to a two-step cDNA synthesis reaction using random primers extended by the T7 RNA polymerase promoter sequence. Synthesis of cRNA was performed using in vitro transcription (16 h, 40°C). cRNA was purified and re-transcribed into cDNA, which was biotin labeled and fragmented using the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: GPCCi001-A were cultured on mouse embryonic fibroblasts (MEFs) feeder layer in standard hiPSC growth medium containing the following: Dulbecco's modified Eagle's medium (DMEM) F12 with L-glutamine; 20% KnockOut Serum Replacement; 1% non-essential amino acid solution; 0.1 mM β-mercaptoethanol; and 0.5% penicillin-streptomycin. Prior to use, the medium was supplemented with fibroblast growth factor 2 (10 ng/ml). ChiPS were cultured Dulbecco's modified Eagle's medium (DMEM) F12 with L-glutamine; 10% FBS and  0.5% penicillin-streptomycin. HC and ACC cells were cultured in  Dulbecco's modified Eagle's medium (DMEM) F12 with L-glutamine; 10% FBS and  0.5% penicillin-streptomycin.

extract_protocol: Total RNA isolation was carried out using the modified Chomczynski method with TRI Reagent (Sigma, St Louis, MO, USA) and RNeasy Mini Elute cleanup Kit (Qiagen, Hilden, Germany), according to the manufacturer's guidelines. The concentration of the total RNA was determined spectrophotometrically by measuring absorbance at 260 nm. The purity of the isolated RNA was determined by using the 260/280 nm absorption ratio, which was > 1.8, as assumed. (NanoDrop spectrophotometer, Thermo Scientific, MA, USA). The quality and integrity of RNA was also checked in a Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) ranged from 8.5 to 10, with a mean of 9.2 (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: GPCCi001-A were cultured for 1 week in a pro-mesodermal medium consisting of the following: DMEM F12 with L-Glutamine, 10% FBS supplemented with FGF-2 (10 ng/ml); BMP-4 (10 ng/ml); and PDGF-BB (10 ng/ml). Then, the medium was replaced with a standard chondrogenic medium  supplemented with TGF-β3 (10 ng/ml) for another week. After that, the medium was replaced with a chondrogenic medium supplemented with TGF-β3 (10 ng/ml) and IGF-1 (10 ng/ml)  for one final week of enhanced chondrogenesis in vitro. We used a standard chondrogenic medium, as follows: DMEM F12 with L-Glutamine; 10% FBS; 50 μM L-proline; 50 μM ascorbic acid; 1 mM sodium pyruvate; 1% ITS + Premix; 1% P/S and 10−7 M dexamethasone.

value: chondrocyte


title: third passage, biological rep1

description:
Gene expression data from the culture of fetal hepatocytes isolated from mid-gestation human livers after 3 passages
P3A


title: N5

value: healthy control


title: chondrocyte cell line:  HC-402-05a, biological rep 1


title: freshly isolated cells, biological rep1

description:
Gene expression data from fresh fetal hepatocytes isolated from mid-gestation human livers
PPA


title: freshly isolated cells, biological rep3

description:
Gene expression data from fresh fetal hepatocytes isolated from mid-gestation human livers
PPC


title: F2


title: F1


title: N4


title: N3


title: primary articular cartilage chondrocyte cell culture , biological rep2

description: Gene expression data from human primary articular cartilage chondrocyte cell culture


title: primary articular cartilage chondrocyte cell culture , biological rep1


title: primary articular cartilage chondrocyte cell culture , biological rep3


title: N2


title: chondrocyte cell line:  HC-402-05a, biological rep2


title: WT cell without VSV infection

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

description: Mouse peritoneal macrophage cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 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 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting.

data_processing: The signal data have been completed after all the Feature Extracted Software processing steps (used for GeneSpring GX (ver11.5.1) data normalization and further analysis)

source_name: Expression profiling in WT cell without VSV infection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse peritoneal macrophages (PM) from wild type (WT) and IFN-I receptor deficient (Ifnar-/-) mice were obtained 3 days after i.p. injected with the thioglycolate and were cultured in DMEM medium with 10% fetal bovine serum.

extract_protocol: RNA was harvested using Trizol reagent.

treatment_protocol: For 2×10^7 cells, 10ul VSV were added to cell culture medium for 9 hours or IFNb was added for 80 mins.

value: 7 weeks

value: peritoneum

value: macrophage

tag: genotype

value: wildtype


title: N1


title: lncRNA-ACOD1-/- liver tissues from mice infected without VSV infection (rep-1)

description:
Expression profiling in liver tissues
KO VSV0h rep-1

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Gene1.0 ST Array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA(Robust Multi-chip Average ) method.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: Mouse liver orgens from wild type (WT) and lncRNA-ACOD1 deficient (lncRNA-ACOD1-/-) mice were isolated 12 hours (12h) after i.p. injected with VSV or without VSV infection (0h).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set

treatment_protocol: After grinding in liquid nitrogen, these liver tissue powders were mixed with Trizol (50mg/1ml).

tag: genotype/variation

tag: infection

value: control


description: Mouse peritoneal macrophage cells

source_name: Expression profiling in WT cell with recombinant mouse IFNb for 80 mins


description: Mouse peritoneal macrophage cells

source_name: Expression profiling in IFN-I receptor deficient (Ifnar-/-) cells with VSV infection

value: Ifnar-/-


title: lncRNA-ACOD1+/+ liver tissues from mice infected with VSV for 12 hrs (rep-2)

description:
Expression profiling in liver tissues
WT VSV12h rep-2

value: VSV


title: lncRNA-ACOD1+/+ liver tissues from mice infected without VSV infection (rep-2)

description:
Expression profiling in liver tissues
WT VSV0h rep-2


title: lncRNA-ACOD1+/+ liver tissues from mice infected without VSV infection (rep-1)

description:
Expression profiling in liver tissues
WT VSV0h rep-1


title: lncRNA-ACOD1-/- liver tissues from mice infected without VSV infection (rep-2)

description:
Expression profiling in liver tissues
KO VSV0h rep-2


title: Experiment4 C57/BL6 mice [G3]

status: Public on Dec 13 2017

type: SRA

city: Utrecht

first: Benedetta

last: Artegiani

address: Upsalalaan 8

country: Netherlands

institute: Hubrecht

description: Hippocampus after depletion of neurons

library_source: transcriptomic

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutt files contain UMI barcode normalised abundance counts
Supplementary_files_format_and_content: Table_S4.csv: normalized transcript counts for all the single cells used in this study after filtering out cells  expressing less than 1500 transcripts/cell. The table S4 contains only filtered data, so it could well be none of the cells from the E4 library were retained after filtering.

source_name: Murine brain

extract_protocol:
Live negative single cells (for GluR1 and Cd24 Abs) were sorted in 384-  well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a  24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA  kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: wild-type

value: Brain


title: Experiment2-second plate C57/BL6 mice [H]

description: Hippocampus after depletion of neurons_the FASTQ files are not the original presented in the paper, but the resequecning of the original libraries used in the paper


title: WT cell with VSV infection

description: Mouse peritoneal macrophage cells

source_name: Expression profiling in WT cell with VSV infection


title: Experiment4 C57/BL6 mice [G4]

description: Hippocampus after depletion of neurons


title: Experiment5-first plate C57/BL6 mice [I]

description: Hippocampus after depletion of neurons


title: lncRNA-ACOD1+/+ liver tissues from mice infected with VSV for 12 hrs (rep-1)

description:
Expression profiling in liver tissues
WT VSV12h rep-1


title: Experiment C57/BL6 mice older than 12 months [old]

description: Hippocampus of mice older than 12 months after depletion of neurons


title: Experiment4 C57/BL6 mice [G2]

description: Hippocampus after depletion of neurons


title: Experiment4 C57/BL6 mice [G1]

description: Hippocampus after depletion of neurons


title: Experiment3-third plate C57/BL6 mice [F3]

description: Hippocampus after depletion of neurons


title: Experiment5-second plate C57/BL6 mice [L]

description: Hippocampus after depletion of neurons


description: Mouse peritoneal macrophage cells

source_name: Expression profiling in IFN-I receptor deficient (Ifnar-/-) cells without VSV infection


title: Control

description: RNA was isolated from the mixed samples of liver tissues from 6 male db/db mice and 6 age-matched male wild-type (WT) mice

source_name: C57 mice

label_protocol: The lncRNAs were labeled using the Agilent mouse lncRNA+mRNA Array V1.0. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to lncRNA arrays.

value: wild type

value: livers

value: 8 weeks


title: DB

source_name: db/db mice

value: db/db

value: Male


title: lncRNA-ACOD1-/- liver tissues from mice infected with VSV for 12 hrs (rep-2)

description:
Expression profiling in liver tissues
KO VSV12h rep-2

value: liver


title: Experiment3-third plate C57/BL6 mice [F2]

description: Hippocampus after depletion of neurons


title: lncRNA-ACOD1-/- liver tissues from mice infected with VSV for 12 hrs (rep-1)

description:
Expression profiling in liver tissues
KO VSV12h rep-1


title: Experiment3-third plate C57/BL6 mice [F4]

description: Hippocampus after depletion of neurons


title: Experiment2-first plate C57/BL6 mice [C3]


title: Experiment2-first plate C57/BL6 mice [C4]


title: Experiment2-first plate C57/BL6 mice [C2]


title: Experiment1-second plate C57/BL6 mice [B7]

description: Hippocampus after depletion of neurons


title: Experiment1-first plate C57/BL6 mice [A4]

description: Hippocampus after depletion of neurons


title: Experiment2-first plate C57/BL6 mice [C1]


title: Experiment1-first plate C57/BL6 mice [A3]

description: Hippocampus after depletion of neurons


title: Experiment1-second plate C57/BL6 mice [B5]

description: Hippocampus after depletion of neurons


title: Experiment1-second plate C57/BL6 mice [B6]

description: Hippocampus after depletion of neurons


title: Experiment1-second plate C57/BL6 mice [B8]

description: Hippocampus after depletion of neurons


title: NestinGFP mouse

description: GFP+ cells from the hippocampus of NestinGFP mice

value: NestinGFP


title: Experiment3 C57/BL6 mice D3

description: Hippocampus after depletion of neurons


title: Experiment3 C57/BL6 mice E1

description: Hippocampus after depletion of neurons


title: Experiment1-first plate C57/BL6 mice [A1]

description: Hippocampus after depletion of neurons


title: Experiment3 C57/BL6 mice E4

description: Hippocampus after depletion of neurons


title: Experiment3 C57/BL6 mice D4

description: Hippocampus after depletion of neurons


title: Experiment3 C57/BL6 mice E3

description: Hippocampus after depletion of neurons


title: Experiment1-first plate C57/BL6 mice [A2]

description: Hippocampus after depletion of neurons


title: Experiment3 C57/BL6 mice D2

description: Hippocampus after depletion of neurons


title: Experiment3 C57/BL6 mice E2

description: Hippocampus after depletion of neurons


title: Experiment3 C57/BL6 mice D1

description: Hippocampus after depletion of neurons


title: B. breve UCC2003 grown on modified rogosa media v. B. breve DRBB25 grown on modified rogosa media.

type: genomic

city: Cork

first: Francesca

last: Bottacini

address: Western Road

department: APC Microbiome Institute & School of Microbiology

country: Ireland

institute: University College Cork

description: CGH array

hyb_protocol: Labelled total gDNA was hybridised as described in the Agilent manual Two-Color Microarray-Based Gene Expression Analysis (v4.0) (publication no. G4140-90050) to the B. breve UCC2003 microarray slides overnight at 65 °C.

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

molecule: genomic DNA

organism: Bifidobacterium breve

source_name: B. breve UCC2003 grown in Modified Rogosa until OD.600 of 0.7

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 was grown in filtered reinforced clostridial medium (RCM; Oxoid Ltd.) and subcultured in modified Rogosa medium. Bifidobacterial cultures were incubated at 37°C, anaerobically in a modular, atmosphere-controlled system (Davidson and Hardy, Belfast, Ireland) to an optical density OD600 of 0.7.

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Cells were collected by centrifugation at 4,500rpm for 5 minutes at room temperature prior to storage in the -80 degree freezer.

source_name: B. breve strain grown in modified Rogosa until OD.600 of 0.7


title: B. breve UCC2003 grown on modified rogosa media v. B. breve DRBB29 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB57 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve DRBB31 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve DRBB26 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 082W4-8 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve DRBB27 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 165W4-19 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 200W4-13 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 180W8-3 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve DRBB28 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 215W4-47a grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 139W4-23 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 144W4-15 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve DRBB30 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 017W4-21 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB55 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB54 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB51 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB53 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB50 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB52 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB44 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB48 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB43 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB49 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB42 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve 017W4-39 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB46 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB41 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB29 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB27 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB39 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB28 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB31 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB24 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB10 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB13 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB35 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB23 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB18 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB12 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB26 grown on modified rogosa media.

description: CGH array


title: Experiment3-third plate C57/BL6 mice [F1]

description: Hippocampus after depletion of neurons


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB09 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB19 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB21 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB25 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB38 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB17 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB30 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB16 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB14 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB06 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB15 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB07 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB11 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB05 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB20 grown on modified rogosa media.

description: CGH array


title: PBSiv_MPP_2

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 transcriptome (ENSEMBL v 81) using STAR
Gene-level expression estimates were calculated using featureCount (Liao et al., 2014).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

source_name: Multipotent progenitors

growth_protocol: Six to ten-week old C57BL/6J, Rag1-/, Ccr2/-, and CD45.1+ B6 mice were purchased from Jackson Laboratories or bred at the RI-MUHC, Montreal, QC, Canada. All experiments were performed with male mice, except parabiosis, which was performed on female mice. All animal studies were conducted in accordance with the guidelines of and approved by the Animal Research Ethics Board of McGill University (project ID: 5860).

extract_protocol: RNA-sequencing libraries were prepared using either the Illumina TruSeq protocol (for BMDMs) or the SMARTer® Stranded RNA-Seq Kit (for HSCs) and sequenced with single-end 100bp reads on an Illumina HiSeq2500.

treatment_protocol:
Throughout the paper, mice were intravenously (iv) or subcutaneously (sc) vaccinated with 1x106 singlesuspended BCG in 100μl PBS, unless otherwise indicated. Image stream analyses were used to identify what cells in the BM were infected with BCG. For the Mtb challenges, mice were either infected with ~50 CFU of Mtb H37Rv in a nose-only aerosol exposure unit (Intox), or with ~1000 CFU Mtb H37Rv via intratracheal instillation. BMDMs were derived as described previously (Coulombe et al., 2014) and infected with Mtb H37Rv at an MOI of 1.
C57BL/6J mice were sc or iv vaccinated with 1x106 singlesuspended BCG or iv PBSinjected. After four weeks, we generated BMDMs that were infected with H37Rv (MOI 0.5) and 0.5x106 cells were intratracheally transferred into naive Rag1-/- mice (Divangahi et al., 2009;; 2010). Parabiosis was performed as previously described (Ensan et al., 2016). Female CD45.1+ B6 mice were either PBSinjected or iv vaccinated with 1x106 singlesuspended BCGTice. After four weeks, CD45.1+ mice were joined to naive, female, weightmatched, and co-housed Ccr2-/- mice through skin suture and attachment of the front and hind legs. Six weeks post surgery the Ccr2-/- mice were intratracheally infected with H37Rv (~1000 CFU). CD45.1+ B6 mice were either PBS-injected or BCG iv-vaccinated (1x106 bacteria). After four weeks, BM cells were harvested and 4x106 cells were intravenously injected into CD45.2+ C57BL/6J mice 16 hours post irradiation with 9 Gy. Chimeric mice were aerosol infected with ~50 CFU Mtb H37Rv after 14 weeks when the hematopoietic compartment was reconstituted as determined by flow cytometry.

tag: mouse id

value: PBS iv

value: Multipotent progenitors

tag: infection status

value: Non Infected


title: PBSiv_MPP_1


title: CD11brGFP-LPS3

city: Québec

first: Hejer

last: Boutej

state: Québec

address: 2601, de la Canardière

department: NEUROBIOLOGY

country: Canada

institute: LAVAL University

description: Ribosomes-associated mRNAs

hyb_protocol: Samples were hybridized with Affymetrix Mouse Gene 2.0 ST microarray. The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Command Console Software (AGCC) (Affymetrix, Santa Clara, CA) to produce the probe cell intensity data (CEL).

data_processing: The image data were analyzed by using the Affymetrix Expression Console Software to perform the quality control, the background subtraction and the normalization of probe set intensities with the method of Robust Multiarray Analysis (RMA). For the visualization of microarray results we used Affymetrix Transcriptome Analysis Console (TAC) Software. A mRNA was considered as variant if the fold change between the two compared samples was higher than 1.2 and the associated ANOVA p-value was lower than 0.05.

source_name: CD11brGFP mice; n=5

label_protocol: Ribosomes-associated mRNA (100 ng per sample) was labeled using the Affymetrix GeneChip® WT cDNA Synthesis and Amplification Kit protocol as described by the manufacturer (Affymetrix).

growth_protocol: CD11brGFP transgenic mice were used at 2-3 months old.

extract_protocol: mRNA was extracted using the Translational Affinity Purification (TRAP) protocol. The purification of the mRNA from the beads was perfomed according to the Absolutely RNA Nanoprep Kit's instructions

treatment_protocol: CD11brGFP transgenic mice received LPS (5mg/kg) or Saline for 24 hrs. Each group contains 5 mice with equal male/female ratio. Three biological replicates were used for control and for LPS injection.

value: injected with LPS (5mg/kg) for 24 hrs

value: Transgenic mice expressing Flag/EGFP-RPL10a under the control of CD11b


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB36 grown on modified rogosa media.

description: CGH array

tag: strain


title: PBSiv_HSC_2

source_name: Hematopoietic stem cell

value: Hematopoietic stem cell


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB02 grown on modified rogosa media.

description: CGH array


title: PBSiv_MPP_4


title: BCGiv_MPP_4

value: BCG iv


title: PBSiv_HSC_1


title: PBSiv_BMDM_3_NI

source_name: Bone marrow-derived macrophages

value: Bone marrow-derived macrophages


title: PBSiv_MPP_3


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB03 grown on modified rogosa media.

description: CGH array


title: CD11brGFP-LPS1

description: Ribosomes-associated mRNAs


title: PBSiv_HSC_4


title: CD11brGFP-LPS2

description: Ribosomes-associated mRNAs


title: PBSiv_BMDM_4_NI


title: CD11brGFP-CTL1

description: Ribosomes-associated mRNAs

value: injected with Saline


title: PBSiv_BMDM_1_NI


title: PBSiv_BMDM_4_Mtb

value: Mtb


title: BCGiv_HSC_4


title: PBSiv_BMDM_2_NI


title: PBSiv_BMDM_1_Mtb


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB04 grown on modified rogosa media.

description: CGH array

value: wild type


title: BCGiv_HSC_2


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB08 grown on modified rogosa media.

description: CGH array


title: PBSiv_BMDM_3_Mtb


title: BCGiv_BMDM_3_NI


title: BCGiv_HSC_1


title: BCGiv_MPP_2


title: BCGiv_BMDM_2_Mtb


title: BCGiv_BMDM_1_Mtb


title: B. breve UCC2003 grown on modified rogosa media v. B. breve UCC2003 grown on modified rogosa media.

description: CGH array


title: B. breve UCC2003 grown on modified rogosa media v. B. breve NRBB01 grown on modified rogosa media.

description: CGH array


title: CD11brGFP-CTL2

description: Ribosomes-associated mRNAs


title: BCGiv_BMDM_3_Mtb


title: BCGiv_MPP_1


title: BCGiv_MPP_3


title: BCGiv_BMDM_4_NI


title: CD11brGFP-CTL3

description: Ribosomes-associated mRNAs


title: PBSiv_BMDM_2_Mtb


title: PBSiv_Mtb_H3K4me1_rep2

library_source: genomic

data_processing:
Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped to the mouse genome reference sequence (GRCm38/mm10) and non-uniquely mapped reads and PCR duplicates were removed.
Peaks were first called on ChIP-seq samples (using respective input IPs as a control) using the MACS2 software suite (Zhang et al., 2008) with the added parameters “g mm -q 0.05 -keep-dup all”. For comparison between samples, all peaks from each sample were merged to provide one set of combined peaks. For quantification of the combined peaks, we used the bamutils count command from NGSUtils (Breese and Liu, 2013) to count the number of overlapping reads for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read count, CPM and RPKM values for each sample.

growth_protocol: Six- to ten-week old C57BL/6J, Rag1-/-, Ccr2-/-, and CD45.1+ B6 mice were purchased from Jackson Laboratories or bred at the RI-MUHC, Montreal, QC,Canada. All experiments were performed with male mice, except parabiosis, which was performed on female mice. All animal studies were conducted in accordance with the guidelines of and approved by the Animal Research Ethics Board of McGill University (project ID: 5860). Throughout the paper, mice were intravenously (iv) or subcutaneously (sc) vaccinated with 1x106 single-suspended BCG in 100µl PBS, unless otherwise indicated. Image stream analyses were used to identify what cells in the BM were infected with BCG. For the Mtb challenges, mice were either infected with ~50 CFU of Mtb H37Rv in a nose-only aerosol exposure unit (Intox), or with ~1000 CFU Mtb H37Rv via intratracheal instillation. BMDMs were derived as described previously (Coulombe et al., 2014).

extract_protocol:
DNA was extracted using the PureGene DNA extraction kit (Gentra Systems).
Samples from BCGvaccinated and non-vaccinated, Mtb-infected and non-infected BMDMs were crosslinked with 37% w/v formaldehyde for 20 minutes at RT and immediately quenched for 5 minutes with 1M Glycine at RT. The formaldehyde fixed samples were then sonicated to 150500 bp using an E220 sonicator (Covaris), and subsequently ChIP-DNA was prepared using a manual chromatin immunoprecipitation method with AntibodiesAntigen incubation for 18 hours, followed by bead incubation for 150 minutes, and 7 5minute washing steps. Approximately 1x106 cells were used for each ChIP and ~50,000 cells for the input. The following antibodies were used: H3K4me1 (Company: CST, Cat. No.: 5326P, Lot No.: 1), H3K4me3 (Thermo Fisher Scientific, MA5-11199), H3K27ac (Abcam, Ab4729, Lot No.: GR2005631). ChIP and Input libraries were prepared using the MicroPlex Library Preparation Kit v2 (C05010013, Diagenode), with alterations including: PCR enrichment (9 to 18 cycles) prior to size selection, and use of Ampure beads for size selection (250-350 bp).

treatment_protocol: BMDMs (1x10^6 cells) were seeded in 6-well plates supplemented with RPMI without penicillin/streptomycin (1 ml), and incubated overnight at 37°C with 5% CO2. Next day, cells were infected with H37Rv (MOI 1), unless otherwise indicated. Cells were incubated for 4 hours at 37°C with 5% CO2. Subsequently, cells were washed 3x with sterile PBS, and then were supplemented with RPMI without penicillin/streptomycin. CFUs were enumerated at 4 hours, day 3 and day 5 post infection.

tag: histone mark


title: PBSiv_Mtb_H3K4me3_rep2


title: PBSiv_Mtb_H3K4me3_rep3


title: BCGiv_BMDM_4_Mtb

tag: tissue


title: PBSiv_Mtb_H3K4me1_rep3


title: BCGiv_BMDM_1_NI


title: PBSiv_NI_H3K27ac_rep3


title: PBSiv_NI_H3K4me1_rep1


title: LUHMES cells, untreated, day 6 of differentiation rep2

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

country: Germany

institute: University of Cologne

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

source_name: human neuronal cells

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer

extract_protocol: Total RNA has  been isolated with  Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

treatment_protocol: all untreated cells

value: female

value: neuronal cells

tag: time

value: day 6 of differentiation

tag: cell state

value: differentiated state


title: BCGiv_NI_H3K27ac_rep2_rep2

tag: treatment


title: BCGiv_Mtb_H3K4me1_rep3


title: PBSiv_Mtb_H3K4me3_rep1


title: LUHMES cells, untreated, day 6 of differentiation rep1

tag: gender


title: PBSiv_NI_H3K4me1_rep3


title: BCGiv_NI_H3K27ac_rep3


title: BCGiv_NI_H3K4me1_rep3


title: BCGiv_BMDM_2_NI


title: PBSiv_Mtb_H3K4me1_rep1


title: PBSiv_Mtb_H3K27ac_rep3


title: PBSiv_NI_H3K27ac_rep2


title: BCGiv_NI_H3K4me1_rep2


title: PBSiv_Mtb_H3K27ac_rep2


title: BCGiv_HSC_3


title: BCGiv_NI_H3K4me3_rep2


title: BCGiv_Mtb_H3K27ac_rep2


title: BCGiv_NI_H3K4me1_rep1


title: BCGiv_Mtb_H3K4me3_rep3


title: BCGiv_NI_H3K27ac_rep1


title: BCGiv_Mtb_H3K4me3_rep2


title: LUHMES cells, untreated, proliferating precursor state rep2

tag: cell type

value: control

value: proliferating state


title: LUHMES cells, untreated, day 6 of differentiation rep3


title: BCGiv_Mtb_H3K4me1_rep1


title: LUHMES cells, untreated, proliferating precursor state rep1


title: BCGiv_Mtb_H3K4me3_rep1


title: PBSiv_NI_H3K4me3_rep1

value: PBS iv


title: PBSiv_NI_rep1

data_processing:
ATAC-seq reads were trimmed for adapter sequences and low quality score bases and were mapped to the mouse reference genome. Mapping was performed using BWA-MEM (Li and Durbin, 2009) in paired-end mode at default parameters. Only reads that were properly paired and had an unique alignment (mapping quality > 10) were retained. PCR duplicates were removed using Picard tools
Peaks were first called on ATAC-seq samples using the MACS2 software suite (Zhang et al., 2008) with the added parameters “g mm -q 0.05 -keep-dup all”. For comparison between samples, all peaks from each sample were merged to provide one set of combined peaks. For quantification of the combined peaks, we used the bamutils count command from NGSUtils (Breese and Liu, 2013) to count the number of overlapping reads for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read count, CPM and RPKM values for each sample.

extract_protocol:
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
ATAC-seq libraries were generated from 100,000 BMDMs, as previously described (Buenrostro et al., 2013) and sequenced on an Illumina HiSeq 2500 using 100-bp paired-end reads. We performed ATAC-seq on non-infected BMDMs from four PBS-control mice and three BCG-iv vaccinated mice.

treatment_protocol: BMDMs (1x106 cells) were seeded in 6-well plates supplemented with RPMI without penicillin/streptomycin (1 ml), and incubated overnight at 37°C with 5% CO2. Next day, cells were infected with H37Rv (MOI 1), unless otherwise indicated. Cells were incubated for 4 hours at 37°C with 5% CO2. Subsequently, cells were washed 3x with sterile PBS, and then were supplemented with RPMI without penicillin/streptomycin. CFUs were enumerated at 4 hours, day 3 and day 5 post infection.


title: LUHMES cells, untreated, day 6 of differentiation rep4


title: LUHMES cells, untreated, day 3 of differentiation rep4

value: day 3 of differentiation


title: LUHMES cells, untreated, day 3 of differentiation rep1


title: LUHMES cells, untreated, day 3 of differentiation rep2


title: MDS-RAS

first: ai

middle: ping

last: jiang

address: No.151, Libing Rd., Zhangjiang Hi-tech Park, Pudong

institute: Shanghai Biotechnology Corporation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

source_name: MDS-RAS sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD34+ cell samples isolated for microarray analysis from eight patients and one healthy individual

treatment_protocol: Heparinized bone marrow samples were obtained by aspiration from the posterior iliac crest after informed consent. Fresh bone marrow was processed immediately after aspiration to select the CD34+ cells or mononuclear cells (MNC) within 4 h.After washing in Hanks balanced salt solution (HBSS; Life Technologies, Gaithersburg, MD), cells were resuspended in magnetic-activated cell separation (MACS) buffer (phosphate-buffered saline [PBS] supplemented with 0.5% bovine serum and 2 mM EDTA [ethylenediaminetetraacetic acid]). After incubation with human immunoglobulin (Ig; Fc receptor [FcR] blocking reagent) and monoclonal hapten-conjugated anti-CD34 antibody for 15 minutes at 6°C to 12°C, cells were washed and resuspended in 500 μL of MACS buffer. Magnetically labeled cells were enriched by passing samples through the positive selection column and magnetic field

tag: subject status

value: myelodysplastic syndrome (MDS) patient

tag: mds subtype

value: RAS

value: bone marrow

value: CD34+ cell


title: MDS-RA1

source_name: MDS-RA sample

value: refractory anemia (RA)


title: MDS-RAEB2

source_name: MDS-RAEB sample

value: refractory anemia with excessive blast (RAEB)


title: PBSiv_NI_rep4


title: BCGiv_NI_rep2

value: BCG iv


title: MDS-RAEB1


title: AML1

source_name: AML sample

value: acute myeloid leukemia (AML)


title: PBSiv_Mtb_H3K27ac_rep1

value: Mtb


title: B. breve UCC2003 grown on modified rogosa media v. B. breve CNCM I-4321 grown on modified rogosa media.

description: CGH array

value: wild type

value: CNCM I-4321


title: LUHMES cells, untreated, day 3 of differentiation rep3

value: female

value: neuronal cells


title: LUHMES cells, untreated, proliferating precursor state rep3

value: control


title: LUHMES cells, untreated, proliferating precursor state rep4

value: proliferating state


title: PBSiv_NI_rep2

value: PBS iv


title: MDS-RA2


title: BCGiv_NI_rep1


title: CAA

source_name: CAA sample

value: chronic aplastic anemia (CAA)


title: BCGiv_NI_H3K4me3_rep1

value: Non Infected


title: BCGiv_Mtb_H3K27ac_rep1


title: BCGiv_NI_rep3


title: NORMAL

source_name: normal people sample

value: normal; healthy


title: Stage7-reference rep5

city: Montpellier

first: Thierry

last: JOET

address: 911 Avenue Agropolis

department: DIADE

country: France

institute: IRD (Institut de Recherche pour le Développement)

description: Each stage was compared to a unique reference (an equimolar pool of each of the seven seed developmental stage)

hyb_protocol: Prior to hybridization, excess oligonucleotide was removed from the arrays by shaking them twice1min in 0.2% SDS. Arrays were then washed 2 times in distilled water. The two labelled aRNA were added to microarray hybridization buffer version 2 (GE Healthcare) in a final concentration of 50% formamide, denaturated at 95°C for 3 min and applied to the microarrays in individual chambers of an automated slide processor (GE Healthcare). Hybridization was carried out at 37°C for 12 h. Hybridized slides were washed at 37°C successively with 1X SSC, 0.2% SDS for 10 min, twice with 0.1X SSC, 0.2% SDS for 10 min, with 0.1X SSC for 1 min and with isopropanol before air drying.

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation.

data_processing: ArrayVision software was used for feature extraction. Spots with high local background or contamination fluorescence were flagged manually. A local background was calculated for each spot as the median values of the fluorescence intensities of 4 squares surrounding the spot. This background was subtracting from the foreground fluorescence intensity.

organism: Coffea arabica

source_name: PC30 - ST7

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according the manufacturer's instructions.

growth_protocol: Experiments were performed with seeds of Coffea arabica cv. ‘Laurina’. Developing seeds were harvested from plants grown at Grand Tampon, Reunion Island (1 015 m asl.) with an average temperature of 18.5°C and mean annual rainfall of 1 300 mm. Coffee trees were planted in 2002 without shade and were in their third (2007) production cycle (about 2 m high) and not yet subject to low or high annual variations in yield. Plant spacing was 2 m between rows and 1 m within rows. Fertilizers were applied and pests and diseases were controlled according to locally recommended practices.

extract_protocol: Total RNA was isolated using the RNeasy™ Lipid Tissue Kit (Qiagen, Hilden Germany) according to the recommendations of the manufacturer. A DNase treatment (RNase free DNase set, Qiagen) was carried out on the RNA during the extraction protocol. Each RNA sample was quantified on a Nanodrop (ThermoFisher Scientific Inc., Waltham MA USA). RNA quality was confirmed on a Bioanalyser (Agilent technologies, CA, USA).

treatment_protocol: Experiments were performed with developing seeds of Coffea arabica cv. ‘Laurina’. For transcriptome analysis, three independent biological samples (pools of ca. 200 seeds) were collected on 20 trees randomly selected in the plot for each of the seven developmental stages studied : ST1 (30–60 days after flowering, DAF); ST2 (60–90 DAF), seed mainly formed of aqueous perisperm; ST3 (90–120 DAF), aqueous endosperm tissue growing and progressively replacing the perisperm in the locule; ST4 (120–150 DAF), soft milky endosperm; ST5 (150–210 DAF), hard white endosperm while the remaining perisperm resembles a thin green pellicle surrounding the endosperm; ST6 (210–240 DAF), seed from ripening cherry fruits with pericarp turning yellow; ST7 (>240 DAF), mature seed from cherry fruits with red pericarp turning purple.

tag: cultivar

value: Laurina

value: Seed

tag: developmental stage

value: Stage 7

source_name: reference mix

tag: developemental stage

value: Equimolar mix of seven developmental stages (Stage1 to Stage 7)


title: Stage7-reference rep3

source_name: PC29 - ST7


title: Stage7-reference rep6


title: Stage5-reference rep2

source_name: PC22 - ST5

value: Stage 5


title: Stage5-reference rep4

source_name: PC23 - ST5


title: Stage7-reference rep2

source_name: PC28 - ST7


title: Stage6-reference rep1

source_name: PC25 - ST6

value: Stage 6


title: Stage7-reference rep1


title: Stage6-reference rep4

source_name: PC26 - ST6


title: Stage7-reference rep4


title: Stage6-reference rep3


title: AML2

value: myelodysplastic syndrome (MDS) patient

value: acute myeloid leukemia (AML)

value: bone marrow

value: CD34+ cell


title: Stage5-reference rep1


title: Stage6-reference rep6

source_name: PC27 - ST6


title: Stage5-reference rep3


title: Stage6-reference rep5


title: Stage4-reference rep6

source_name: PC21 - ST4

value: Stage 4


title: Stage5-reference rep6

source_name: PC24 - ST5


title: Stage3-reference rep5

source_name: PC18 - ST3

value: Stage 3


title: Stage3-reference rep4

source_name: PC17 - ST3


title: Stage4-reference rep3

source_name: PC20 - ST4


title: Stage4-reference rep1

source_name: PC19 - ST4


title: Stage3-reference rep2

source_name: PC16 - ST3


title: Stage6-reference rep2


title: Stage4-reference rep4


title: Stage5-reference rep5


title: Stage4-reference rep2


title: Stage3-reference rep6


title: Stage2-reference rep4

source_name: PC14 - ST2

value: Stage 2


title: Stage2-reference rep1

source_name: PC13 - ST2


title: Stage3-reference rep1

source_name: reference mix


title: Stage1-reference rep6

source_name: Pcc - ST1

value: Stage 1


title: Stage4-reference rep5


title: Psgl1-/- DsRed+ CD11b+ CD45hi cells [GrKO_6]

city: Berlin

first: Ria

last: Göttert

address: Charitéplatz 1

department: experimental Neurology

institute: Charité

description: bone marrow chimeras

hyb_protocol: For hybridisation, the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) was used. 600 ng of each cRNA was hybridised on 8x60K microarrays at 65 °C for 17 h using Agilent's recommended hybridisation chamber and oven. Afterwards, microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37 °C) Gene Expression Wash Buffer 2 for one minute.

scan_protocol: The SurePrint G3 Gene Expression Microarray Scanner (Agilent Technologies) at a resolution of 3 micron was used to generate a 20 bit TIFF file

data_processing: Prior to normalisation of the background substracted signals, the following processing steps are performed: (1) removal of signals from control probes (2) mean of signals from replicate probes (3) mean of signals from all probes of a target. Data of all samples were quantile normalised using the ranked mean quantiles according to Bolstad et al. A comparison of normalisation methods for high density oligonucleotide array data based on variance and bias, Bioinformatics (19), 2003, Oxford Univ Press. Briefly, the mean signal of each target was ranked relative to all other targets. The ranked signal value was replaced with the mean quantile value of the same rank. Thus, the highest value in all samples became the mean of the highest values, the second highest value became the mean of the second highest values, and so on. Raw and normalised data were provided in different sheets of one Excel file. Further annotation was added to the data indicating miRNA target genes (sourced from miRTarBase release 6.1).

source_name: Psgl1-/- DsRed+ CD11b+ CD45hi cells

label_protocol: For labeling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) was used to generate fluorescent cRNA (complementary RNA). For 1st strand synthesis, random primer was used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labeled with cyanine 3-CTP was performed. Yield of cRNA ranges from 12.5 to 14.4 µg, Cy3 incorporation rate ranges from 35.5 to 38.1 pmol/µg.

extract_protocol: All RNA samples underwent a quality control to determine the quality and quantity of total RNA. This quality control was done with the 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 Pico Kit for total RNA samples. For quantity control, a photometric measurement with the Nanodrop 2000 spectrophotometer (Thermo Scientific) was used. A sample's quality was evaluated based on the Bioanalyzer's RNA integrity number (RIN) and the two distinct peaks representing 18S and 28S rRNA as well as the overall electropherogram. After successfully passing quality control, RNA samples were used for further processing.

treatment_protocol: Brain tissue was dissected and dissociated with the Neuronal Tissue Dissociation Kit (Miltenyi Biotec). CD11b+ cells were magnetically sorted using myelin removal in conjunction with CD11b microbeads (Miltenyi Biotec). Then, cells were sorted for the following markers: Pi- DsRed+ CD11b+ Ly6G- CD3- CD45hi.

value: ischemic brain

tag: timepoint

value: 7 days post 30 min MCAo

tag: genotype/variation

value: Psgl1-/- DsRed+ CD11b+ CD45hi cells


title: Psgl1-/- DsRed+ CD11b+ CD45hi cells [GrKO_8]

description: bone marrow chimeras


title: ISC

first: Pingping

last: Zhu

state: Beijing

address: Datun Road 15#

institute: Institute of Biophysics, Chinese Academy of Sciences

description: This is intestinal stem cells (ISCs)

hyb_protocol: hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000 and analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

data_processing: All resulting .CEL files for each array type were processed as a single group via the Affymetrix Power Tools (APT) package using sketch normalization and the RMA algorithm to summarize probeset signal.

source_name: Lgr5GFP+ ISCs

label_protocol: 10 mg of cRNA was carried into the second cycle, first strand cDNA synthesis reaction. 5.5 mg of single-stranded cDNA was fragmented and biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: cell collection protocol: 2´105 Non-ISCs and ISCs were isolated from Lgr5GFP-CreERT2 mice. For FACS enrichment, 8 week-old mice were anesthetized and small intestine cells were collected, followed by ILCreg cell sorting through a BD AriaIII sorter.

value: intestinal stem cells (ISCs)

tag: genotype

value: Wild-type


title: Stage3-reference rep3

value: Laurina

value: Seed


title: Psgl1+/+ DsRed+ CD11b+ CD45hi cells [GrWT_4]

description: bone marrow chimeras

source_name: Psgl1+/+ DsRed+ CD11b+ CD45hi cells

value: Psgl1+/+ DsRed+ CD11b+ CD45hi cells


title: Psgl1-/- DsRed+ CD11b+ CD45hi cells [GrKO_7]

description: bone marrow chimeras


title: ISC_LncG6Mut

description: This is LncGata6 mutant ISCs

source_name: LncGata6Mut Lgr5GFP+ ISCs

value: LncGata6 mut


title: Psgl1+/+ DsRed+ CD11b+ CD45hi cells [GrWT_3]

description: bone marrow chimeras


title: Stage1-reference rep5

value: Equimolar mix of seven developmental stages (Stage1 to Stage 7)


title: Stage1-reference rep4

source_name: PC12 - ST1


title: Stage2-reference rep5

source_name: PC15 - ST2


title: Stage1-reference rep3


title: Stage2-reference rep2


title: Stage2-reference rep3


title: quiescent beta cell, replicate 2

city: Vic

first: NOELIA

last: TELLEZ

state: Barcelona

address: Can Baumann. Carretera de Roda, 70

department: Department of Medicine

country: Spain

institute: UVIC-UCC

description:
Q_2
isolated pancreatic cells islets

hyb_protocol: 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized to Agilent SurePrint G3 Rat Gene Expression v2 8x60K Microarray (amadid ID: 074036) for 40h at 65ºC in a rotating Agilent hybridization oven

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).  The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Rattus norvegicus

source_name: rat pancreas

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of double stranded cDNA using the SureTag Complete DNA Labeling kit (Agilent 5190-4240) according to manufacturer’s instructions

extract_protocol: Total RNA was extracted with RNeasy FFPE kit (Qiagen, Crawley, UK) according to manufacturer’s instructions with the following variation. Cell sorted cells were directly collected in PKD buffer, immediately treated with 200μg/ml proteinase K (Qiagen) at 56ºC for 3h with continuous shaking

value: beta cells

value: pancreas


title: replicating beta cell, replicate 3

description:
R_4
isolated pancreatic cells islets


title: quiescent beta cell, replicate 3

description:
Q_4
isolated pancreatic cells islets


title: Psgl1-/- DsRed+ CD11b+ CD45hi cells [GrKO_5]

description: bone marrow chimeras


title: ISC_EhfKO

description: This is Ehf knockout ISCs

source_name: Ehf-/- Lgr5GFP+ ISCs

value: Ehf knockout


title: replicating beta cell, replicate 2

description:
R_2
isolated pancreatic cells islets


title: Stage2-reference rep6


title: Non-ISC

description: This is non-intestinal stem cells (non-ISCs)

source_name: Lgr5GFP- non-ISCs

value: non-intestinal stem cells (non-ISCs)


title: B. breve UCC2003 grown on Difco MRS medium (log phase) - Replicate 1

type: mixed

description: Tiling arrays - replicate 1

hyb_protocol: Labelled total gDNA was hybridized as described in the Agilent manual Two-Color Microarray-Based Gene Expression Analysis (v4.0) (publication no. G4140-90050) to the B. breve UCC2003 microarray slides overnight at 65 °C.

data_processing:
Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).
DNA-microarray data sets were processed as previously described (Garcia De La Nava et al., 2003). Differential signal intensity between gDNA (baseline) and mRNA (transcriptome) were analyzed using the Limma package implemented in the statistical environment R (https://cran.r-project.org)

organism: Bifidobacterium breve UCC2003

source_name: B. breve UCC2003 grown in Difco MRS OD.600 of 0.5

label_protocol: Labelling was performed using the Kreatech ULS labelling kit according to the manufacturer’s instructions (Kreatech, Amsterdam, The Netherlands)

growth_protocol: Bifidobacterium breve UCC2003 was grown in Difco MRS. Bifidobacterial cultures were incubated at 37°C, anaerobically in a modular, atmosphere-controlled system (Davidson and Hardy, Belfast, Ireland) to an optical density OD600 of 0.5.

extract_protocol: Bacterial DNA and RNA was isolated as described previously (O' Connell Motherway et al., 2011).

value: wild type


title: Psgl1+/+ DsRed+ CD11b+ CD45hi cells [GrWT_2]

description: bone marrow chimeras


title: human converted naïve state pluripotent stem cell

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

country: Japan

institute: Kindai Universty Hospital

hyb_protocol: Following fragmentation, 2.3 mg of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45℃ on GeneChip Clariom S array, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene chip Scanner 7G, affymetrix.

data_processing: Command Console CHP file version 1

source_name: human induced pluripotent stem cell

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Gene Chip WT PLUS Reagent kit, Affymetrix).

tag: cell line

value: 409b2 hiPSC


title: WT spinal cord_P4_LMC_#3

status: Public on Dec 12 2017

city: New York

first: George

middle: Z

last: Mentis

address: 630 W 168th Street

department: Dept of Pathology&Cell Biology

institute: Columbia University

description:
WT LMC_#3
5513075037_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data was translated into intensities with Illumina Genome Studio. Intensities were normalized with Lumi using the variance stabilizing transformation (VST) method followed by Robust Spline Normalization.
probes were included if their probability of detection was less than or equal to 0.05.

source_name: spinal cord

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total cellular RNA was isolated using Absolutely RNA Nanoprep Kit (Stratagene).cDNA amplification  and performed with WT-Ovation Pico RNA Amplification System (NuGen).

tag: age

tag: strain

value: FVB

value: spinal cord

tag: group (tissue subtype)

value: Lateral Motor Column


title: replicating beta cell, replicate 1

description:
R_1
isolated pancreatic cells islets

tag: tissue


title: WT spinal cord_P4_LMC_#1

description:
WT LMC_#1
5513075037_A


title: pre-conversion hiPSCs

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


title: Psgl1+/+ DsRed+ CD11b+ CD45hi cells [GrWT_1]

description: bone marrow chimeras

value: ischemic brain

value: 7 days post 30 min MCAo


title: SMA spinal cord_P4_MMC_#2

description:
SMA MMC_#2
5513075042_E

value: Medial Motor Column


title: SMA spinal cord_P4_LMC_#3

description:
SMA LMC_#3
5513075037_F


title: Alveolar_macrophage_H6_at_T1_biological replicate_6

city: Edinburgh

first: Anna

middle: Eleonora

last: Karagianni

address: Easter Bush Campus

country: United Kingdom

institute: The Royal (Dick) School of Veterinary Studies and The Roslin Institute

description: Gene expression data from untreated alveolar macrophages derived from Standardbred racehorses during the training period (T1)

hyb_protocol: Biotin labelled transcripts were prepared for hybridisation following the Nugen protocol for Gene Titan hybridisation (Affymetrix, Santa Clara, CA), using the Affymetrix Gene Titan Hybridization Wash and Stain Kit for WT Array Plates (PN 901622). The samples were hybridised to Equine Gene 1.0 ST Array Strips from Affymetrix, including 30,559 probe sets.

scan_protocol: The appropriate Hyb-Wash Scan protocol and the Gene Titan Hyb-Wash Stain Kit for the reagents (Affymetrix, Santa Clara, CA) was performed

data_processing: The data were analyzed with Partek Genomic Suite 6.6 and BioLayout Express3D softwares and  using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Equus caballus

source_name: Untreated alveolar macrophages at T1

label_protocol: Total RNA (50ng) was amplified by the Nugen Pico SL kit (Agilent, the Netherlands). Two and a half micrograms (2.5μg) of the cDNA produced was biotin labelled using the Nugen Encore labelling kit.

growth_protocol: Alveolar macrophages were isolated from the lungs from systemically healthy Standardbred racehorses using standard protocol

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

treatment_protocol: Isolated cells from the bronchoalveolar and peritoneal lavage were seeded in plastic plates at 1x106 cells per mL in complete medium: RPMI-1640 medium supplemented with GlutaMAX™-I Supplement (Invitrogen Ltd, Paisley, UK), penicillin/streptomycin (Invitrogen Ltd, Paisley, UK) and 10% heat-inactivated horse serum (HS - Sigma Aldrich, cat no: H1138). Plates were incubated at 370C in 5% CO2 overnight. The following day, nonadherent cells were removed.

tag: time point

value: T1 during training period (1.5 to 7 weeks in training)


title: Alveolar_macrophage_H2_at_T1_biological replicate_2


title: Alveolar_macrophage_H6_at_T0_biological replicate_6

description: Gene expression data from untreated alveolar macrophages derived from Standardbred racehorses before the training period (T0)

source_name: Untreated alveolar macrophages at T0

value: T0 before training period


title: Stage1-reference rep2

source_name: PC11 - ST1

value: Laurina

value: Seed

value: Stage 1


title: B. breve UCC2003 grown on Difco MRS medium (log phase) - Replicate 2

description: Tiling arrays - replicate 2


title: Alveolar_macrophage_H5_at_T1_biological replicate_5


title: Alveolar_macrophage_H3_at_T1_biological replicate_3


title: WT spinal cord_P4_MMC_#2

description:
WT MMC_#2
5513075042_B


title: Alveolar_macrophage_H4_at_T1_biological replicate_4


title: quiescent beta cell, replicate 1

description:
Q_1
isolated pancreatic cells islets

value: beta cells


title: Alveolar_macrophage_H3_at_T0_biological replicate_3


title: SMA spinal cord_P4_MMC_#1

description:
SMA MMC_#1
5513075042_D


title: Stage1-reference rep1

source_name: reference mix

value: Equimolar mix of seven developmental stages (Stage1 to Stage 7)


title: WT spinal cord_P4_LMC_#2

description:
WT LMC_#2
5513075037_B


title: SMA spinal cord_P4_MMC_#3

description:
SMA MMC_#3
5513075042_F


title: SMA spinal cord_P4_LMC_#2

description:
SMA LMC_#2
5513075037_E


title: WT spinal cord_P4_MMC_#1

description:
WT MMC_#1
5513075042_A


title: WT spinal cord_P4_MMC_#3

description:
WT MMC_#3
5513075042_C.


title: Alveolar_macrophage_H4_at_T0_biological replicate_4


title: SMA spinal cord_P4_LMC_#1

description:
SMA LMC_#1
5513075037_D


title: Alveolar_macrophage_H5_at_T0_biological replicate_5


title: Alveolar_macrophage_H2_at_T0_biological replicate_2


title: Alveolar_macrophage_H1_at_T1_biological replicate_1


title: Alveolar_macrophage_H1_at_T0_biological replicate_1


title: converted naïve state pluripotent stem cell rep1

data_processing:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46


title: converted naïve state pluripotent stem cell rep2


title: Patient_14

city: Memphis

first: Tong

last: Lin

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

institute: St. Jude Children's Research Hospital

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using BeadArray reader

data_processing: R library minfi

label: Cy5, Cy3

source_name: Tumor resection

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

value: malignant rhabdoid tumor

tag: subject id

tag: location

value: CNS Tumor


title: mouse epiblast stem cell rep2

source_name: mouse epiblast stem cell

tag: cell type

value: epiblast stem cell


title: Patient_12_2

value: Extra-CNS Tumor


title: mouse epiblast stem cell rep1


title: Patient_7_1


title: Patient_4


title: Patient_12_1


title: Patient_8_2


title: Patient_3


title: Patient_5


title: Patient_9_1


title: Patient_15_2


title: Patient_19_1


title: Patient_19_2


title: Patient_16


title: Patient_2


title: Patient_9_2


title: mouse embryonic stem cell rep2

source_name: mouse embryonic stem cell

value: embryonic stem cell


title: Patient_7_2


title: Patient_18


title: mouse embryonic stem cell rep1


title: Patient_21


title: Patient_13


title: Patient_6


title: Patient_15_1


title: Patient_11_2


title: Patient_10


title: Patient_11_1


title: Liver, finishing, rep8

status: Public on Dec 11 2017

city: Lexington

first: James

last: Matthews

state: KY

address: 207 W.P. Garrigus Buidling

department: Animal and Food Sciences

institute: University of Kentucky

description: steer

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Gene 1.0 ST Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the .cel files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO, USA). The algorithm of Robust Multichip Averaging data were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

source_name: Liver, finishing

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

growth_protocol: The growth protocol has been described in the overall design section above.

extract_protocol: Trizol extraction of total RNA was perfomed according to the manufacturer's instruction.

treatment_protocol: The treatment protocol has been described in the overall design section above.

value: Liver

tag: gender

value: male

value: finishing


title: Liver, finishing, rep7

description: steer


title: Liver, finishing, rep5

description: steer


title: Liver, finishing, rep4

description: steer


title: Liver, growing, rep8

description: steer

source_name: Liver, growing

value: growing


title: Patient_8_1


title: Liver, finishing, rep3

description: steer


title: Patient_20


title: Liver, growing, rep6

description: steer


title: Liver, finishing, rep1

description: steer


title: Liver, growing, rep5

description: steer


title: Liver, growing, rep3

description: steer


title: Liver, growing, rep7

description: steer


title: Liver, growing, rep2

description: steer


title: G3_blood_normal_rep1

city: Tongliao

first: Batudeligen

last: Duan

state: Inn Mongolian

address: 1742 Huolinhe Street

department: Affiliated hospital of Inner Mongolian University for the nationalities

institute: Institute of clinical pharmacology of traditional Mongolian Medicine

hyb_protocol: 1 Preheat the heat block to 95°C.  2 Preheat the Illumina Hybridization Oven to 48°C and set the rocker speed to 5.Assemble the Hybridization Chambers  3 .Place the resuspended MSA4 plate on the heat block to denature the samples at 95°C for  20 minutes.   4 Remove the BeadChips from 2°C to 8°C storage, leaving the BeadChips in their plastic bags  and mylar packages until you are ready to begin hybridization3 During the 20-minute incubation, prepare the Hyb Chambers.   a Place the BeadChip Hyb Chamber gaskets into the BeadChip Hyb Chambers.   b Dispense 400 μl PB2 into the humidifying buffer reservoirs in the Hyb Chambers.  c After you fill the Hyb Chamber reservoirs with PB2, place the lid on the Hyb Chamber  right away to prevent evaporation. It is not necessary to lock the lid.  d Leave the closed Hyb Chambers on the bench at room temperature until the BeadChips  are loaded with DNA sample. Load BeadChips into the Hyb Chamber within 1 hour.4 After the 20-minute incubation, remove the MSA4 plate from the heat block and place it on  the benchtop at room temperature for 30 minutes.  5 After the 30-minute cool down, pulse centrifuge the MSA4 plate to 280 × g. Remove the foil  seal.

scan_protocol: scanned with iScan (Illumina) in accordance with the manufacturer’s protocol. Following scanning,  raw data in the form of IDAT files were funnelled through the ChAMP analysis  pipeline implemented in R (http://www.R-project.org/). ChAMP is an integrated  workflow that ues a number of Bioconductor packages. Within ChAMP, IDAT files  were loaded and normalized using minfi

data_processing:
SWAN (subset-quantile within array normalization) introduced sub-quantile normalization for the methylated and unmethylated channels separately, assuming that the distribution of the probes with similar number of CpGs should be similar, irrespective of probe type
Raw Illumina data files were processed with the minfi Bioconductor package. Using the P-values of detection from this package, we next estimated coverage of each sample and probe. All samples and probes had reasonable coverage. P-values larger than 0.05 were assigned not available (NAs) and later imputed using the impute.knn (k=5) function from the impute Bioconductor package
the non_normalized.txt contain Unmethylated and methylated signal intensities and Average Beta value

label: Cy5 and Cy3

source_name: normal blood sample

label_protocol: 1 Follow the instructions in the Zymo EZ DNA Methylation Kit to denature the genomic DNA  and add conversion reagent.  2 Incubate in a thermal cycler using the following conditions for 16 cycles:  • 95°C for 30 seconds  • 50°C for 1 hour   3 Hold DNA at 4°C for 10 minutes in the thermal cycler until you are ready to do the clean-up.  1 Follow the instructions in the Zymo EZ DNA Methylation Kit to do the following:  a Wash off the conversion reagent.  b Desulphonate the column or plate with desulphonation buffer. Incubate at room  temperature for 15 minutes.  c Wash off the desulphonation buffer.  d Add elution buffer.  e Centrifuge to elute.  2 Transfer the bisulfite-converted DNA (BCD) samples to the BCD plate.  3 Heat-seal the plate and store it at -25C° to -15°C.  4 Proceed to Make MSA4 Plate (Pre-AMP).

growth_protocol: Pulmonary tuberculosis patient and normal people who have genetic relationship wtih each other.

extract_protocol: 1. Cut tissue (up to 25 mg; up to 10 mg spleen) into small pieces, and place in 1.5 ml microcentrifuge tube. For rodent tails, use one (rat) or two (mouse) 0.4–0.6 cm lengths of tail. Add 180 μl Buffer ATL.  2. Add 20 μl proteinase K. Mix by vortexing, and incubate at 56°C until completely lysed. Vortex occasionally during incubation, or place in a thermomixer, in a shaking water bath, or on a rocking platform. Lysis is usually complete in 1–3 h or, for rodent tails, 6–8 h. Samples can be lysedovernight.  3. Vortex for 15 s. Add 200 μl Buffer AL to the sample. Mix thoroughly by vortexing. Then add 200 μl ethanol (96–100%). Mix again thoroughly. Alternatively, premix Buffer AL and ethanol, and add together.  4. Pipet the mixture into a DNeasy Mini spin column in a 2 ml collection tube. Centrifuge at _6000 x g (8000 rpm) for 1 min. Discard flow-through and collection tube.  5. Place the spin column in a new 2 ml collection tube. Add 500 μl Buffer AW1. Centrifuge for 1 min at _6000 x g. Discard flow-through and collection tube.  6. Place the spin column in a new 2 ml collection tube. Add 500 μl Buffer AW2. Centrifuge for 3 min at 20,000 x g (14,000 rpm). Discard flow-through and collection tube. Remove the spin column carefully so that it does not come into contact with the flow-through.  7. Transfer the spin column to a new 1.5 ml or 2 ml microcentrifuge tube, and add 200 μl Buffer AE for elution. Incubate for 1 min at room temperature. Centrifuge for 1 min at _6000 x g.  Recommended: Repeat this step for maximum yield.

treatment_protocol: Blood samples were obtained in January 2017 in a Blood RNA tube (4 ml) and an EDTA-containing tube (2 ml). Samples were stored at -80°C.

value: has a genetic relationship with G5

tag: disease state

value: normal

value: blood


title: Liver, finishing, rep2

description: steer


title: Liver, finishing, rep6

description: steer


title: G5_blood_ disease_rep1

source_name: Pulmonary tuberculosis blood sample

value: has a genetic relationship with G3

value: Pulmonary tuberculosis


title: Liver, growing, rep1

description: steer


title: Hawk tea extracts vs. DMSO_2

status: Public on Dec 10 2017

city: Beijing

first: Juan

last: Feng

address: No.30, Shuangqing Road, Haidian District

department: School of Medicine

institute: Tsinghua University

description: Analysis used DMSO-treated RNA as control samples for comparison to the experimental samples treated with hawk tea extracts

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from the ratio value of processed Red signal/processed Green signal. Agilent software was used.

source_name: DMSO treated

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

growth_protocol: HepG2 cells  were maintained in high-glucose Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin at 37°C in a humidified incubator under 5% carbon dioxide.

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

treatment_protocol: HepG2 cells  were treated hawk tea extracts for 24 h at a dose of 200 µg/mL. DMSO (1‰）was set as the control group.

source_name: Hawk tea extracts treated


title: Hawk tea extracts vs. DMSO_1

source_name: DMSO-treated


title: Glomerulus ob mouse, 4 weeks, replicate 2

city: Regensburg

first: Dominik

last: Chittka

address: Franz-Josef-Strauss-Allee 11

department: Nephrology

institute: University hospital Regensburg

hyb_protocol: 5,2 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Mouse Whole Transcriptome 1.0 ST array for 16 h at 45°C in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software.

source_name: Glomerulus, ob 4 weeks

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 15 µg of subsequently synthesized cDNA was purified, and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: After cervical dislocation kidneys were explanted and passed through a series of stainless steel sieves (150 µm, 100 µm, 70 µm, 50 µm). Glomeruli were collected, and the purity of the respective isolated glomeruli fractions was controlled by an Axiostar plus microscope (Zeiss, Jena, Germany).  Subsequent RNA extraction was conducted using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). RNA concentration and purity were determined by a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) prior to storage at  80°C.

extract_protocol: Total RNA extraction was conducted using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions.

value: isolated glomeruli

value: BTBR ob/ob

value: female

value: 4 weeks


title: Glomerulus WT mouse, 4 weeks, replicate 2

source_name: Glomerulus, WT 4 weeks

value: BTBR WT


title: Glomerulus WT mouse, 4 weeks, replicate 1


title: Glomerulus ob mouse, 4 weeks, replicate 1


title: G2_blood_ disease_rep1

value: has a genetic relationship with G4


title: Glomerulus WT mouse, 4 weeks, replicate 3


title: Glomerulus ob mouse, 4 weeks, replicate 3


title: Glomerulus WT mouse, 8 weeks, replicate 2

source_name: Glomerulus, WT 8 weeks

value: 8 weeks


title: Glomerulus WT mouse, 8 weeks, replicate 4


title: G4_blood_normal_rep1

value: has a genetic relationship with G2


title: Glomerulus ob mouse, 8 weeks, replicate 1

source_name: Glomerulus, ob 8 weeks


title: Glomerulus WT mouse, 8 weeks, replicate 3


title: Glomerulus ob mouse, 8 weeks, replicate 3