title: BAT from adipocyte-specific Sel1L-deficient mouse after 5h of fasting at 4℃, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.50.0).

source_name: Brown adipose tissue, isolated from an adipocyte-specific Sel1L-deficient mouse, fasted for 5h at 4℃

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Sel1Lf/f mice on the C57BL/6J background were crossed with Adiponectin-Cre mice (B6.FVB-Tg(Adipoq-cre)1Evdr/J; JAX 028020) on the C57BL/6J background to generate adipocyte-specific Sel1L (Sel1LAdipCre) deficient mice with respective control littermates (Sel1L f/f). Mice were subjected to 5h of fasting either at room temperature or 4℃.

extract_protocol: Brown adipose tissue was snap-frozen in liquid nitrogen.Total RNA was extracted using Trizol and further purified with RNeasy Minikit columns (Qiagen). RNA concentration was determined using NanoDrop 2000 UV-Vis Spectrophotometer. The quality and concentration were determined using the RNA 6000 Nano kit on an Agilent 2100 bioanalyser.

treatment_protocol: Sel1LAdipCre mice and control littermates (Sel1L f/f) were subjected to 5h of fasting either at room temperature or 4℃.

value: adipocyte-specific Sel1L KO

tag: exposure (temperature)

value: cold (4℃)

tag: nutritional status

value: fasted for 5h


title: AE43 (spleen)

status: Public on Apr 24 2020

type: SRA

city: Newcastle Upon Tyne

first: Olaf

last: Heidenreich

address: Brewery Lane

department: Wolfson Childhood Cancer Research Centre

country: United Kingdom

institute: Newcastle University

library_source: genomic

data_processing:
Sequencing data was analysed using a custom python script to extract barcode sequences and frequencies.Sequencing data was analysed using a python script (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558874/bin/leu2017140x2.txt) to extract barcode sequences and frequencies.
Sequences which did not match the expected fixed triplets were processed to create a list of ‘rejected’ barcodes, which had the correct vector sequence leading up to the barcode, but contained mismatches or insertions/deletions within the barcode region.
Supplementary_files_format_and_content: Excel files providing barcode sequence and number of reads (1st tab) and 'rejected' barcodes not matching the correct fixed barcode sequence (2nd tab)

molecule: genomic DNA

organism: synthetic construct

source_name: ALL primograft harvested from mouse

growth_protocol: ALL primograft samples were transduced with a lentiviral vector barcode library with an estimated complexity in excess of 100,000 barcodes and transplanted intrafemorally into NSG mice. Samples were collected from spleen, bone marrow and meninges, certain samples were transplanted into secondary and tertiary recipients.

extract_protocol:
Genomic DNA was extracted using a Qiagen Dneasy kit.
Barcode regions were amplified by PCR, and Illumina adaptors added by further cycles of PCR. Products were gel extracted, pooled and sequenced using a 50bp Illumina MiSeq run

tag: sample type

value: secondary of AE12 spleen

tag: sample

tag: transduction

tag: cells transplanted


title: AE44 (spleen)


title: BAT from adipocyte-specific Sel1L-deficient mouse after 5h of fasting at 4℃, replicate 2

type: RNA

label: biotin

molecule: total RNA

organism: Mus musculus

tag: genotype


title: AE42 (spleen)


title: AE41 (right femur)


title: TTKO_m3_d17 (Amplicon Bisulfite)

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Mock-Cre transduction day 17

data_processing:
Alignment: For amplicon bisulfite samples, the last 100 base pairs were trimmed due to reduced sequencing quality using the preprocessReads function from the Bioconductor QuasR package with the truncateEndBases = 100 parameter.  Amplicon sequences were then aligned to the mm9 build using Rbowtie in the QuasR package and the following parameters: genome="BSgenome.Mmusculus.UCSC.mm9", paired="fr", bisulfite="undir".  For SureSelect samples, reads were aligned to the mm9 build using Rbowtie in the QuasR environment as for amplicon sequencing above except with the parameter bisulfie = "dir".
Methylation level determination: Methylation levels for CpGs in amplicons was determined using the AmpliconViews function from the R package AmpliconBiSeq with the parameters ‘conv = 80’ and exp.var = ‘90’. Methylation levels for SureSelect samples was calculated using the qMeth function in the QuasR package.  For the SureSelect methylation data (Supplemental_Table4), read counts for replicates of the same time points were added together before determining methylation levels. Coverage columns for Supplemental_Table4 reflect summed counts for the triplicate experiments.
Filtering: A minimum of 100x coverage was required for all methylation calls in the amplicon bisulfite data. If coverage did not reach this threshold for any time point, the respective methylation level was set to NA. We further removed all CpGs with NA at day 0 or with more than one NA during the time course across all replicates. In addition, we filtered out one amplicon (chr7:149767665-149767784) containing 9 CpGs due to high variability in methylation calls. From a total of 588 CpGs initially quantified, this filtering procedure resulted in 405 CpGs. For SureSelect, a minimum of 50x coverage in all time points and replicates was used to filter CpGs for further analysis.
Rate determination: For methylation and demethylation rate determination, please see text.
Genome_build: mm9
Supplementary_files_format_and_content: Table files with CpG coordinates, methylation level, coverage, rate of methylation, rate of demethylation and tet activity (SureSelect only). For sample identication in Supplemental tables, there are 4 elements in the sample name that reflect the sample composition. Taking the sample name 'TTKO_cre1_d4_methylation' as an example, the TTKO refers to 'Tet Triple Knock-Out', while the 'cre1' refers to 'Cre transduction, replicate 1', the element 'd4' refers to 'Day 4 post transduction' and finally 'methylation' is the percent methylated alleles at that CpG. Other acronyms used are 'WT' for 'Wild-type', 'coverage' for number of reads covering that particular CpG in the sample, and 'mock' refers to the negative control in cre transduction. More specifically, 'm' refers to 'mock' and indicates addition of DMSO to the cells instead of Cre protein. The column 'MLE_kMe' reflects the rate of methylation while 'MLE_kDe' reflects the rate of demethylation (described in detail in the manuscript). The confidence column reflects the confidence level of rate inferrence. Lastly, the 'tag' column in Supplemental Table 2 and 3 reflects whether the CpG resides in an LMR (Low Methylated Region), FMR (Fully Methylated Region), UMR (Unmethylated Region), metIsland (Methylated CpG Island), NP-specific (Neural Progenitor specific) and ES-specific (Embyonic Stem cell specific) region. The designation 'Constitutive' reflects that the CpG resides in regions with the methylation state of interest in different cell types. In Supplemental Table 2, 'inferredInWTandTET' indicates rates inferred in wild-type and TTKO timecourse, while 'kDeWT_predicted' indicates predicted demethylation rates in wild-type cells using TTKO time course information and wild-type steady state measurements.

source_name: TET triple knockout mESCs

extract_protocol: Approximately 2ug of extracted genomic DNA from days 0, 4, 8, 10, 13, 17 and 29 were first mixed with 3.2pg of both unmethylated Lambda bacteriophage and in vitro methylated T7 bacteriophage DNA. Addition of the bacteriophage DNA was used to control for bisulfite conversion efficiency. Samples were then bisulfite converted using the EpiTect kit from Qiagen per the manufacturer’s instructions. Primers designed to amplify UMRs, LMR and FMR regions (88 in total, Supplemental Table 1) were distributed in 96 well plates and amplification was carried out using Amplitaq gold using the following thermocycler settings (all temperatures are in celcius and all incubation times are 30” unless specified): 1 cycle of 95⁰ for 9’, 20 cycles of touchdown with 95⁰ melt, 55⁰-51⁰ annealing, and extension at 72⁰, followed by 36 cycles of 95⁰ melt, 51⁰ annealing and 72⁰ extension. The amplicon reactions were then mixed, run out on an agarose gel and DNA extracted. Libraries were then constructed using the NEBNext ChIP-seq Library Prep kit (#E6240) as per the manufacturers instructions, indexed, pooled and sequenced using the Illumina MiSeq platform in 250bp paired-end mode.

tag: strain

tag: tissue

value: mESCs

tag: genotype/variation

value: TET triple knockout (TTKO)

value: Dnmt3a/3b intact

tag: timepoint

value: day 17

tag: replicate

value: replicate 3


title: TTKO_m1_d29 (Amplicon Bisulfite)

description: Mock-Cre transduction day 29

value: day 29

value: replicate 1


title: BAT from adipocyte-specific Sel1L-deficient mouse after 5h of fasting at 4℃, replicate 1


title: TTKO_m2_d17 (Amplicon Bisulfite)

description: Mock-Cre transduction day 17

value: replicate 2


title: TTKO_m3_d29 (Amplicon Bisulfite)

description: Mock-Cre transduction day 29


title: AE41 (meninges)


title: TTKO_m1_d17 (Amplicon Bisulfite)

description: Mock-Cre transduction day 17


title: BAT from adipocyte-specific Sel1L-deficient mouse after 5h of fasting at room temperature, replicate 2

source_name: Brown adipose tissue, isolated from an adipocyte-specific Sel1L-deficient mouse, fasted for 5h at room temperature

value: room temperature (RT)


title: BAT from wildtype mouse after 5h of fasting at 4℃, replicate 3

source_name: Brown adipose tissue, isolated from wildtype (C57BL/6J) mouse, fasted for 5h at 4℃

value: wildtype (C57BL/6J; Sel1L f/f)


title: AE41 (spleen)


title: BAT from adipocyte-specific Sel1L-deficient mouse after 5h of fasting at room temperature, replicate 1


title: AE40 (left femur)


title: AE40 (meninges)


title: TTKO_m3_d13 (Amplicon Bisulfite)

description: Mock-Cre transduction day 13

value: day 13


title: AE40 (spleen)


title: BAT from adipocyte-specific Sel1L-deficient mouse after 5h of fasting at room temperature, replicate 3


title: AE40 (right femur)


title: BAT from wildtype mouse after 5h of fasting at 4℃, replicate 2


title: AE37 (right femur)

value: secondary of AE6 spleen


title: AE37 (left femur)


title: AE41 (left femur)


title: AE37 (spleen)


title: AE37 (meninges)


title: AE36 (right femur)


title: TTKO_m3_d10 (Amplicon Bisulfite)

description: Mock-Cre transduction day 10

value: day 10


title: TTKO_m1_d13 (Amplicon Bisulfite)

description: Mock-Cre transduction day 13


title: AE36 (left femur)


title: TTKO_m2_d10 (Amplicon Bisulfite)

description: Mock-Cre transduction day 10


title: BAT from wildtype mouse after 5h of fasting at room temperature, replicate 3


title: BAT from wildtype mouse after 5h of fasting at 4℃, replicate 1


title: BAT from wildtype mouse after 5h of fasting at room temperature, replicate 2

source_name: Brown adipose tissue, isolated from wildtype (C57BL/6J) mouse, fasted for 5h at room temperature


title: TTKO_m2_d13 (Amplicon Bisulfite)

description: Mock-Cre transduction day 13


title: AE36 (meninges)


title: AE36 (spleen)


title: WT_IL22_24h_3

city: Oxford

first: Fiona

last: Powrie

address: Roosevelt Drive

department: Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences

institute: University of Oxford

description:
processed data file: IL22KRAS_featurecounts.csv
processed data file: IL22KRAS_log2RPKM1.csv

library_source: transcriptomic

data_processing:
Basecalling was performed using bcl2fastq version 2.17.1.14.
Adapter trimming was performed using cutadapt. Alignment was performed using hisat2. Indexing was performed with SAMBAMBA.
Mapped reads were quantified using featurecounts. Data was normalized to log2(RPKM)+1 expression. Genes with no expression were filtered out.
Genome_build: GRCh37.EBVB95-8wt.ERCC
Supplementary_files_format_and_content: IL22KRAS_featurecounts.csv: Matrix with unprocessed number of counts determined using featurecounts. Sample names in row 1 correspond to sample titles listed above.
Supplementary_files_format_and_content: IL22KRAS_log2RPKM1.csv: Matrix with log2(RPKM)+1 expression with genes with no expression filtered out. Sample names in row 1 correspond to sample titles listed above.

organism: Homo sapiens

source_name: colorectal cancer cell line

growth_protocol: DLD-1 KRAS MUT (Parental) and WT (KRAS(+/-)) cells were grown in RPMI, 1% Penicillin/Streptomycin (P/S) and 10% FBS in T75 flasks.

extract_protocol:
Following in vitro cytokine stimulation, cells were harvested by lysing the pellet in Qiagen Buffer RLT with 10μL β-mercaptoethanol/1 mL RLT. RNA was then immediately extracted from cell lysates using Qiagen RNeasy Columns according to the manufacturer’s protocol. Note that the optional on-column DNase digestion was performed. RNA integrity was subsequently analyzed using the Bioanalyzer 2100 Eukaryote Total RNA Nano chip. All samples had RIN = 10.
Samples were normalized to 1ug total RNA and the mRNA fraction was isolated by polyA selection. Libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina).

treatment_protocol: For experimentation, DLD-1 isogenic cells were pelleted by centrifugation at 500g for 5 minutes and plated in 12-well plates in 800μL RPMI, P/S + 1X Insulin, selenium, transferrin (ITS) per well, 24 hours prior to cytokine stimulation. After 24 hours, 200μL of 50ng/mL recombinant human interleukin 22 (rhIL-22) [R&D systems] or recombinant human interleukin 6 (rhIL-6) [Peprotech] for a final concentration of 10ng/mL in 1000μL of media were added to the cytokine treatment and non-treatment wells respectively. Cells were harvested after 2 hours or 24 hours for RNA extraction.

tag: cell line

tag: tissue source

value: colon (Colon adenocarcinoma Dukes Type C)

value: KRAS WT

tag: cytokine stimulation

value: 10ng/mL IL-22

tag: stimulation time

tag: experimental replicate

tag: passage


title: TTKO_m1_d10 (Amplicon Bisulfite)

description: Mock-Cre transduction day 10


title: AE33 (right femur)

value: secondary of AE12 spleen


title: WT_NT_24h_3

value: untreated


title: TTKO_m3_d8 (Amplicon Bisulfite)

description: Mock-Cre transduction day 8

value: mESCs

value: TET triple knockout (TTKO)

value: day 8


title: TTKO_m2_d8 (Amplicon Bisulfite)

description: Mock-Cre transduction day 8

value: Dnmt3a/3b intact


title: AE33 (meninges)


title: AE33 (left femur)


title: AE33 (spleen)


title: AE32 (right femur)


title: MUT_IL22_24h_3

value: DLD-1 Parental (HD-PAR-111 P4)

value: KRAS MUT


title: BAT from wildtype mouse after 5h of fasting at room temperature, replicate 1

tag: exposure (temperature)

tag: nutritional status

value: fasted for 5h


title: TTKO_m1_d8 (Amplicon Bisulfite)

description: Mock-Cre transduction day 8

value: replicate 1


title: AE32 (spleen)

tag: sample type

tag: sample


title: AE32 (meninges)

tag: transduction

tag: cells transplanted


title: AE32 (left femur)


title: MUT_NT_24h_3


title: WT_IL6_24h_3

value: 10ng/mL IL-6


title: AE31 (right femur)


title: WT_IL6_24h_2


title: AE31 (meninges)


title: AE31 (spleen)


title: TTKO_m2_d4 (Amplicon Bisulfite)

description: Mock-Cre transduction day 4

tag: strain

value: day 4

value: replicate 2


title: TTKO_m1_d4 (Amplicon Bisulfite)

description: Mock-Cre transduction day 4

tag: tissue


title: AE30 (left femur)


title: AE30 (spleen)


title: AE29 (right femur)

value: primary transplant


title: TTKO_cre3_d29 (Amplicon Bisulfite)

description: Post-Cre transduction day 29

tag: genotype/variation

value: Dnmt3a/3b catalytic dead

value: day 29

value: replicate 3


title: AE29 (left femur)


title: MUT_IL6_24h_3

value: colon (Colon adenocarcinoma Dukes Type C)


title: MUT_IL6_24h_2


title: MUT_IL22_24h_2

value: 10ng/mL IL-22


title: TTKO_cre2_d29 (Amplicon Bisulfite)

description: Post-Cre transduction day 29

value: mESCs

tag: timepoint


title: AE29 (meninges)


title: AE29 (spleen)


title: TTKO_cre1_d29 (Amplicon Bisulfite)

description: Post-Cre transduction day 29

value: TET triple knockout (TTKO)

tag: replicate


title: TTKO_m3_d4 (Amplicon Bisulfite)

description: Mock-Cre transduction day 4


title: AE28 (meninges)


title: MUT_NT_24h_2

tag: cell line

value: untreated


title: AE28 (right femur)


title: WT_IL6_24h_1

tag: tissue source

value: KRAS WT


title: TTKO_cre3_d17 (Amplicon Bisulfite)

description: Post-Cre transduction day 17

value: day 17


title: WT_IL22_24h_1

tag: cytokine stimulation


title: AE27 (right femur)


title: AE27 (spleen)


title: WT_IL22_24h_2

tag: stimulation time


title: AE26 (right femur)


title: AE28 (spleen)


title: WT_NT_24h_2

tag: experimental replicate


title: TTKO_cre2_d17 (Amplicon Bisulfite)

description: Post-Cre transduction day 17


title: WT_NT_24h_1

tag: passage


title: AE27 (left femur)


title: TTKO_cre3_d13 (Amplicon Bisulfite)

description: Post-Cre transduction day 13

value: day 13


title: AE26 (left femur)


title: AE26 (spleen part 2)


title: AE26 (meninges)


title: AE26 (spleen part 1)


title: MUT_IL6_24h_1

value: DLD-1 Parental (HD-PAR-111 P4)

value: KRAS MUT


title: TTKO_cre1_d17 (Amplicon Bisulfite)

description: Post-Cre transduction day 17

value: replicate 1


title: MUT_IL22_24h_1


title: AE25 (left femur)


title: TTKO_cre2_d13 (Amplicon Bisulfite)

description: Post-Cre transduction day 13


title: AE25 (meninges)


title: AE25 (spleen)


title: TTKO_cre1_d13 (Amplicon Bisulfite)

description: Post-Cre transduction day 13


title: TTKO_cre3_d10 (Amplicon Bisulfite)

description: Post-Cre transduction day 10

value: day 10


title: MUT_NT_24h_1


title: WT_IL6_2h_3

value: 10ng/mL IL-6


title: AE24 (left femur)

value: primary transplant


title: AE24 (meninges)


title: TTKO_cre2_d10 (Amplicon Bisulfite)

description: Post-Cre transduction day 10

value: Dnmt3a/3b catalytic dead

value: replicate 2


title: AE19 (meninges)


title: AE24 (spleen)


title: WT_IL22_2h_3


title: WT_NT_2h_3


title: AE19 (spleen part 2)


title: AE18 (left femur)


title: TTKO_cre3_d8 (Amplicon Bisulfite)

description: Post-Cre transduction day 8

value: day 8

value: replicate 3


title: TTKO_cre1_d10 (Amplicon Bisulfite)

description: Post-Cre transduction day 10


title: AE18 (meninges)


title: MUT_IL6_2h_3

value: colon (Colon adenocarcinoma Dukes Type C)


title: AE18 (spleen)


title: MUT_IL22_2h_3

value: 10ng/mL IL-22


title: TTKO_cre2_d8 (Amplicon Bisulfite)

description: Post-Cre transduction day 8

value: mESCs

value: TET triple knockout (TTKO)


title: MUT_NT_2h_3

value: untreated


title: AE15 (left femur)


title: AE16 (spleen)


title: AE14 (left tibia)


title: AE15 (spleen)


title: TTKO_cre3_d4 (Amplicon Bisulfite)

description: Post-Cre transduction day 4

value: day 4


title: WT_IL6_2h_2

value: KRAS WT


title: TTKO_cre2_d4 (Amplicon Bisulfite)

description: Post-Cre transduction day 4


title: AE14 (right femur)


title: TTKO_cre1_d4 (Amplicon Bisulfite)

description: Post-Cre transduction day 4


title: AE14 (left femur)


title: AE14 (meninges)


title: WT_IL22_2h_2


title: TTKO_3_d0 (Amplicon Bisulfite)

description: Non-transduced

value: Dnmt3a/3b intact

value: day 0


title: AE14 (spleen part 2)


title: AE13 (meninges)


title: MUT_IL6_2h_2

value: DLD-1 Parental (HD-PAR-111 P4)

value: KRAS MUT


title: TTKO_cre1_d8 (Amplicon Bisulfite)

description: Post-Cre transduction day 8

value: replicate 1


title: AE19 (spleen part 1)

value: primary transplant


title: MUT_IL22_2h_2


title: AE13 (left femur)


title: AE16 (meninges)


title: AE16 (left femur)


title: MUT_NT_2h_2


title: AE12 (left tibia)


title: TTKO_2_d0 (Amplicon Bisulfite)

description: Non-transduced


title: AE12 (left femur)


title: WT_IL6_2h_1

value: 10ng/mL IL-6


title: AE12 (right femur)


title: AE13 (spleen)


title: TTKO_cre2_d29 (SureSelect)

description: Post-Cre transduction day 29

extract_protocol: SureSelect enrichment and subsequent sequencing of bisulfite DNA was carried out as per the manufacturer’s instructions. Briefly, genomic DNA isolated from the time points above was sonicated down to 150-200 base pairs in size using a Covaris S220, followed by library construction. The libraries were then hybridized to probes (Mouse Methyl-Seq XT, 931052), bound to streptavidin beads, washed and bisulfite converted using the EZ DNA methylation Gold kit from Zymo (D5005). Bisulfite converted DNA libraries were then amplified and indexed, pooled and sequenced in 51bp paired-end mode using the Illumina HiSeq platform.

value: Dnmt3a/3b catalytic dead

value: day 29

value: replicate 2


title: WT_IL22_2h_1

value: colon (Colon adenocarcinoma Dukes Type C)


title: WT_NT_2h_2


title: AE12 (meninges)


title: TTKO_cre1_d29 (SureSelect)

description: Post-Cre transduction day 29


title: AE14 (spleen part 1)


title: TTKO_cre3_d17 (SureSelect)

description: Post-Cre transduction day 17

value: day 17

value: replicate 3


title: AE11 (right femur)


title: AE12 (spleen part 1)


title: AE11 (left tibia)


title: MUT_IL6_2h_1


title: AE12 (right tibia)


title: AE11 (meninges)


title: TTKO_cre2_d17 (SureSelect)

description: Post-Cre transduction day 17

value: mESCs

value: TET triple knockout (TTKO)


title: AE10 (left femur)


title: TTKO_cre1_d17 (SureSelect)

description: Post-Cre transduction day 17


title: MUT_IL22_2h_1

value: 10ng/mL IL-22


title: AE10 (spleen)


title: TTKO_cre3_d29 (SureSelect)

description: Post-Cre transduction day 29


title: MUT_NT_2h_1

value: untreated


title: AE11 (spleen)


title: AE12 (spleen part 2)


title: AE8 (right tibia)


title: TTKO_cre2_d13 (SureSelect)

description: Post-Cre transduction day 13

value: day 13


title: AE9 (spleen)


title: AE8 (right femur)


title: TTKO_cre1_d13 (SureSelect)

description: Post-Cre transduction day 13


title: WT_NT_2h_1

value: KRAS WT


title: AE8 (left femur)


title: Spleen_3_IP

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

description: Ip sample

data_processing:
Basecalls performed using illumina bcl2fastq2.
Adapters were trimmed with cutadapt.
Clean reads were mapped to the reference genome with Tophat2
m6A peak analysis was then performed. Each gene was split into the 100-nucleotide sliding windows and an enrichment fold (winscore) was calculated for each window
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph with genome-wide raw read coverage (converted from BAM format).

molecule: polyA RNA

source_name: Spleen,tissue

extract_protocol:
Total RNA was isolated from tissues using chloroform and isopropanol following the manufacturer’s protocol. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
RNA samples were fragmented in 1X NEB Next Magnesium RNA Fragmentation Buffer at 94℃ for 5min and fragmented RNA was then cleaned up using ethanol precipitation. 10ng fragmented RNA was used to construct input control library with VAHTS Stranded mRNA-seq library prep kit (Vazyme). 15-40ug fragmented RNA was further incubated with 5ug rabbit anti-m6A polyclonal antibody in IPP buffer overnight at 4℃. The m6A-Ab mixture was then immunoprecipitated by incubation with protein-G magnetic beads at 4℃ for another 2h. After washing with IPP buffer, bound RNA was competitively eluted from the beads with 0.5mgml-1 N6-methyladenosine (Sigma-Aldrich), followed by ethanol precipitation. RNA was resuspended in 8μl water and used for library construction.

value: Spleen

tag: rip antibody


title: AE8 (spleen)


title: AE7 (right tibia)


title: Spleen_2_IP

description: Ip sample


title: Spleen_2_Input

description: Input sample


title: TTKO_cre3_d10 (SureSelect)

description: Post-Cre transduction day 10

value: day 10


title: AE7 (right femur)


title: AE7 (left femur)


title: TTKO_cre2_d10 (SureSelect)

description: Post-Cre transduction day 10


title: AE7 (spleen)


title: AE9 (right femur)


title: Spleen_1_IP

description: Ip sample


title: TTKO_cre1_d10 (SureSelect)

description: Post-Cre transduction day 10

value: replicate 1


title: AE6 (right tibia)

value: primary transplant


title: AE6 (right femur)


title: TTKO_cre3_d8 (SureSelect)

description: Post-Cre transduction day 8

value: day 8


title: AE6 (left tibia)


title: Spleen_1_Input

description: Input sample


title: Spleen_3_Input

description: Input sample


title: Muscle_3_IP

description: Ip sample

source_name: Muscle,tissue

value: Muscle


title: AE6 (left femur)


title: TTKO_cre2_d8 (SureSelect)

description: Post-Cre transduction day 8

value: Dnmt3a/3b catalytic dead


title: TTKO_cre1_d8 (SureSelect)

description: Post-Cre transduction day 8


title: AE6 (spleen part 3)


title: AE6 (spleen part 1)


title: AE6 (spleen part 2)


title: Muscle_3_Input

description: Input sample


title: AE5 (spleen)

value: 100000 barcoded & 900000 unlabelled


title: TTKO_cre3_d4 (SureSelect)

description: Post-Cre transduction day 4

value: day 4


title: AE4 (spleen)


title: AE3 (spleen)


title: Δire1Δopi3+ ire1ΔLD+choline_replicate 3

city: Singapore

first: Nurulain

last: Ho

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Probes were hybridized on a Custom Microarray Agilent GE 8x60K array.

data_processing: Data were analyzed using GeneSpring GX software (Agilent Technologies).  Processed data file includes: Base 2 logarithmic fold changes in gene expression normalized to untreated WT cells. The average of the log2 fold change was calculated for the genes.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae_Δire1Δopi3+ ire1ΔLD+choline (overnight)_replicate 3

label_protocol: Probes were prepared using the Low Input Quick Amp Labeling System with 100 ng of Total RNA as starting material following manufacturer’s instructions, which included One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5 (Agilent Technologies). Arrays were scanned using a high-resolution DNA Microarry Scanner, model G2505C (Agilent Technologies)

growth_protocol: Cultures were grown to an OD600/ml of 0.25 at 30°C in selective synthetic complete media

extract_protocol: Total RNA was extracted by the hot acid phenol method as previously described {PMID: 9843569}. Total RNA was subsequently cleaned up using the RNeasy Mini Kit (Qiagen). RNA quality control was carried out using the Agilent RNA Nano 6000 Chip (Agilent Technologies)

treatment_protocol: Cells were subjected to 1h incubation of 2 mM DTT when indicated and overnight 1 mM choline when indicated. Cells were harvested from cultures at cell density of less than 0.5 OD600/mL.

tag: gender

value: Mat a

tag: genotype

value: delta_ire1 delta_opi3 with  ire1 delta_LD

tag: treated with

value: choline


title: Barcode plasmid library

source_name: plasmid DNA

tag: sample type

value: barcode plasmid DNA library

tag: sample

tag: transduction

tag: molecule subtype

value: plasmid DNA


title: TTKO_cre1_d4 (SureSelect)

description: Post-Cre transduction day 4

tag: strain

tag: tissue

value: mESCs

tag: genotype/variation

value: TET triple knockout (TTKO)


title: Δire1Δopi3+IRE1+choline_replicate 3

scan_protocol: Arrays were scanned using a high-resolution DNA Microarry Scanner, model G2505C (Agilent Technologies)

value: delta_ire1 delta_opi3 with IRE1


title: TTKO_cre2_d4 (SureSelect)

description: Post-Cre transduction day 4

tag: timepoint

tag: replicate

value: replicate 2


title: Δire1Δopi3+ ire1ΔLD_replicate 3


title: Muscle_1_IP

description: Ip sample


title: Δire1Δopi3+IRE1_replicate 3


title: Muscle_1_Input

description: Input sample


title: Lung_3_IP

description: Ip sample

source_name: Lung,tissue

value: Lung


title: Δire1+ ire1ΔLD+DTT_replicate 3

source_name: S.cerevisiae_Δire1+ ire1ΔLD+DTT (1 hour)_replicate 3

value: delta_ire1 with ire1 delta_LD

value: DTT


title: AE6 (meninges)

value: primary transplant

tag: cells transplanted


title: TTKO_3_d0 (SureSelect)

description: Non-transduced

value: Dnmt3a/3b intact

value: day 0

value: replicate 3


title: Muscle_2_Input

description: Input sample

value: Muscle


title: TTKO_2_d0 (SureSelect)

description: Non-transduced


title: Muscle_2_IP

description: Ip sample


title: Δire1Δopi3+ ire1ΔLD+choline_replicate 2

source_name: S.cerevisiae_Δire1Δopi3+ ire1ΔLD+choline (overnight)_replicate 2

value: Mat a


title: TTKO_1_d0 (SureSelect)

description: Non-transduced

value: replicate 1


title: Lung_2_IP

description: Ip sample


title: Δire1+ ire1ΔLD_replicate 3

source_name: S.cerevisiae_Δire1+ ire1ΔLD_replicate 3


title: WT_3_d0 (SureSelect)

description: Non-transduced

source_name: Wild-type mESCs

value: Wild-type TET


title: Δire1+IRE1+DTT_replicate 3

source_name: S.cerevisiae_Δire1+IRE1+DTT (1 hour)_replicate 3

value: delta_ire1 with IRE1


title: Lung_3_Input

description: Input sample


title: Δire1+IRE1_replicate 3

source_name: S.cerevisiae_Δire1+IRE1_replicate 3


title: Δire1Δopi3+IRE1+choline_replicate 2

value: choline


title: Δire1Δopi3+ ire1ΔLD_replicate 2

value: delta_ire1 delta_opi3 with  ire1 delta_LD


title: Lung_2_Input

description: Input sample


title: TTKO_cre3_d13 (SureSelect)

description: Post-Cre transduction day 13

value: mESCs

value: TET triple knockout (TTKO)

value: Dnmt3a/3b catalytic dead

value: day 13


title: Δire1+ ire1ΔLD+DTT_replicate 2

source_name: S.cerevisiae_Δire1+ ire1ΔLD+DTT (1 hour)_replicate 2

value: delta_ire1 with ire1 delta_LD


title: WT_1_d0 (SureSelect)

description: Non-transduced


title: Lung_1_IP

description: Ip sample

value: Lung


title: Lung_1_Input

description: Input sample


title: Liver_3_IP

description: Ip sample

source_name: Liver,tissue

value: Liver


title: Δire1+IRE1+DTT_replicate 2

source_name: S.cerevisiae_Δire1+IRE1+DTT (1 hour)_replicate 2

value: DTT


title: Δire1+ ire1ΔLD_replicate 2

source_name: S.cerevisiae_Δire1+ ire1ΔLD_replicate 2


title: Δire1+IRE1_replicate 2

source_name: S.cerevisiae_Δire1+IRE1_replicate 2


title: Δire1Δopi3+IRE1+choline_replicate 1

value: delta_ire1 delta_opi3 with IRE1


title: K510 DAZAP1 Si1

city: Jinan

first: Yan

last: Zheng

state: Shandong

address: No.440 Jiyan road

department: Shandong Provincial Key Laboratory of Radiation Oncology

institute: Shandong Cancer Hospital Affiliated to Shandong University

description: processed data file: gene.count.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole transcriptome using tophat2 with default parameters.
Reads count of three samples were calculated by HT-Seq based on the gtf file of Ensembl human.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: gene.count.txt: Tab-delimited text files includes gene count values for each Sample.

growth_protocol: Human KYSE510 cells were cultured in RPMI-1640 media supplied with 10% fetal bovine serum (Hyclone) at 37°C with 5% CO2.

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

treatment_protocol: Small interfering RNA (siRNA) duplexes (siDAZAP1-1, siDAZAP1-2) were products of Genepharma (Shanghai, China). The negative control RNA duplex (NC) for siRNAs (Genepharma, Shanghai, China) was nonhomologous to any human genome sequence. All small RNAs were transfected into KYSE510 cells with INTERFERin® (Polyplus).

tag: cell line

tag: cell type

value: Esophageal squamous cell carcinoma

tag: transfection

value: DAZAP1 siRNA


title: Liver_3_Input

description: Input sample

tag: rip antibody


title: Δire1Δopi3+ ire1ΔLD+choline_replicate 1

source_name: S.cerevisiae_Δire1Δopi3+ ire1ΔLD+choline (overnight)_replicate 1

tag: gender

value: Mat a

value: delta_ire1 delta_opi3 with ire1 delta_LD


title: Δire1Δopi3+ ire1ΔLD_replicate 1

tag: genotype


title: K510NC

description: processed data file: gene.count.txt

value: NC RNA


title: Δire1+IRE1+DTT_replicate 1

source_name: S.cerevisiae_Δire1+IRE1+DTT (1 hour)_replicate 1

value: delta_ire1 with IRE1

tag: treated with


title: Liver_2_Input

description: Input sample


title: Δire1Δopi3+IRE1_replicate 1


title: Liver_2_IP

description: Ip sample


title: Δire1+ ire1ΔLD+DTT_replicate 1

source_name: S.cerevisiae_Δire1+ ire1ΔLD+DTT (1 hour)_replicate 1

value: delta_ire1 with  ire1 delta_LD


title: Δire1+ ire1ΔLD_replicate 1

source_name: S.cerevisiae_Δire1+ ire1ΔLD_replicate 1


title: Δire1+IRE1_replicate 1

source_name: S.cerevisiae_Δire1+IRE1_replicate 1


title: LIver_1_IP

description: Ip sample


title: PGK.RAG2.d15.N9

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description:
X6463
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498270

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 500 ng of each fluorescently labelled cRNA population were used for hybridization.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2565CA).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’. Data was analyzed using R/Bioconductor. The data was analyzed using R 3.5.1 and Bioconductor 3.741. Raw files were read in separately for each array design with the function “read.maimages” from the R package “limma”. A merged dataset was created by extracting all probes derived from the original Agilent Mouse Genome Oligo Microarray 4x44K v2 array (A_XX_PXXXXXX) from the four array platforms and combining them using the function “cbind.EList” from “limma”. The probe with the ID “A_55_P2337033“ interrogating the gene “2310065F04Rik” was manually excluded from the dataset since it strongly cross-reacted with the sequence of EGFP. The Raw data was log2-transformed and quantile-normalized using the ”limma” package. The four within-array replicates of each probe were collapsed using the “avereps” function from the R package “limma”. Batch correction between different SAGA assays was performed on quantile-normalized log2-values using the parametric ComBat algorithm as implemented in the R package “sva”.

label: Alexa Fluor 555

label_protocol: 100 ng of total RNA were used to prepare Aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. Prior to the reverse transcription reaction, 1 µl of a 1:5000 dilution of Agilent’s One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100 ng of total RNA of each analysed sample. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

growth_protocol: Lineage negative cells were isolated from 8-12 week old female C57BL/6J mice using the mouse lineage cell depletion kit (Miltenyi). After thawing, one aliquot per assay was cultured for 48 hours in StemSpan (STEMCELL Technologies) supplemented with 50 ng/ml rm-SCF, 100 ng/ml rh-Flt-3L, 100 ng/ml rh-IL-11, 20 ng/ml rm-IL-3 (Peprotech). For transduction, 250 µl of viral supernatant was preloaded on RetroNectin (TaKaRa)-coated 24-well plates. 1x105 cells were added and incubated overnight. The preloading procedure was repeated for the second round of transduction. Cells from the first transduction round were harvested and cells still bound to the RetroNectin were incubated with cell dissociation buffer (Gibco), pelleted and resuspended in 250 µl of fresh culture medium before being added to the suspension harvest. Subsequently, the 750 µl of cell suspension were added to the wells preloaded for the second transduction. Cells were incubated for 24 hours, harvested, mixed with 1.6 ml IMDM containing 10% FBS, 1% Penicillin/Streptomycin, 2 mM glutamine and cytokines as described above (IMDM+), and seeded onto 12-well suspension plates. On day 4 1.9 ml medium was added, cells were incubated for 48 hours on 6-well suspension plates, before adding another 2.2 ml of medium. On day 8 post-transduction samples were diluted (~ 1:10) by seeding 1 x106 cells in 4 ml of IMDM+ in 6-well suspension plates. On days 11 and 13 p.t., cells were given with 1.2 ml of IMDM+.

extract_protocol: RNAzol B (WAK-Chemie Medical) and Direct-Zol RNA MiniPrep Kit (Zymo Research) according to manufacturers instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.

tag: facs

tag: immortalized

value: No

tag: vector

tag: assay batch id

tag: batch variable


title: Δire1Δopi3+IRE1_replicate 2

tag: strain


title: WT_2_d0 (SureSelect)

description: Non-transduced

tag: tissue

value: mESCs

tag: genotype/variation

value: Wild-type TET

value: Dnmt3a/3b intact

value: day 0

value: replicate 2


title: MND.RAG2.d15.N9

description:
X6462
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498269

tag: comment

value: IVIM phenotype unknown; not used for limma and prediction


title: MND.RAG2.d15.N8

description:
X6461
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498268


title: Liver_1_Input

description: Input sample

value: Liver


title: K510 DAZAP1 Si2

description: processed data file: gene.count.txt


title: Kidney_3_IP

description: Ip sample

source_name: Kidney,tissue

value: Kidney


title: MND.RAG2.d15.N7

description:
X6458
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498265


title: E12.0PG_Tead_CUTnRUN_rep2

city: Los Angeles

first: Neil

last: Segil

state: CA

address: 1425 san pablo st, BCC 503K

department: BCC

country: USA

institute: University of Southern California

data_processing:
Library strategy: CUT&RUN
The quality of the libraries was confirmed using a Bioanalyzer (Quick Biology Inc.). Reads were mapped to GRCm38/mm10 genome assembly using STAR.
For RNAseq, genes.results files provided for each sample contain length, effective length, and expected counts for each gene.
For ATAC and CUTnRUN libraries, Endcode pipeline was used; PCR duplicates were removed based on genomic coordinates for ATAC-seq, or by MIDs using UMI-tools for CUT&RUN.
Peaks were called by Model-based analysis of ChIP-Seq (MACS2) with FDR< 0.01 and the dynamic lambda (--nolambda) option for individual replicates.
NarrowPeak files provide the list of called peaks of significant signal enrichment.
Genome_build: GRCm38/mm10 genome
Supplementary_files_format_and_content: *.genes.results.txt
Supplementary_files_format_and_content: *.narrowPeak

source_name: Organ of Corti

extract_protocol:
Progenitors (Sox2-GFP+) were purified from E12 cochlea by FACS sorting. Chromatin were digested by CUT&RUN technique, and DNA fragments were purified by phenol-chloroform method.
Libraries were prepared using Accel 2S Plus DNA library kit with MID and single indexed adapters.

value: Organ of Corti progenitor cells (Sox2-GFP+)

tag: age

tag: antibody

value: pan-Tead (Cell Signaling)


title: PGK.RAG2.d15.N8

description:
X6459
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498266


title: MND.RAG1.d15.N9

description:
X6460
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498267


title: Kidney_3_Input

description: Input sample


title: RV.SF.d15.Y42

description:
X6456
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498263

value: Yes


title: E12.0PG_Tead_CUTnRUN_rep1

extract_protocol:
Progenitors (Sox2-GFP+) were purified from E12 cochlea by FACS sorting. Chromatin were digested by CUT&RUN technique, and DNA fragments were purified by phenol-chloroform method.
Libraries were prepared using KAPA HTP Library Preparation Kit Illumina® platforms.

tag: cell type


title: Kidney_2_IP

description: Ip sample


title: E13.5PG_H3K27Ac_CUTnRUN_rep2

extract_protocol:
Progenitors (p27-GFP+) were purified from E13 cochlea by FACS sorting. Chromatin were digested by CUT&RUN technique, and DNA fragments were purified by phenol-chloroform method.
Libraries were prepared using Accel 2S Plus DNA library kit with MID and single indexed adapters.

value: Organ of Corti progenitor cells (p27-GFP+)

value: H3K27Ac (Active Motif)


title: MND.RAG1.d15.N7

description:
X6454
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498261


title: E13.5PG_H3K27Ac_CUTnRUN_rep1


title: Kidney_2_Input

description: Input sample


title: E12.0PG_H3K27Ac_CUTnRUN_rep2


title: MND.RAG2.d15.Y6

description:
X6408
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498257


title: Kidney_1_IP

description: Ip sample


title: PGK.RAG2.d15.N6

description:
X6409
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498258


title: MND.RAG1.d15.N6

description:
X6406
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498255


title: Kidney_1_Input

description: Input sample


title: E12.0PG_H3K27Ac_CUTnRUN_rep1


title: Heart_3_IP

description: Ip sample

source_name: Heart,tissue

value: Heart


title: MND.RAG2.d15.N5

description:
X6404
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498253


title: RSF91-Cer-WA.d15.N6

description:
X6405
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498254


title: PGK.RAG2.d15.N7

description:
X6455
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498262


title: E13.5PG_ATACseq_rep3

data_processing:
The quality of the libraries was confirmed using a Bioanalyzer (Quick Biology Inc.). Reads were mapped to GRCm38/mm10 genome assembly using STAR.
For RNAseq, genes.results files provided for each sample contain length, effective length, and expected counts for each gene.
For ATAC and CUTnRUN libraries, Endcode pipeline was used; PCR duplicates were removed based on genomic coordinates for ATAC-seq, or by MIDs using UMI-tools for CUT&RUN.
Peaks were called by Model-based analysis of ChIP-Seq (MACS2) with FDR< 0.01 and the dynamic lambda (--nolambda) option for individual replicates.
NarrowPeak files provide the list of called peaks of significant signal enrichment.
Genome_build: GRCm38/mm10 genome
Supplementary_files_format_and_content: *.genes.results.txt
Supplementary_files_format_and_content: *.narrowPeak

extract_protocol:
Progenitors (p27-GFP+) were purified from E13 cochlea by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were amplified by PCR with indexed primers.


title: E13.5PG_ATACseq_rep2


title: PGK.RAG2.d15.N5

description:
X6402
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498251


title: Heart_2_IP

description: Ip sample


title: E13.5PG_ATACseq_rep1


title: RSF91-Cer-WA.d15.Y5

description:
X6401
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498250


title: PGK.RAG2.d15.N4

description:
X6400
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498249


title: Mock.d15.N43

description:
X6399
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498248


title: Mock.d15.N44

description:
X6452
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498259


title: Heart_3_Input

description: Input sample


title: RV.SF.d15.Y41

description:
X6453
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498260


title: Heart_2_Input

description: Input sample


title: RV.SF.d15.N40

description:
X6407
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498256


title: E12.0PG_ATACseq_rep3

extract_protocol:
Progenitors (Sox2-GFP+) were purified from E12 cochlea by FACS sorting. Nuclei were extracted and chromatin were digested by tn5 transposase at 37°C for 20 minutes. DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
Libraries were amplified by PCR with indexed primers.


title: MND.RAG1.d15.N5

description:
X6398
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498247


title: RSF91-Cer-WA.d15.Y4

description:
X6397
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498246


title: MND.RAG1.d15.N8

description:
X6457
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498264


title: MND.RAG2.d15.N4

description:
X6396
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498245


title: MND.RAG1.d15.N4

description:
X6395
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498244


title: Heart_1_IP

description: Ip sample


title: E12.0PG_ATACseq_rep2


title: Heart_1_Input

description: Input sample


title: Mock.d15.N42

description:
X6394
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498243


title: RSF91-Cer-WX.d15.N3

description:
X6385
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498242


title: FrontalCortex_3_IP

description: Ip sample

source_name: FrotalCortex,tissue

value: FrotalCortex


title: RV.SF.d15.Y39

description:
X6403
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498252


title: E13.5PG_RNAseq_rep2

extract_protocol:
Progenitors (p27-GFP+) were purified from E13 cochlea by FACS sorting. RNA was extracted using Quick RNA micro-kit (Zymo).
PolyA RNA were enriched and used for library with Illumina TruSeq RNA library kit.


title: TTKO_1_d0 (Amplicon Bisulfite)

description: Non-transduced

source_name: TET triple knockout mESCs

value: TET triple knockout (TTKO)

tag: timepoint

tag: replicate

value: replicate 1


title: RSF91-Cer-WX.d15.N2

description:
X6384
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498241

value: No


title: RSF91-Cer-WA.d15.N3

description:
X6383
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498240


title: E13.5PG_RNAseq_rep1


title: RSF91-Cer-WX.d15.N1

description:
X6381
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498238


title: FrontalCortex_2_IP

description: Ip sample

tag: rip antibody


title: Mock.d15.N41

description:
X6379.1
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498237

value: duplicate, removed after RMA and COMBAT; not used for limma


title: Mock.d15.N40

description:
X6374.1
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498236


title: RSF91-Cer-WT.d15.N3

description:
X6382
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498239


title: RSF91-Cer-WA.d15.N2

description:
X6380
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498235


title: mOC [RNA-seq]

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

institute: Third Military Medical University

data_processing:
FastQC software was used for reads quality evaluation.
Fastp software was used for reads filtering to get clean reads.
Hisat2 software was used for spliced mapping with mouse genome GRCm38.
Circos software was used for chromosomal mapping.
Stringtie software was used for counting of fragments and trimmed mean of M values (TMM) was used for normalization.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited xls files include FPKM values for each Sample concerning miRNA

source_name: Bone marrow

growth_protocol: BMMs were used to generate preosteoclast (pOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 24 h and mature osteoclast (mOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 72 h or more.

extract_protocol:
Femurs and tibia were dissected from mice and flushed using complete medium to acquire whole bone marrow. The whole cells were cultured using alpha-MEM complete media for 24 h and the floating cells were collected for further treatment of M-CSF (50ng/mL) for 72 h to generate BMMs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of alendronate (500 μM for 12 h) to cell culture medium to induce the generation of apoptotic bodies.

value: Bone marrow

value: mature osteoclast

value: post natal week 11


title: FrontalCortex_1_IP

description: Ip sample


title: FrontalCortex_1_Input

description: Input sample


title: Cerebellum_3_IP

description: Ip sample

source_name: Cerebellum,tissue

value: Cerebellum


title: Mock.d15.N39

description:
X6379
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498234


title: RSF91-Cer-WT.d15.Y2

description:
X6378
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498233


title: BMM [RNA-seq]

value: BMM


title: pOC [RNA-seq]

value: preosteoclast


title: FrontalCortex_2_Input

description: Input sample


title: CD8 T cells

city: Boston

first: George

middle: C

last: Tsokos

state: Massachusetts

address: CLS-928, 3 Blackfan Circle

department: Rheumatology/BIDMC

institute: Harvard Medical School

data_processing:
Library strategy: TCR-seq
The alignment and assembly of the RNA-seq reads and the exporting of the clonotypes were conducted using MiXCR.
Supplementary_files_format_and_content: clonotype-report

source_name: spleen

extract_protocol:
mRNAs were extracted from 1 millon of each subset using Qiagen RNA isolation kit
Takara SMARTer Mouse TCRa/b profiling kit

treatment_protocol: Splenic CD4, CD8 and DN T cells were FACS sorted from a 16 week-old MRL.lpr mouse

value: spleen

value: CD8 T cells

value: 16 weeks


title: CD4 T cells

value: CD4 T cells


title: DN T cells

value: DN T cells


title: E12.0PG_ATACseq_rep1

value: Organ of Corti progenitor cells (Sox2-GFP+)


title: BM 3  immune profiling

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: BM 3

data_processing:
The Cell Ranger Single Cell Software Suite 2.1.1 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting for transcriptome wirh refdata-cellranger-mm10-1.2.0 ar reference and expected-cells number of 3000 for each sample.
For immune profiling Cell Ranger Single Cell Software Suite 3.0.2 was used for demultiplexing, barcode processing and assembly of the BCR sequences, using the vdj command and refdata-cellranger-vdj_GRCm38_alts_ensembl-mouse-2.2.0 as reference.
Genome_build: mm10
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcode information for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. fastq: high-confidence contig sequences of immune receptors annotated with the corresponding cellular barcode and contig-id; csv: results from the signle cell immune profiling comprising including the receptor type, VDJ-Genes annotation, CDR3 nucleotide and amino acid sequense as well as the count for the corresponding cellular barcode and contig.

source_name: IgG+ CD38+ CD138- GL7- CD19+ cells bone marrow

extract_protocol:
Single-cell suspensions from BM of 3x NP-CGG immunized C57BL/6 mice were prepared and CD19+ cells were enriched by magnetic cell sorting using anti-CD19 microbeads (Miltenyi Biotech). Ex vivo IgG1+/IgG2b+CD19+CD38+GL7-CD138-IgM-IgD- memory B cells were isolated by FACS (Influx cell sorter (BD Bioscience)) and applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
The amplified cDNA was used for simultaneous 5’ gene expression (GEX) and murine BCR library preparation. BCR transcripts were additionally amplified by Chromium Single Cell V(D)J Enrichment Kit for murine B cells (10x Genomics). Upon adapter ligation and index PCR, the quality of the obtained cDNA library was assessed by Qubit quantification, Bioanalyzer fragment analysis (HS DNA Kit, Agilent) and KAPA library quantification qPCR (Roche). The sequencing was performed on a NextSeq500 device (Illumina) using a High Output v2 Kit (150 cycles) with the recommended sequencing conditions (read1: 26nt, read2: 98nt, index1: 8 nt, index2: n.a.) for the transcriptome and Mid Output v2 Kit (300 cycles) for BCR repertoire analysis (read1: 150nt, read2: 150nt, index1: 8nt, index2: n.a., 20% PhiX spike-in).

treatment_protocol: 3x NP-CGG immunized C57BL/6 mice

value: bone marrow

tag: mouseid


title: BM 2  immune profiling

description: BM 2


title: RSF91-Cer-WA.d15.N1

description:
X6377
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498232

value: IVIM phenotype unknown; not used for limma and prediction


title: Cerebellum_3_Input

description: Input sample


title: FrontalCortex_3_Input

description: Input sample

value: FrotalCortex


title: TLC_S84

city: Bruxelles

first: Alessia

last: Centonze

address: Route de Lennik 808

country: Belgium

institute: Université libre de Bruxelles

data_processing:
Approximately 19 million of paired-end reads per sample were mapped against the mouse reference genome (GRCm38/mm10) using STAR software to generate read alignments for each sample.
Annotations Mus_musculus.GRCm38.87.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTSeq. These counts were normalized for 20 millions of mapped reads.
The fold changes of mean gene expression for the duplicates were used to calculate the level of differential gene expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include raw counts.

source_name: Mammary gland

extract_protocol:
Mammary gland cells were isolated by FACS and collected into kit lysis buffer. RNA was extracted with Qiagen RNeasy Micro Kit.
The multiplexed libraries (18 pM) were loaded on flow cells and sequences were produced using a NovaSeq 6000 S2 Reagent Kit (200 cycles) from a NovaSeq 6000 System (Illumina).
Indexed cDNA libraries were obtained using the Ovation Solo RNA-Seq System (NuGen) following manufacturer recommendation.

treatment_protocol: Single cell suspension from mammary gland was stained with different primary antibodies for the markers of interest.

value: Mammary gland

value: Tomato luminal cells (TLC)

tag: treatment

value: Luminal cell ablation


title: THC_S83

value: Tomato hybrid cells (THC)


title: Spleen 3 immune profiling

description: Spleen 3

source_name: IgG+ CD38+ CD138- GL7- CD19+ cells spleen


title: Cerebellum_2_IP

description: Ip sample


title: RSF91-Cer-WT.d15.Y1

description:
X6376
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498231

tag: facs

value: Yes


title: Cerebellum_2_Input

description: Input sample

value: Cerebellum


title: TBC_S82

value: Tomato basal cells (TBC)


title: Spleen 2 immune profiling

description: Spleen 2


title: RV.SF.d15.Y38

description:
X6375
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498230

tag: immortalized


title: BM 3

description: BM 3


title: LC-WT_S81

value: Luminal cells (LC-WT)


title: Cerebellum_1_IP

description: Ip sample


title: Mock.d15.N38

description:
X6374
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498229

value: No

tag: vector


title: BC-WT_S80

value: Basal cells (BC-WT)


title: PGK.RAG2.d15.N2

description:
X6368
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498227

tag: assay batch id


title: PGK.RAG2.d15.N3

description:
X6369
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498228

tag: batch variable


title: Cerebellum_1_Input

description: Input sample


title: Spleen 3

description: Spleen 3

value: spleen


title: TBC_S46


title: THC_S47


title: Spleen 2

description: Spleen 2


title: Bmem 3 Sp H 2

data_processing:
Samples were demultiplexed by MIGEC-1.2.4a using checkout and '-cute' as settings.
Different Ig-isotypes were further demultiplexed according to the presents of the IgG1/2, IgG3 and IgA specific primer sequence: AGTGGATAGACMGATG, AAGGGATAGACAGATG and TCAGTGGGTAGATGGTG allowing one mismatch.
Each isotype and sample were further analysed by MIGEC using UMI-guided correction in default parameter settings and segment file, adjusted to include only C57BL/6-specific V genes for mapping.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: tab-seperated values including clonal counts, fractions, the VDJ-Gene annotation and the nucleotide and aminoacid sequence of the CDR3 region for each sample and isotype.

extract_protocol:
Cells from BM (tibiae, femurae and pelvic bones) and spleen of three times NP-CGG immunized-mice were isolated and Bsm were magnetically enriched using a “Memory B cell Isolation Kit” (130-095-838 Miltenyi). Bsm were further enriched by FACSorting of CD19+CD38+CD138-CD11c-GL7-IgM-IgD-small lymphocytes. Sorted cells of Mouse 1 and 2 were split into two equal aliquots (samples A, B) for BM and spleen samples as cellular (biological) replicates. Sorted cells of Mouse 3 were split into 4 samples (A, B, C, D). Biological replicates were processed independently from this point on. Cell samples were lysed in RNA lysis buffer (R1060-1-50, Zymo Research) and stored at -80°C. Total RNA was extracted from samples using the ZR RNA Miniprep Kit (Zymo Research) according to the manufacturer’s protocol (Catalog nos. R1064 & R1065). Isolated RNA was split and library preparation was performed in technical duplicates.
First-strand cDNA was synthesized with SMARTScribe Reverse Transcriptase (Clontech) using total RNA, a cDNA synthesis primer mix (mIgG12ab_r1(KKACAGTCACTGAGCTGCT), mIgG3_r (GTACAGTCACCAAGCTGCT), mIgA_r (CCAGGTCACATTCATCGTG) by metabion international AG) and a 5’ – template-switch adaptor with unique molecular identifiers (UMI) (SmartNNNa (AAGCAGUGGTAUCAACGCAGAGUNNNNUNNNNUNNNNUCTT(rG)4)) according to the protocol “high-quality full length immunoglobulin profiling with unique molecular barcoding” by the Chudakov lab46. cDNA was purified with MinElute PCR purification Kit (Qiagen) and eluted in 10 µL 70°C nuclease-free H2O (Qiagen). The first PCR was performed according to the protocol of the Chudakov lab 46 using a Step-out primer M1SS (AAGCAGTGGTATCAACGCA) (annealing on the switch adaptor) and a mouse IgH reverse primer mix (mIgG12_r2 (ATTGGGCAGC CCTGATTAGTGGATAGACMGATG), mIgG3_r2 (ATTGGGCAGCCCTGATTAAGGGATAGA CAGATG), mIgA_r2 (ATTGGGCAGCCCTGATTTCAGTGGGTAGATGGTG) binding to the constant region of certain Ig heavy chains). The first PCR was performed with Q5 Hot Start High-Fidelity DNA polymerase (NEB) in a 50µL reaction volume using 7.5 µL of cDNA product with following PCR parameters: 1 cycle of 95°C for 1 min 30 sec; 20 cycles of 95°C for 10 sec, 60°C for 20 sec, 72°C for 40 sec; 1 cycle of 72°C for 4 min; storage at 4°C. PCR 1 products were purified with MinElute PCR purification Kit (Qiagen) and eluted in 25 µL 70°C nuclease-free H2O (Qiagen). Within the second PCR amplification46 a M1S primer ((N)4–6(XXXXX)CAGTGGTATCAACGCAGAG) (annealing on M1SS) and a step-out primer Z ((N)4-6(XXXXX)ATTGGGCAGCCCTGATT), both with sample barcodes, were used. PCR 2 was performed with Q5 Hot Start High-Fidelity DNA polymerase (NEB) in a 50µL reaction volume using 2 µL of PCR 1 product with following PCR parameters: 1 cycle of 95°C for 1 min 30 sec; 14-15 cycles of 95°C for 10 sec, 60°C for 20 sec, 72°C for 40 sec; 1 cycle of 72°C for 4 min; storage at 4°C. PCR 2 products were purified with MinElute PCR purification Kit (Qiagen) and eluted in 25 µL 70°C nuclease-free H2O (Qiagen). The products were also gel-purified from 2% agarose gels (extraction with MinElute gel extraction Kit (Qiagen); elution in 15 µL 70°C nuclease-free H2O (Qiagen).  Adapter ligation was performed using the TruSeq® DNA PCR-Free Library Prep protocol (Illumina). The products were gel-purified from 2% agarose gels instead of bead purification as mentioned in the protocol (extraction with MinElute gel extraction Kit (Qiagen); elution in 10 µL 70°C nuclease-free H2O (Qiagen)). The quality of amplified libraries was verified using an Agilent 2100 Bioanalyzer (2100 expert High Sensitivity DNA Assay). According to the fragment size, the libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).


title: Bmem 3 Sp H 1


title: PGK.RAG2.d15.N1

description:
X6365
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498224


title: BM 2

description: BM 2


title: Bmem 3 Sp G 2


title: BC_S44

value: Basal cells (BC)


title: TLC_S48


title: MND.RAG2.d15.N2

description:
X6364
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498223


title: LC_S45

value: Luminal cells (LC)


title: Ad-Bmal1

city: Nanjing

first: Jiangyi

last: Yu

address: No. 155, Hanzhong Rd

institute: Affiliated Hospital of Nanjing University of Chinese Medicine

description: RNA expression in HK-2 cells which were infected with adenovirus expressing RNA expression Bmal1 CDS

data_processing:
Quality of RNA libraries was evaluated using the Agilent 2100 bioanalyzer (Agilent Technologies, USA).
Library sequencing was performed on HiSeq 3000 sequencing platform (Illumina Company, USA).
All sequenced reads were trimmed for adaptor sequence, were masked for low-complexity or low-quality sequence, and then were mapped to reference human genome GRCh38(hg38) using HISAT2.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: HK-2 cells

growth_protocol: HK-2 cells (ATCC, Manassas, VA, USA) were cultured at 37°C and 5% CO2 in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin and streptomycin)

extract_protocol:
Cells were collected, and total RNA was extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq3000 by a 2X150 bp run.

treatment_protocol: HK-2 cells were infected with adenovirus expressing either Bmal1 CDS domain or GFP for 24 h

tag: cell line

value: HK-2 (human kidney 3) is a proximal tubular cell (PTC) line derived from normal kidney

tag: passages

tag: transfection

value: Bmal1 CDS domain


title: Bmem 3 Sp G 1

tag: tissue


title: Bmem 3 Sp F 2


title: MND.RAG1.d15.N3

description:
X6366
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498225


title: MND.RAG2.d15.N1

description:
X6361
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498220

tag: comment

value: IVIM phenotype unknown; not used for limma and prediction


title: Bmem 3 Sp F 1


title: Bmem 3 Sp E 2


title: MND.RAG2.d15.Y3

description:
X6367
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498226


title: MND.RAG1.d15.N1

description:
X6360
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498219


title: RV.SF.d15.Y36

description:
X6359
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498218


title: Bmem 3 Sp E 1


title: Mock.d15.N37

description:
X6358
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498217


title: LV.EFS.d15.N29

description:
X6257
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498216


title: Bmem 3 BM D 2

value: bone marrow


title: Bmem 3 BM D 1


title: MND.RAG1.d15.N2

description:
X6363
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498222


title: Bmem 3 BM C 2


title: LV.EFS.d15.N28

description:
X6256
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498215


title: LV.EFS.d15.N27

description:
X6255
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498214


title: RV.SF.d15.Y37

description:
X6362
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498221


title: LV.EFS.d15.N26

description:
X6254
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498213


title: Ad-GFP

description: RNA expression in HK-2 cells which were infected with adenovirus expressing GFP

value: HK-2 (human kidney 2) is a proximal tubular cell (PTC) line derived from normal kidney

value: GFP


title: RV.SF.d15.N35

description:
X6253
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498212


title: RV.SF.d15.Y34

description:
X6252
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498211


title: Bmem 3 BM B 2


title: Bmem 3 BM B 1


title: Bmem 3 BM A 2


title: Mock.d15.N36

description:
X6251
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498210


title: Bmem 3 BM A 1


title: LV.EFS.d15.N25

description:
X6250
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498209


title: 12mon_14day_L_2

first: Wenjun

last: Deng

state: MA

address: 175 Cambridge street

institute: Massachusetts General Hospital

description:
Gene expression in microglia isolated from the contralateral hemisphere of 12-month old rat 14 day after stroke
130917-107-L_2048G

hyb_protocol: Following fragmentation, 5 μg of cDNA were hybridized for 16 hr at 45°C on GeneChip Rat 1.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450, and scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with Affymetrix Expression Console using RMA algorithm. Raw data were processed by RMA algorithm. Expression data were quantile normalized and probes with mean log-transformed intensity less than 3 were removed.

organism: Rattus norvegicus

source_name: Microglia isolated from the contralateral hemisphere of 12-month old rat 14 day after stroke

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA using amplification kit NuGEN Ovation Pico WTA System V2, followed by labeling 5 μg of cDNA using kit NuGEN Encore Biotin Module.

growth_protocol: Male spontaneously hypertensive rats

extract_protocol: Total RNAs were extracted using miRNeasy kit (Qiagen) according to the manufacturer’s instructions. All RNA samples had initial RIN scores above 7.0.

treatment_protocol: Transient focal cerebral ischemia was induced by 75 min monofilament occlusion of the middle cerebral artery in 3-month- and 12-month-old male spontaneously hypertensive rats (SHRs) (Charles River Laboratories Wilmington, MA, USA) under 1.2% isoflurane anesthesia and with Laser Doppler monitoring. Rectal temperature was maintained at 37°C±1 with a thermostat-controlled heating pad. Right femoral arteries were cannulated to confirm that the blood pressure, pH and gases were all within normal range.

tag: strain

value: Wistar Kyoto

tag: Sex

value: male

tag: age

value: 12 month

tag: condition/time point

value: 14 day after stroke

tag: hemisphere

value: Contralateral


title: 12mon_3day_R_3

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 12-month old rat 3 day after stroke
130926-91-R_2048R

source_name: Microglia isolated from the ipsilateral hemisphere of 12-month old rat 3 day after stroke

value: 3 day after stroke

value: Ipsilateral


title: 12mon_14day_R_3

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 12-month old rat 14 day after stroke
130917-111-R_2048L

source_name: Microglia isolated from the ipsilateral hemisphere of 12-month old rat 14 day after stroke


title: 12mon_14day_L_1

description:
Gene expression in microglia isolated from the contralateral hemisphere of 12-month old rat 14 day after stroke
130916-102-L_2048A


title: 12mon_3day_R_2

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 12-month old rat 3 day after stroke
130926-90-R_2048P


title: 12mon_14day_L_3

description:
Gene expression in microglia isolated from the contralateral hemisphere of 12-month old rat 14 day after stroke
130917-111-L_2048K


title: LV.EFS.d15.N24

description:
X6249
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498208

value: No


title: Bmem 2 Sp B 2

value: spleen

tag: mouseid


title: 12mon_14day_R_2

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 12-month old rat 14 day after stroke
130917-107-R_2048H


title: 12mon_3day_R_1

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 12-month old rat 3 day after stroke
130926-89-R_2048N


title: Bmem 3 BM C 1


title: Bmem 2 Sp A 2


title: 12mon_14day_R_1

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 12-month old rat 14 day after stroke
130916-102-R_2048B


title: Bmem 2 Sp B 1


title: LV.EFS.d15.N23

description:
X6248
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498207


title: 12mon_3day_L_3

description:
Gene expression in microglia isolated from the contralateral hemisphere of 12-month old rat 3 day after stroke
130926-91-L_2048Q

source_name: Microglia isolated from the contralateral hemisphere of 12-month old rat 3 day after stroke


title: 12mon_3day_L_2

description:
Gene expression in microglia isolated from the contralateral hemisphere of 12-month old rat 3 day after stroke
130926-90-L_2048O


title: LV.EFS.d15.N22

description:
X6247
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498206


title: 12mon_3day_L_1

description:
Gene expression in microglia isolated from the contralateral hemisphere of 12-month old rat 3 day after stroke
130926-89-L_2048M


title: 12mon_Sham_2

description:
Gene expression in microglia isolated from 12-month old Sham control
Sham2_2048T

source_name: Microglia isolated from 12-month old Sham control

value: Sham


title: 12mon_Sham_3

description:
Gene expression in microglia isolated from 12-month old Sham control
Sham3_2048U


title: RV.SF.d15.Y33

description:
X6246
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498205

value: Yes


title: RV.SF.d15.Y32

description:
X6245
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498204


title: Mock.d15.N35

description:
X6244
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498203


title: LV.EFS.d15.N21

description:
X6212
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498202


title: Bmem 2 BM B 2


title: Bmem 1 Sp B 2


title: Bmem 1 Sp B 1


title: LV.EFS.d15.N20

description:
X6208
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498201


title: Bmem 2 BM A 1


title: 3mon_14day_R_2

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 3-month old rat 14 day after stroke
130212-36-R_1955F

source_name: Microglia isolated from the ipsilateral hemisphere of 3-month old rat 14 day after stroke

value: 3 month


title: RV.SF.d15.Y31

description:
X6207
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498200


title: Bmem 1 Sp A 2


title: Bmem 1 Sp A 1


title: 3mon_14day_R_3

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 3-month old rat 14 day after stroke
130212-39-R_1955H


title: 3mon_14day_R_1

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 3-month old rat 14 day after stroke
130205-27-R_1955D


title: Bmem 2 Sp A 1


title: Mock.d15.N34

description:
X6206
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498199


title: Bmem 1 BM B 2


title: 3mon_14day_L_3

description:
Gene expression in microglia isolated from the contralateral hemisphere of 3-month old rat 14 day after stroke
130212-39-L_1955G

source_name: Microglia isolated from the contralateral hemisphere of 3-month old rat 14 day after stroke


title: Bmem 1 BM B 1


title: RV.SF.d15.Y30

description:
X6203
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498197


title: Bmem 2 BM A 2


title: 3mon_14day_L_1

description:
Gene expression in microglia isolated from the contralateral hemisphere of 3-month old rat 14 day after stroke
130205-27-L_1955C


title: Mock.d15.N33

description:
X6202
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498196


title: Bmem 2 BM B 1


title: 3mon_3day_R_3

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 3-month old rat 3 day after stroke
121220-13R_1897F

source_name: Microglia isolated from the ipsilateral hemisphere of 3-month old rat 3 day after stroke


title: Bmem 1 BM A 2


title: 3mon_3day_R_2

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 3-month old rat 3 day after stroke
121220-12R_1897D


title: LV.EFS.d15.N18

description:
X6200
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498195


title: RV.SF.d15.N29

description:
X6199
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498194


title: 3mon_14day_L_2

description:
Gene expression in microglia isolated from the contralateral hemisphere of 3-month old rat 14 day after stroke
130212-36-L_1955E


title: LV.WASP.d15.N5

description:
X6018
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498192


title: LV.WASP.d15.N4

description:
X6017
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498191


title: SRS.SF.d15.Y.3

description:
X6016
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498190


title: LV.EFS.d15.N19

description:
X6204
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498198


title: Bmem 1 BM A 1


title: SRS.SF.d15.N.1

description:
X6014
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498188


title: SRS.EFS.d15.N.8

description:
X6013
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498187


title: 3mon_3day_R_1

description:
Gene expression in microglia isolated from the ipsilateral hemisphere of 3-month old rat 3 day after stroke
121220-10R_1897B


title: LSPE_low_cell_conc_5

city: Tsukuba

first: Sotaro

last: Takano

state: Ibaraki

address: Central 6-10, Higashi 1-1-1

department: Bioproduction

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: 3 ug of cDNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Microarray data were extracted based on the finite hybridization model (Ono et al, 2018) and the thermo-dynamic model of non-specific binding (Furusawa et al. 2009). We obtained the noramlized log10 mRNA signals.
Normalized_data.txt
After data processing, we removed expression data which were less than -1.5 to avoid effects of noise, and then selected expression data were quantile-normalized as previously described (Bolstad et al., 2003).

label: Biotin

organism: Escherichia coli

source_name: MDS42, LSP supernatant at 10^7 cells/mL

label_protocol: Fragmented cRNA were biotinylated according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were then shaken at 160 rpm in a BR-21FP air incubator (Taitec, Saitama, Japan) at 37°C aerobically.

extract_protocol: The cell cultures were mixed into chilled phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) and centrifuged at 7500 × g for 3 min at 4 °C. After eliminating the supernatants, the cell pellets were frozen by liquid nitrogen and stored at -80 °C. Total RNA was extracted using a PureLink Mini kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's protocol.

treatment_protocol:
GLC late_log cell cultures were centrifuged at 7500 × g for 3 min and resuspended by M63  without glucose for three times and inoculated into the supernatant of long-term statipnary phase culture at 10^7 cells/mL.
All cell cultures were first grown on M63 minimal medium with glucose, washed by M63 without glucose, and then inoculated into each condition.

tag: substrain


title: LSPE_low_cell_conc_4


title: LSPE_low_cell_conc_3


title: 3mon_3day_L_2

description:
Gene expression in microglia isolated from the contralateral hemisphere of 3-month old rat 3 day after stroke
121220-12L_1897C

source_name: Microglia isolated from the contralateral hemisphere of 3-month old rat 3 day after stroke


title: LSPE_low_cell_conc_2


title: Mock.d15.N32

description:
X6198
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498193

tag: facs


title: 3mon_Sham_2

description:
Gene expression in microglia isolated from 3-month old Sham control
N2_2078B

source_name: Microglia isolated from 3-month old Sham control


title: 3mon_3day_L_1

description:
Gene expression in microglia isolated from the contralateral hemisphere of 3-month old rat 3 day after stroke
121220-10L_1897A


title: 3mon_Sham_1

description:
Gene expression in microglia isolated from 3-month old Sham control
N1_2078A


title: 3mon_3day_L_3

description:
Gene expression in microglia isolated from the contralateral hemisphere of 3-month old rat 3 day after stroke
121220-13L_1897E


title: AV.EFS.d15.N3

description:
X5848
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498184

tag: immortalized


title: SRS.EFS.d15.Y.1

description:
X6011
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498185

tag: vector


title: AV.EFS.d15.N2

description:
X5847
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498183

tag: assay batch id


title: LSPE_low_cell_conc_1


title: LSPE_5

source_name: MDS42, LSP supernatant at 10^9 cells/mL

treatment_protocol:
GLC late_log cell cultures were centrifuged at 7500 × g for 3 min and resuspended by M63  without glucose for three times and inoculated into the supernatant of long-term statipnary phase culture at 10^9 cells/mL.
All cell cultures were first grown on M63 minimal medium with glucose, washed by M63 without glucose, and then inoculated into each condition.


title: AV.EFS.d15.N1

description:
X5846
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498182

tag: batch variable


title: AV.SF.d15.Y1

description:
X5845
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498181


title: 3mon_Sham_3

description:
Gene expression in microglia isolated from 3-month old Sham control
N3_2078C


title: SRS.SF.d15.Y.2

description:
X6015
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498189


title: AV.SF.d15.N2

description:
X5844
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498180


title: LSPE_low_cell_conc_6


title: LSPE_4


title: SRS.EFS.d15.N.7

description:
X6012
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498186


title: AV.SF.d15.N1

description:
X5843
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498179


title: LSPE_3


title: LSPE_2


title: LSPE_1


title: RV.SF.d15.Y.27

description:
X5842
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498178


title: Mock.d15.N.26

description:
X5841
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498177


title: GLC_starved_4

source_name: MDS42, M63 without glucose

treatment_protocol:
GLC late_log cell cultures were centrifuged at 7500 × g for 3 min and resuspended by M63  without glucose for three times and inoculated into M63 without glucose at 10^7 cells/mL.
All cell cultures were first grown on M63 minimal medium with glucose, washed by M63 without glucose, and then inoculated into each condition.


title: BRLF1 expressing cells_1 round

type: genomic

city: Miaoli

first: Huang

last: Sheng-Yen

address: No.35, Keyan Road

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

description: 1 round of BRLF1 expression

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, V6.0

scan_protocol: Agilent Microarray Scanner

data_processing: Agilent Feature Extraction 10.5.1.1. Agilent Genomic Workbench version 7.0.4.0 (Agilent Technologies). The filtering strategy used in processed data worksheet was as follows: Aberration Algorithm: z-score, Threshold: 2.5, Aberration Filter:  (Minimum Number of Probes for Amplification >= 5 AND Minimum Size (Kb) of Region for Amplification >= 0.0 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.125) OR (Minimum Number of Probes for Deletion >= 5 AND Minimum Size (Kb) of Region for Deletion >= 0.0 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.125)

source_name: R1 cells

label_protocol: Agilent SureTaq Genomic DNA Labeling Kit: 1mg DNA labeled with Cy3-dUTP or Cy5-dUTP

growth_protocol: The TW01-TetER cells are cultured in Dulbecco’s modified Eagle’s medium (Thermo Fisher Scientific) supplemented with 10% tetracycline-free fetal bovine serum and incubated at 37°C and 5% CO2. To maintain the selected inducible clones, the cells are further supplemented with 12.5 μg/ml blasticidin and 250 μg/ml zeocin. For the induction of EBV BRLF1 expression, the cells were treated with 50 ng/ml doxycycline (Sigma-Aldrich).

extract_protocol: WelPrep DNA kit

treatment_protocol: The NPC cells were seeded. After seeding for 24 h, cells were mock or treated with 50 ng/ml doxycycline for 24 h. After incubation for 24 h, the cells were recovered by replacing with fresh medium and incubated for 24h. The resulting cells were defined as passage 1 (P1) or BRLF1 expression 1 (R1). The procedure was repeated for 15 rounds and the resulting cells were defined as passage 15 (P15) or BRLF1 expression 15 (R15).

tag: cell line

value: TW01-TetER cells

tag: tissure

value: nasopharyngeal epithelial cells

tag: passage

tag: treatment

value: 50 ng/ml doxycycline for 24 h

source_name: P1 cells


title: BB694.d15.N1

description:
X5748
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498176


title: GLC_starved_3


title: GLC_starved_2


title: SRS.EFS.d15.N.5

description:
X5746
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498174


title: RV.SF.d15.Y.26

description:
X5744
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498172


title: SRS.EFS.d15.N.6

description:
X5747
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498175


title: GLC_ST_2

source_name: MDS42, M63, glucose in stationary phase

growth_protocol: Cells were shaken at 160 rpm in a BR-21FP air incubator (Taitec, Saitama, Japan) at 37°C aerobically.

treatment_protocol: GLC late_log cell cultures were further incubated  at 37 °C for 16 h.


title: RV.SF.d15.Y.25

description:
X5743
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498171


title: Mock.d15.N.25

description:
X5742
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498170


title: Passage cells_15 rounds

description: passage control

source_name: P15 cells

value: mock


title: GLC_late_log_5

source_name: MDS42, M63, glucose in late-log

growth_protocol: Cells were  shaken at 160 rpm in a BR-21FP air incubator (Taitec, Saitama, Japan) at 37°C aerobically.

treatment_protocol: The E. coli cells were inoculated into fresh M63 medium with glucose from glycerol stock and grown for 20 h at a density of approximately 10^9 cells/mL


title: Mock.d15.N.24

description:
X5741
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498169


title: GLC_ST_1


title: GLC_late_log_4


title: BRLF1 expressing cells_15 rounds

description: 15 rounds of BRLF1 expression

source_name: R15 cells

value: 50 ng/ml doxycycline for 24 h, repeated 15 rounds


title: GLC_late_log_3


title: GLC_starved_1


title: GLC_late_log_2


title: GLC_late_log_1


title: SRS.EFS.d15.N.4

description:
X5745
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498173


title: GLC_ST_3


title: SVAR_A4_Vanco_RPMI_2

city: La Jolla

first: Henrique

last: Machado

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

data_processing:
The phred quality scores for the Illumina sequencing reads were generated using FastQC package
Bowtie2 was used to align the raw reads to TCH1516 genome (GCA_000017085.1) and to calculate alignment percentage
The aligned reads were then normalized to transcripts per million (TPM) with DESeq2
Genome_build: GCA_000017085.1
Supplementary_files_format_and_content: csv file with deseq2 TPM values for all samples

organism: Staphylococcus aureus

growth_protocol: The strains were grown in each respective media, with and without vancomycin (at 1/2 MIC). At OD 0.2, cultures without vancomycin were harvested. At the same OD, cultures were treated with 0.5x MIC of vancomycin, and harvested for RNA 30min after. Harvesting of the cells consisted in mixing of 3 mL of culture with two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m.. The supernatant was decanted, and the cell pellet was stored at −80 °C.

extract_protocol:
Total RNA was isolated using the Quick RNA Fungal/Bacterial Microprep (Zymo Research), following vendor procedures, including an on-column DNase treatment. RNA quality and purity was assessed using Nanodrop and Bioanalyzer RNA nano chip. Ribosomal RNA was removed from total RNA preparations using RNaseH.
RNA was used to build a cDNA library for sequencing using a KAPA Stranded RNA-seq Library Preparation Kit.

tag: gentotype/variation

tag: culture media

value: vancomycin


title: SVAR_A5_Vanco_RPMI_2

treatment_protocol: cultures were treated with 0.5x MIC of vancomycin

tag: strain


title: SVAR_A5_Vanco_RPMI_1


title: SVAR_A3_Vanco_RPMI_2


title: SVAR_A4_Vanco_RPMI_1


title: SVAR_STR1_Vanco_RPMI_1


title: LV.EFS.d15.N.6

description:
X5120
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498168

extract_protocol: RNAzol B (WAK-Chemie Medical) and Direct-Zol RNA MiniPrep Kit (Zymo Research) according to manufacturers instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.


title: RV.SF.d15.Y.8

description:
X5119
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498167


title: SVAR_A2_Vanco_RPMI_2


title: SVAR_A3_Vanco_RPMI_1


title: SVAR_A2_Vanco_RPMI_1


title: SVAR_TCH1516_Vanco_RPMI_2

value: WT


title: SVAR_A5_RPMI_2

source_name: SVAR_A5_RPMI+10%LB_no vancomycin

value: no vancomycin


title: SVAR_TCH1516_Vanco_RPMI_1


title: Mock.d15.N.8

description:
X5118
Gene expression data from murine Lineage-negative bone marrow cells transduced with GSM4498166


title: Lhx2GFP_negative_Fucci_Positive_rep2

city: New York

first: Irina

last: Matos

address: 1230 York Av

institute: The Rockefeller University

description:
processed data column (in AllValuesConf_Irina.xls):
Lhx2GFP_negative_Fucci_Positive

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7).
Unique reads mapped to a single genomic location (allowing two mismatches) were kept.
Transcript Assembly: Aligned reads were assembled into transcripts using Cufflinks (version 2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff gene expression files

extract_protocol:
Keratinocytes were isolated by fluorescence-activated cell sorting (FACS) and total RNA was extracted using the ZYMO Direct-Zol RNA miniprep kit (R2050) according to manufacturer instructions. Purification was done using the sorter markers a6, GFP and either tdTOM (Samples 1-20) or mKO2 (Samples 21-29).
mRNA libarary was prepared using Illumina TruSeq mRNA sample preparation kit and single end sequencing was performed using Illumina HiSeq 2500.

treatment_protocol: For samples 1 to 20: E9.5 Embryos were mosaically transduced with a lentivirus harbouring CRE recombinase and a WNT reporter tagged to GFP.

tag: age

tag: genotype/variation

value: WildType Lhx2GFP- mKO2 +

tag: tissue

value: developing epidermis

tag: cell type

value: Epidermal keratinocytes


title: Rosiglitazone-treated VCT vs control VCT Replicate 5

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

country: France

institute: INSERM UMRS-1139

description: Biological replicate 5 of 5. Rosiglitazone-treated villous cytotrophoblast (RT-VCT) vs not treated/control villous cytotrophoblast (VCT)

hyb_protocol: The labeled cDNA mixtures were hybridized according to the protocol described at http://cmgm.stanford.edu/pbrown/protocols/index

scan_protocol: The arrays were immediately scanned using a GenePix 4000A confocal Scanner (Axon Instruments). Images were analyzed using GenePix pro 3 software

data_processing: A print-tip loess normalization of the microarray experiments was performed after the log-transformation of the background-corrected expression measurements. Raw data files include a column of 'ID_REF' which matches the ID_REF on platform GPL21609.

source_name: RT-VCT 5

label_protocol: Three micrograms of amplified RNA  (aRNA) was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit  (Amersham Biosciences)

growth_protocol: VCT were isolated from term placenta by trypsin and purified on percoll gradient, then plated onto  Cells were cultured DMEM/10% FBS, and rosiglitazone-treated (RT-VCT) or not (VCT) as control for 24h. RT-VCT/VCT pellets were then snap-frozen and stored at -80°C until RNA extraction.

extract_protocol:
Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions
amplification protocol: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit  (Ambion)

value: villous cytotrophoblast (VCT)

tag: culture time

value: rosiglitazone

source_name: VCT 5

value: not treated/control


title: Rosiglitazone-treated VCT vs control VCT Replicate 3

description: Biological replicate 3 of 5. Rosiglitazone-treated villous cytotrophoblast (RT-VCT) vs not treated/control villous cytotrophoblast (VCT)

source_name: RT-VCT 3

source_name: VCT 3


title: Lhx2GFP_negative_Fucci_Negative_rep2

description:
processed data column (in AllValuesConf_Irina.xls):
Lhx2GFP_negative_Fucci_Negative

value: WildType Lhx2GFP- mKO2 -


title: Rosiglitazone-treated VCT vs control VCT Replicate 2

description: Biological replicate 2 of 5. Rosiglitazone-treated villous cytotrophoblast (RT-VCT) vs not treated/control villous cytotrophoblast (VCT)

source_name: RT-VCT 2

source_name: VCT 2


title: Rosiglitazone-treated VCT vs control VCT Replicate 4

description: Biological replicate 4 of 5. Rosiglitazone-treated villous cytotrophoblast (RT-VCT) vs not treated/control villous cytotrophoblast (VCT)

source_name: RT-VCT 4

source_name: VCT 4


title: Lhx2GFP_positive_Fucci_Positive_rep3

description:
processed data column (in AllValuesConf_Irina.xls):
Lhx2GFP_positive_Fucci_Positive

value: WildType Lhx2GFP+ mKO2 +


title: SVAR_A4_RPMI_1

source_name: SVAR_A4_RPMI+10%LB_no vancomycin


title: SVAR_A4_RPMI_2


title: SVAR_STR1_Vanco_RPMI_2


title: Rosiglitazone-treated VCT vs control VCT Replicate 1

description: Biological replicate 1 of 5. Rosiglitazone-treated villous cytotrophoblast (RT-VCT) vs not treated/control villous cytotrophoblast (VCT)

source_name: RT-VCT 1

source_name: VCT 1


title: SVAR_STR1_RPMI_2

source_name: STR1_RPMI+10%LB_no vancomycin


title: SVAR_A5_RPMI_1


title: Lhx2GFP_positive_Fucci_Negative_rep2

description:
processed data column (in AllValuesConf_Irina.xls):
Lhx2GFP_positive_Fucci_Negative

value: WildType Lhx2GFP+ mKO2 -


title: Lhx2GFP_positive_Fucci_Positive_rep2


title: SVAR_A3_RPMI_2

source_name: SVAR_A3_RPMI+10%LB_no vancomycin


title: Lhx2GFP_negative_Fucci_Negative_rep1


title: SVAR_STR1_RPMI_1


title: SVAR_A3_RPMI_1


title: Lhx2GFP_negative_Fucci_Positive_rep1


title: SVAR_A2_RPMI_2

source_name: SVAR_A2_RPMI+10%LB_no vancomycin


title: Lhx2GFP_positive_Fucci_Negative_rep1


title: Lhx2GFP_positive_Fucci_Positive_rep1


title: APCnull tdTOM_positive_WNT_positive_rep2

description:
processed data column (in AllValuesConf_Irina.xls):
APCnull tdTOM_positive_WNT _positive

value: APC fl/fl tdTOM R26 fl/+


title: SVAR_TCH1516_RPMI_2

source_name: WT_RPMI+10%LB_no vancomycin


title: SVAR_A2_RPMI_1


title: APCnull tdTOM_positive_WNT_positive_rep1


title: SVAR_TCH1516_RPMI_1


title: APCnull tdTOM_positive_WNT_negative_rep4

description:
processed data column (in AllValuesConf_Irina.xls):
APCnull tdTOM_positive_WNT _negative


title: APCnull tdTOM_positive_WNT_negative_rep3


title: APCnull tdTOM_negative_WNT_negative_rep4

description:
processed data column (in AllValuesConf_Irina.xls):
APCnull tdTOM_negative_WNT _negative


title: SVAM_A12_Vanco_MHB_2

value: CA-MHB


title: SVAM_A12_Vanco_MHB_1


title: SVAM_A10_Vanco_MHB_1


title: APChet tdTOM_positive_WNT_positive_rep1

description:
processed data column (in AllValuesConf_Irina.xls):
APChet tdTOM_positive_WNT _positive

value: APC fl/+ tdTOM R26 fl/+


title: SVAM_A9_Vanco_MHB_1


title: APCnull tdTOM_negative_WNT_negative_rep3


title: SVAM_A9_Vanco_MHB_2


title: SVAM_STM3_Vanco_MHB_2


title: APChet tdTOM_positive_WNT_negative_rep3

description:
processed data column (in AllValuesConf_Irina.xls):
APChet tdTOM_positive_WNT _negative


title: 12mon_Sham_1

description:
Gene expression in microglia isolated from 12-month old Sham control
Sham1_2048S

source_name: Microglia isolated from 12-month old Sham control

value: Wistar Kyoto

tag: Sex

value: male

value: 12 month

tag: condition/time point

value: Sham


title: APChet tdTOM_positive_WNT_negative_rep4


title: SVAM_STM3_Vanco_MHB_1

value: vancomycin