title: the hindgut tissue of healthy fetal rats 3

city: beijing

first: hui

last: xiao

address: yabao road 2#

institute: capital institute of pediatric

hyb_protocol: 0.6 ug of Cy-3 labelled cRNA (specific activity>10.0 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 min in a reaction volume of 22.5ul containing 1X Agilent fragmentation buffer and 2X Agilent blocking agent following the manufacture instructions. On completion of the fragmentation reaction, 22.5ul of 2X Agilent hybridization buffer was added to the fragmentation mixtue and hybridized to Agilent rats Gene expression for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE wash buffer 1 (Agilent) and 1 min with 37 ℃ GE wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner (G2505C) using one color scan setting for 4X180k array slides (SCan area 61X21.6 mm,sacn resolution 3um,Dye channel is set to Green and Green PMT is set to 100%)

data_processing: the sacnned images were analyzed with feature extraction software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring13.0(Agilent). Probe that at least 1 out of 2 samples flagged as "detected " were maintained

source_name: terminal hindgut tissue

label_protocol: Cy3 lableed cRNA was prepared from 0.2ug RNA using the one-color low RNA input Linear Amplification PLUS kit (Agilent) according to the manufactue instruction, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and ceRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The Beijing Vital River Laboratory Animal Technology Co.Ltd. provided 12 mature and healthy Sprague Dawley (SD) rats of similar weight (8 females, 4 males) . The presence of sperm in a vaginal smear was considered as gestational day 0 after overnight mating (2 female rats were mated to 1 male rat. Then the pregnant rats were randomly divided into experimental and control group. On gestational day 10, 4 pregnant rats of the experimental group received stomach perfusion of 1% ethylenethiourea (ETU, 125 mg/kg), while in the control group, the pregnant rats received an stomach perfusion of distilled water correspondingly

extract_protocol: RNA was extracted by mirVanaTM RNA isolation kit (Applied biosystem p/n AM1556) following the manufactures instructions.

treatment_protocol: Embryo day 20 embryos were obtained from cesarean section. Through observing the presence of ARM under light microscope, the embryos were divided into ARM and control group. To prepare for the extraction of RNA, 1 cm of terminal hindgut tissue from the embryos was resected, and then frozen in liquid nitrogen immediately.

value: hindgut tissue of fetal rat


title: Healthy_Skin substitute_F22

status: Public on Sep 26 2018

type: RNA

city: Québec

first: Roxane

last: Pouliot

state: Québec

address: 1401, 18ème rue, aile R

country: Canada

institute: Centre de recherche en organogenese expérimentale de l'Université Laval/LOEX

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: Healthy skin substitute

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50-200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: Fibroblasts were cultured in Dulbecco-Vogt modification of Eagle's medium (DMEM) supplemented with 10% bovine growth serum, 100UI/mL penicillin and 25μg/mL gentamicin. Keratinocytes were cultured in a combination of DMEM with Ham's F12 (3:1), supplemented with 5% Fetal Clone II serum, 5μg/mL insulin, 0.4μg/mL hydrocortisone, 1e-10M cholera toxin, 10ng/mL human epidermal growth factors, 100UI/mL penicillin and 25 μg/mL gentamicin.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104).

treatment_protocol: Biopsies of skin substitute were taken after 21 days of culture at the air-liquid interface.

tag: condition

value: Healthy

tag: Sex

value: Female

tag: age


title: Non-lesional_Skin substitute_M70

source_name: Psoriatic skin substitute

value: Non-lesional

value: Male


title: WT PSA-NCAM- iNeurons after 13 days BAM (I15)

type: SRA

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology & University of Milano, Italy

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned with TopHat v2.0.1041, first to the mm10 Refseq transcriptome, and genes without a perfect alignment were realigned to genome (--read-realign-edit-dist=1), tolerating an edit distance of 3.
Quantification was performed on the Refseq transcriptome using Cuffquant v2.2.1, with multi-read correction (-u).
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-level count matrix

organism: Mus musculus

source_name: iNeurons (MEFs after 13 days of BAM transdifferentiation, sorted for PSA-NCAM- cells)

growth_protocol: MEF were cultured in the medium published in Vierbuchen et al., 2010, at 37° C, 3% O2 and 5% CO2.

extract_protocol:
Total RNA was depleted of rRNA using Ribozero
Illumina TruSeq Stranded Total RNA

treatment_protocol: Control and cKO MEFs at P1-P3 were treated for 5 days with 4-Hydroxytamoxifen (4-OHT), added to the MEF medium in a final concentration of 1000ng/ml, and then left either 2 or 7 days in medium not supplemented with 4-OHT.  Transdifferentiation was performed according to the protocol in Vierbuchen et al. (2010).

tag: cell type

value: iNeurons

tag: genotype

value: Wildtype

tag: sorting fraction

value: PSA-NCAM negative

tag: library type

value: Single-end


title: the hindgut tissue of healthy fetal rats 2

country: China

organism: Rattus norvegicus

tag: tissue


title: WT PSA-NCAM- iNeurons after 13 days BAM (I17)


title: Non-lesional_Skin substitute_F64


title: Lesional_Skin substitute_M70

value: Lesional


title: Healthy_Skin substitute_F46


title: Lesional_Skin substitute_F64


title: Healthy_Skin substitute_F38


title: Healthy_Skin substitute_F18


title: Kmt2b-/- PSA-NCAM- iNeurons after 13 days BAM (F16)


title: d03-m4539-plate2

city: New York

first: Efthymia

last: Papalexi

state: NY

address: 101 avenue of americas

country: USA

institute: New York Genome Center

description:
RNA1_counts.csv
modified Smart seq2 library

data_processing:
Modified Smart Seq 2 data were processed using Drop-seq tools v1.12 (Macosko et al., 2015)
R1 reads: cell barcode, UMI read
R2 reads: cDNA read
Genome_build: Mus_musculus.GRCm38.84
Supplementary_files_format_and_content: comma separated values files for modified Smart-Seq 2 data
Supplementary_files_format_and_content: RNA1_counts.csv: raw counts for samples 1-9
Supplementary_files_format_and_content: RNA2_counts.csv: raw counts for samples 10-14

molecule: polyA RNA

source_name: Lin- Tom+ mouse cells

extract_protocol:
We used a modified version of Smart Seq 2 protocol that allows for sequencing of the 3' end of each transcript. Detailed protocol can be found here: dx.doi.org/10.17504/protocols.io.nkgdctw
Lin-  Tom+ single cells were sorted into 96well plates and a modified version of Smart Seq 2 protocol that allows for sequencing of the 3' end of each transcript was used. Protocol can be found here dx.doi.org/10.17504/protocols.io.nkgdctw

value: Lin- Tom+  cells


title: Kmt2b-/- PSA-NCAM- iNeurons after 13 days BAM (E11)


title: WT PSA-NCAM- iNeurons after 13 days BAM (H6)


title: the hindgut tissue with ETU-induced ARMs 1


title: Kmt2b-/- PSA-NCAM- iNeurons after 13 days BAM (F11)


title: Kmt2b-/- PSA-NCAM+ iNeurons after 13 days BAM (F11)

source_name: iNeurons (MEFs after 13 days of BAM transdifferentiation, sorted for PSA-NCAM+ cells)

value: PSA-NCAM positive

value: Paired-end


title: the hindgut tissue with ETU-induced ARMs 3


title: Kmt2b-/- PSA-NCAM+ iNeurons after 13 days BAM (F16)


title: the hindgut tissue of healthy fetal rats 1


title: d03-m4539-plate1


title: the hindgut tissue with ETU-induced ARMs 2


title: WT PSA-NCAM+ iNeurons after 13 days BAM (I17)


title: Condition D rep1

city: Merritt Island

first: Wayne

last: Nicholson

state: FL

address: Space Life Sciences Laboratory 505 Odyssey Way Room 201B

department: Microbiology and Cell Science

institute: University of Florida

data_processing:
Illumina HiSeq Control Software v2.2.37 was used for basecalling.
Sequenced reads were trimmed to remove low-quality base-calls. Trimmed sequences were mapped to the ATCC 27592 genome using bowtie2 v2.3.2. Aligned sequences were quantified at the gene level using HTSeq v0.6.1.
Gene counts for each sample were imported into R v3.4.2 using limma v3.33.7. Differential expression analysis was done using the default parameters in limma and a significance cut-off of 2 fold with a p value < 0.01.
Genome_build: RefSeq NC_021741.1
Supplementary_files_format_and_content: .csv files include the raw count values for each sample, and the limma normalized abundant output for each condition comparison.

organism: Serratia liquefaciens

extract_protocol:
Cells were collected using a bench top centrifuge, and RNA was extracted using the RiboPureTM RNA Purification Kit (Thermo Fisher Scientific, Waltham, MA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: atmosphere

tag: temperature

tag: pressure

value: 1013 mbar


title: Condition D rep3


title: Condition D rep2


title: WT PSA-NCAM+ iNeurons after 13 days BAM (I15)


title: WT PSA-NCAM+ iNeurons after 13 days BAM (A6)


title: Condition C rep2


title: Kmt2b-/- PSA-NCAM+ iNeurons after 13 days BAM (E11)


title: Kmt2b-/- PSA-NCAM+ iNeurons after 13 days BAM (E10)


title: Condition C rep3


title: WT PSA-NCAM+ iNeurons after 13 days BAM (A1)


title: WT_E

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

country: United Kingdom

institute: University of Leicester

hyb_protocol: Labelled cRNA was then hybridized over night at 65˚C onto the SurePrint G3 Mouse Gene Exp v2 Array)  (Agilent, Santa Clara, CA, USA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters

label_protocol: A total of 100ng of total RNA was reverse transcribed, converted into complementary RNA (cRNA) and labelled with Cy3 using the LowInput QuickAmp Labeling Kit One-Color according to manufacturer’s protocol (Agilent, Santa Clara, CA, USA).

extract_protocol: Total RNA was purified from CD4+ T-cells isolated from Roquinsan/+ and wildtype mice on a Promega Maxwell 16 robot using the simplyRNA cell purification Kit (Promega, Madison, WI, USA). RNA quality was checked on a Bioanalyzer 2100 (Agilent, UK). All the RNA samples had a RNA Integration Number (RIN) > 7.

tag: genotype/variation

value: Wild Type


title: WT PSA-NCAM+ iNeurons after 13 days BAM (A3)


title: Kmt2b-/- PSA-NCAM+ iNeurons after 13 days BAM (E17)


title: Condition C rep1


title: Condition B rep1


title: Condition B rep3


title: Condition A rep3

value: 7 mbar


title: WT_B


title: Condition A rep1


title: WT_G


title: WT_D


title: WT_A


title: WT_C


title: Condition B rep2


title: WT_F


title: SRQ_E

value: Roquinsan/+


title: SRQ_D


title: SRQ_G


title: SRQ_F


title: SRQ_C


title: SRQ_B


title: SRQ_A


title: Condition A rep2


title: H4Lu1_3 [BS-seq]

status: Public on Sep 25 2018

city: Chicago

first: Lauren

middle: Elizabeth

last: Blake

state: Illinois

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Caucasian

library_source: genomic

data_processing:
50 bp single-end RNA-seq reads from each species were trimmed and mapped to the appropriate genome (hg19, panTro3, rheMac2) using the Bismark aligner (version 0.8.1) (Krueger et al. 2011). We permitted one mismatch in the seed of the alignment, and by default Bismark reports only uniquely mapped reads. We applied the Bismark deduplication script to each technical replicate to remove reads mapped to the same starting genomic position, which likely arise through PCR amplification of the same DNA fragments during library preparation (Bock 2012).
We estimated the percentage of methylation at an individual cytosine site by the ratio of the number of cytosines (unconverted) found in mapped reads at this position, to the total number of reads covering this position (sequenced as cytosine or thymine, i.e., converted or unconverted). We calculated methylation estimates genome-wide at CpG sites using the methylation extractor tool from Bismark (version 0.8.1). We additionally collapsed information from both DNA strands (because CpG methylation status is highly symmetrical on opposite strands (Lister et al. 2009) to achieve better precision in methylation estimates across the genome.
To obtain CpGs that mapped to multiple species, the chimpanzee and rhesus macaque CpG sites were mapped to human coordinates (hg19) using chain files from ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/ and the LiftOver tool from the UCSC genome browser [35]. These files had previously been filtered for paralogous regions and repeats, but we also removed positions that were not remapped to their original position when we mapped from human back to their original genome. Chimpanzee and rhesus macaque CpG sites were mapped to human, even if their orthologous positions was not a CpG site in human.
Genome_build: hg19, panTro3, rheMac2
Supplementary_files_format_and_content: Per CpG methylation level and coverage for all individuals (hg19 coordinates). Object of type 'BSseq' (Hansen et al. 2012).

molecule: genomic DNA

source_name: post mortem frozen tissue

extract_protocol:
We prepared a total of 48 whole-genome bisulfite sequencing libraries (BS-seq) from extracted DNA as previously described (Tung et al. 2012, Banovich et al. 2014).
For each sample, we prepared at least two libraries, with independent PCR amplifications to minimize PCR duplication rates. The BS-seq libraries were sequenced on 111 lanes on 17 flow-cells on an Illumina HiSeq 2500 sequencer in the Gilad lab or at the University of Chicago Genomics Facility

treatment_protocol: Tissues were received postmortem.

tag: individual

value: lung

value: male


title: H4Li2 [BS-seq]

description: Caucasian

value: liver


title: H4Lu1_15 [BS-seq]

description: Caucasian


title: H4Lu2 [BS-seq]

description: Caucasian


title: H4Li1 [BS-seq]

description: Caucasian


title: H4K4 [BS-seq]

description: Caucasian

value: kidney


title: H4K3 [BS-seq]

description: Caucasian


title: A-M - Non Lesional Skin

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description: 18_HGU133 plus 2.0_Irma_062712.CEL

hyb_protocol: The labeled target was fragmented and hybridized to probe arrays, using Encore Biotin Module from NuGen (San Carlos, Calif).

scan_protocol: The chips were washed, stained with streptavidin-phycoerythrin, and scanned (HP GeneArray Scanner; Hewlett-Packard Company, Palo Alto, Calif) On each chip, the human housekeeping genes β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) served as controls. Suite 5.0 software normalized the expression level values using these controls.

data_processing:
Affymetrix CEL files for the HGU133Plus2.0 chips were scrutinized for spatial artifacts using the Harshlight package.E9 Classic microarray quality control was obtained by the Bioconductor’s array Quality Metrics package.
Expression measures obtained using GCRMA algorithm (using GCRMA package from R package/Bioconductor). To follow normality assumptions required by most statistical methods used, the expressions were log2-transformed

label: biotin

source_name: AD_non lesional skin

label_protocol: DNA was removed with on-column DNAse digestion by the Qiagen RNAse-free DNAse Set. Total RNA (50 ng) was reverse transcribed and amplified with Ovation Whole Blood Solution from NuGen (San Carlos, Calif).

extract_protocol: Total RNA was extracted by using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, Calif), and DNA was removed with the Qiagen RNAse-free DNAse Set.

tag: patient id

value: A-M

value: Non Lesional Skin

tag: atopic dermatitis (ad) history

value: Yes

tag: patient with positive dust mite reaction

tag: patient with positive fragrance reaction

value: No

tag: patient with positive nickel reaction


title: G-L - Dust Mite Atopic Patch Skin

description: 87_HGU133 plus 2.0_Irma_080712.CEL

source_name: NonAD_dust mite atopic patch skin

value: G-L

value: Dust Mite Atopic Patch Skin


title: L-M - Dust Mite Atopic Patch Skin

description: 36_HGU133 plus 2.0_Irma_062712.CEL

value: L-M


title: ASK - Dust Mite Atopic Patch Skin

description: 101_HGU133 plus 2.0_Irma_080712.CEL

value: ASK


title: N-A - Non Lesional Skin

description: 49_HGU133 plus 2.0_Irma_071012.CEL

source_name: NonAD_non lesional skin

value: N-A


title: S-L - Non Lesional Skin

description: 72_HGU133 plus 2.0_Irma_071112.CEL

value: S-L


title: GFP3 [iCLIP-seq]

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

institute: University of Naples “Federico II”

data_processing:
iCLIP data was processed following the iCount pipeline (Curk et al., 2016; https://github.com/tomazc/iCount). Briefly, 'iCount demultiplex' was used to separate and trim off molecular and sample barcodes as well as adapter sequences. The reads were then mapped to the human genome (GRCh38) using the STAR aligner (Dobin et al., 2013) (Curk et al., 2016). 'iCount xlsites' was used to determine the number of unique crosslinked sites (unique cDNA molecules) for any given position.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab separated text file. Contains peak coordinates.

source_name: HeLa cells

growth_protocol: HeLa cells were grown on 15-cm dishes until were approximately 85% confluent

extract_protocol:
SDOS-eGFP cells were photoactivable ribonucleoside-cross-linked on ice at and 0.30 J cm−2 with UV light at 365 nM. eGFP cells were cross-linked on ice at 0.15 J cm−2 with UV light at 254 nM. Immediately after irradiation, cells were lysed in 1 mL of lysis buffer (NaCl 100mM, MgCl2 5mM, Tris pH 7.5 10mM, NP40 0.5%, SDS 0.1%, Na deoxycholate 0.5%, DTT 1mM (fresh), 1x AEBSF (fresh). The cell lysate was passed 3 times through 27 1/2G needle and sonicated using a bioruptor (Digenode) for 3 cycles of 10 seconds (pause 15 seconds), level M at 4ºC, then it was cleared by centrifugation at 17900g for 10 min at 4°C.
RNA was then partially digested by adding 10 μl of 1:100 dilution of RNase I (Ambion, AM2295), as well as 2 μl of Turbo DNase (Ambion, AM 2238). After 3 min of incubation at 37°C under shaking at 1100 rpm 11 μl of Ribolock (Invitrogen) were added to each lysate. The lysates were precleared by incubation with 50 µL of equilibrated control agarose beads (Thermo Scientific) for 30 min at 4°C under gentle rotation. eGFP-fusion proteins were then captured from precleared lysates by incubation with 40 µL of GFP-Trap agarose beads (GFP-Trap_A, Chromotek) per mL of lysate for 2 h, 4°C, gentle rotation. Beads were collected by centrifugation and washed twice with High salt buffer (NaCl 500mM, Tris HCL pH7.5 20mM, MgCl2 1mM, NP40 0.05%, SDS 0.10%, 1x AEBSF (fresh)); twice with Medium salt buffer (NaCl 250mM, Tris HCl pH7.5 20mM, MgCl2 1mM, NP40 0.05%, 1x AEBSF (fresh)) and twice with Low salt buffer (NaCl 150mM, Tris HCl pH7.5 20mM, MgCl2 1mM, NP40 0.01%, 1x AEBSF (fresh)). The RNA was then dephosphorylated, and 3’-linker ligated as described in [16]. The protein/RNA complexes were isolated as described in [17]. Samples were processed for subsequent steps as described in Huppertz et al 2014. cDNA libraries obtained after PCR amplification with universal Solexa primers (25 cycles) were multiplexed and sequenced using an Illumina Next-generation sequencing platform.

treatment_protocol: Cells were treated with doxycycline (1 ug/mL) for 16 hrs to induce the expression of GFP-fusion proteins. HeLa SDOS-eGFP cells were treated with 100 μM 4-thiouridine for 16 hrs before the lysis.

value: T-REx-HeLa Cell Line

value: eGFP under Tet repressor


title: A-M - Dust Mite Atopic Patch Skin

description: 21_HGU133 plus 2.0_Irma_062712.CEL

source_name: AD_dust mite atopic patch skin


title: SYA - Non Lesional Skin

description: 29_HGU133 plus 2.0_Irma_062712.CEL

value: SYA


title: Z-Y - Dust Mite Atopic Patch Skin

description: 58_HGU133 plus 2.0_Irma_071012.CEL

value: Z-Y


title: C-C - Dust Mite Atopic Patch Skin

description: 48_HGU133 plus 2.0_Irma_071012.CEL

value: C-C


title: G-N - Dust Mite Atopic Patch Skin

description: 13_HGU133 plus 2.0_Irma_062112.CEL

value: G-N


title: H-R - Dust Mite Atopic Patch Skin

description: 28_HGU133 plus 2.0_Irma_062712.CEL

value: H-R


title: Z-Y - Non Lesional Skin

description: 54_HGU133 plus 2.0_Irma_071012.CEL


title: SYA - Dust Mite Atopic Patch Skin

description: 32_HGU133 plus 2.0_Irma_062712_2.CEL


title: H4H1 [BS-seq]

description: Caucasian

value: heart

tag: Sex

value: male


title: D-R - Dust Mite Atopic Patch Skin

description: 96_HGU133 plus 2.0_Irma_080712.CEL

value: D-R

value: Yes


title: G-L - Non Lesional Skin

description: 84_HGU133 plus 2.0_Irma_071112.CEL

value: G-L

value: Non Lesional Skin

value: No


title: B-A - Non Lesional Skin

description: 103_HGU133 plus 2.0_Irma_080812.CEL

value: B-A


title: S-L - Dust Mite Atopic Patch Skin

description: 75_HGU133 plus 2.0_Irma_071112.CEL

value: Dust Mite Atopic Patch Skin


title: D-R - Non Lesional Skin

description: 95_HGU133 plus 2.0_Irma_080712.CEL


title: T-A - Dust Mite Atopic Patch Skin

description: 108_HGU133 plus 2.0_Irma_080812.CEL

value: T-A


title: H3Lu4 [BS-seq]

description: Caucasian

value: lung


title: N-A - Dust Mite Atopic Patch Skin

description: 53_HGU133 plus 2.0_Irma_071012.CEL

value: N-A


title: H3Li1 [BS-seq]

description: Caucasian

value: liver


title: H3Lu3 [BS-seq]

description: Caucasian


title: H3K1 [BS-seq]

description: Caucasian

value: kidney


title: H3H2 [BS-seq]

description: Caucasian


title: H3H1 [BS-seq]

description: Caucasian


title: H3K2 [BS-seq]

description: Caucasian


title: B-A - Dust Mite Atopic Patch Skin

description: 105_HGU133 plus 2.0_Irma_080812.CEL


title: H4H2 [BS-seq]

description: Caucasian


title: H2Lu4 [BS-seq]

description: Caucasian


title: H2Lu3_17 [BS-seq]

description: Caucasian


title: H2Lu3_14 [BS-seq]

description: Caucasian


title: mLN_SPF_migDC_3

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

description:
processed data file:
DESeq2_genes_diffexp_by_fc_Migr_mLN_SPF_vs_Migr_pLN_SPF.csv

data_processing:
Libraries were aligned versus the mouse reference genome (assembly: GRCm38) using the splice junction mapper Tophat2 v1.2.0 with default parameterization.
Reads aligned to annotated genes were quantified with the htseq-count program [Anders, Pyl, Huber, 2015, Bioinformatics 31, 166-169].
Determined read counts served as input to DESeq2 [Love, Huber, Anders, 2014, Genome Biology 15, 550] for pairwise detection and quantification of differential gene expression.
RPKM (reads per kilobase maximal transcript length per million mapped reads) values were computed for each library from the raw gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: .csv files include RPKM values, q-value and log2(FC) for each pair-wise comparison

growth_protocol: ex vivo

extract_protocol:
Total RNA was extracted from FACS‑sorted migratory DCs using the RNeasy Plus Micro Kit (Qiagen).
cDNA was synthesized and amplified using template switching technology of the SMART‑Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories), followed by purification using the Agencourt AMPure XP Kit (Beckman Coulter). Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina). The Agilent Technologies 2100 Bioanalyzer was used to control quality and integrity of nucleic acids after each step.

treatment_protocol: For RNA‑seq analysis, CD45+ cells enriched with autoMACS were stained using fluorescence‑coupled antibodies and sorted for migratory DCs by FACS (Aria II, 100 μm nozzle).

tag: strain background

value: BALB/c

tag: ln

value: gut-draining

tag: transplanted

value: no

tag: cell type

value: FACS-sorted migratory DCs


title: mLN_SPF_migDC_1


title: mLN_SPF_migDC_2


title: mLN_SPF_Tx_migDC_7

description:
processed data file:
DESeq2_genes_diffexp_by_fc_Migr_mLN_SPF_Tx_vs_Migr_pLN_SPF_Tx.csv

value: yes


title: mLN_SPF_migDC_4


title: H2Li2 [BS-seq]

description: Caucasian

tag: tissue

value: male


title: mLN_SPF_Tx_migDC_6


title: H2Lu3_15 [BS-seq]

description: Caucasian


title: H2K2 [BS-seq]

description: Caucasian


title: H2Li1 [BS-seq]

description: Caucasian


title: mLN_SPF_migDC_5


title: H1Lu2_17 [BS-seq]

description: Caucasian


title: H2H1 [BS-seq]

description: Caucasian

value: heart


title: H1Lu2_6 [BS-seq]

description: Caucasian


title: pLN_SPF_migDC_4

value: skin-draining


title: mLN_SPF_Tx_migDC_3


title: H2H2 [BS-seq]

description: Caucasian


title: H1Lu1 [BS-seq]

description: Caucasian


title: H2K1 [BS-seq]

description: Caucasian


title: mLN_SPF_Tx_migDC_4


title: mLN_SPF_Tx_migDC_2


title: pLN_SPF_migDC_3


title: H1Li2 [BS-seq]

description: Caucasian


title: H3Li2 [BS-seq]

description: Caucasian


title: pLN_SPF_migDC_2


title: pLN_SPF_migDC_1


title: H1Li1.gz

description: Caucasian


title: H1K2 [BS-seq]

description: Caucasian


title: pLN_SPF_Tx_migDC_3


title: H1K1 [BS-seq]

description: Caucasian


title: pLN_SPF_Tx_migDC_2


title: mLN_SPF_Tx_migDC_5


title: H1H3 [BS-seq]

description: Caucasian

value: heart (later reclassified as liver)


title: mLN_SPF_Tx_migDC_1


title: pLN_SPF_Tx_migDC_4


title: H1H1 [BS-seq]

description: Caucasian


title: pLN_SPF_Tx_migDC_1


title: H4Lu

description: Caucasian

data_processing:
50 bp single-end RNA-seq reads from each species were trimmed and mapped to the appropriate genome (hg19, panTro3, rheMac2) using Tophat2 (version 2.0.11) (Kim et al. 2013). We kept only reads that mapped uniquely.
The number of reads falling into orthologous meta-exons across 30,030 Ensembl genes from hg19, panTro3 and rheMac2 (Blekhman et al. 2010) was determined using featureCounts within SubRead (version 1.4.4) (Liao et al. 2014).
Genome_build: hg19, panTro3, rheMac2
Supplementary_files_format_and_content: RNA-seq counts for orthologous genes for all individuals

growth_protocol: Tissues were received postmortem.

extract_protocol:
We extracted RNA from each tissue sample using TRIzol (Invitrogen, as described in Blekhman et al. 2010).
Samples were pooled together in 2 pools for RNA-seq library generation (as described in Blekhman et al. 2010).  50 bp single-end RNA-seq libraries were sequenced on 26 lanes on 4 different flow-cells on an Illumina HiSeq 2500 sequencer in the Gilad lab or at the University of Chicago Genomics Facility, following the manufacturer's protocols.


title: H3Lu

description: Caucasian


title: H4K

description: Caucasian


title: H3Li

description: Caucasian


title: H4Li

description: Caucasian


title: H1H4 [BS-seq]

description: Caucasian


title: H3K

description: Caucasian


title: H4H

description: Caucasian


title: H1H2 [BS-seq]

description: Caucasian


title: H2Lu

description: Caucasian


title: H2Li

description: Caucasian


title: H2K

description: Caucasian


title: H2H

description: Caucasian


title: H1Lu

description: Caucasian


title: TLR4-KO ethanol rep1

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description:
small RNA
KE_1

data_processing:
A quality control analysis of the resulting fastq sequencing files was performed using FastQC, version 0.11.6
Then the adapter sequences from Cutadapt version 1 were trimmed 8
The trimmed reads were mapped against the databases for homologous non-coding RNAs (ncRNAs) with Bowtie, version 2.2.5, and with version 2.1.0 of the TopHat software
Normalization and post-alignment filters were used to remove low-quality reads, alignments characterized by sequencing errors or multiple mismatches
Read counts were generated using the Python and PERL programming  software, which allows putative miRNAs of interest to be detected and annotated.
Genome_build: Ensembl GRCm38 ncRNA
Supplementary_files_format_and_content: tab-delimited text file include normalized values for each sample

source_name: mice brain cortex

extract_protocol:
Cortex were removed and frozen on nitrogen liquid. RNA was isolated using miRNeasy mini Kit (Appendix A, Qiagen, Hilden, Germany). Libraries were prepared with Truseq library prep Small RNA Sample Preparation kit (Illumina, San Diego, USA) 100ng of smallRNA fraction was used for the construction of sequencing libraries.
The small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For chronic alcohol treatment, the mice were housed (4 animals/cage) and maintained with water (WT and TLR4-KO control) or with water containing 10% (v/v) alcohol. They were placed on a solid diet ad libitum for 5 months

tag: strain

value: brain

value: TLR4-KO ethanol


title: wild type rep2

description:
small RNA
WT_2

value: wild type


title: wild type rep1

description:
small RNA
WT_1


title: wild type ethanol rep2

description:
small RNA
WE_2

value: wild type ethanol


title: TLR4-KO rep3

description:
small RNA
KO_3


title: TLR4-KO ethanol rep2

description:
small RNA
KE_2


title: TLR4-KO rep2

description:
small RNA
KO_2


title: wild type rep3

description:
small RNA
WT_3


title: TLR4-KO rep1

description:
small RNA
KO_1


title: wild type ethanol rep1

description:
small RNA
WE_1


title: R4Lu2 [BS-seq]

description: Indian origin

organism: Macaca mulatta

value: lung


title: H3H

description: Caucasian


title: H1H

description: Caucasian


title: R4Lu1 [BS-seq]

description: Indian origin


title: wild type ethanol rep3

description:
small RNA
WE_3


title: R4Li2 [BS-seq]

description: Indian origin


title: R4Li1 [BS-seq]

description: Indian origin


title: H1Li

description: Caucasian


title: R4K2 [BS-seq]

description: Indian origin


title: H1K

description: Caucasian


title: R4K1 [BS-seq]

description: Indian origin


title: R3Lu4 [BS-seq]

description: Indian origin


title: R4Lu3 [BS-seq]

description: Indian origin


title: R4H2 [BS-seq]

description: Indian origin


title: TLR4-KO ethanol rep3

description:
small RNA
KE_3


title: R3Lu3 [BS-seq]

description: Indian origin


title: R3Lu2 [BS-seq]

description: Indian origin


title: R3Li4 [BS-seq]

description: Indian origin


title: R3Li3 [BS-seq]

description: Indian origin


title: NCH644_Hypoxia

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

country: Germany

institute: University Hospital Heidelberg

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw-intensity data were obtained after image analysis of the fluorescent spot intensity reads. All preprocessing and normalization steps were performed in the R programming environment [www.r-project.org]. Inter-array normalization was conducted using vsn normalization in the vsn package.

source_name: glioma stem cell line

label_protocol: Standard labeling protocol of Genomic Core Facility of the German Cancer Research Center (DKFZ, Heidelberg, Germany)

growth_protocol: Cells were grown as floating neurospheres in DMEM/F-12 medium containing 20% BIT serum-free supplement, basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) at 20ng/ml each (all Provitro, Berlin, Germany). To study expression changes, IDH1mut and IDH1wt GSCs were grown under normoxic and hypoxic conditions. Hypoxic conditions (1.5% O2, 5% CO2, 93.5% N2) were established in an O2- and CO2-controlled tissue culture incubator (Nunc, Langenselbold, Germany) as previously described.

extract_protocol: Total RNA was extracted from tissue using the AllPrep Kit (Qiagen) according to manufacturer's instructions. RNA integrity was assessed by the Agilent 2100 Bioanalyzer.

tag: oxygen

value: Hypoxia

tag: idh1 mutation status

tag: source tissue

value: primary Glioblastoma

tag: gender

value: female

tag: age at diagnosis


title: R4H1 [BS-seq]

description: Indian origin

tag: individual


title: NCH660h_Hypoxia


title: NCH601_Hypoxia


title: NCH421k_Hypoxia


title: C4Lu4 [BS-seq]

description: Subspecies/admixture- Western

organism: Pan troglodytes


title: C4Lu3 [BS-seq]

description: Subspecies/admixture- Western


title: R3K1 [BS-seq]

description: Indian origin

value: kidney


title: R3K2 [BS-seq]

description: Indian origin


title: NCH644_Normoxia

value: Normoxia


title: NCH601_Normoxia


title: NCH645_Hypoxia

value: secondary Glioblastoma


title: R3H1 [BS-seq]

description: Indian origin


title: R3H2 [BS-seq]

description: Indian origin


title: NCH551b_Hypoxia


title: NCH620_Normoxia


title: C4Li1 [BS-seq]

description: Subspecies/admixture- Western

value: liver


title: C4Li2 [BS-seq]

description: Subspecies/admixture- Western


title: NCH612_Hypoxia

value: Oligo°III


title: R2Lu2 [BS-seq]

description: Indian origin


title: NCH612_Normoxia

value: male


title: NCH551b_Normoxia


title: C4K2 [BS-seq]

description: Subspecies/admixture- Western


title: NCH620_Hypoxia


title: R2Lu1 [BS-seq]

description: Indian origin


title: NCH645_Normoxia


title: NCH660h_Normoxia


title: C4K3 [BS-seq]

description: Subspecies/admixture- Western


title: NCH421k_Normoxia


title: C4K1 [BS-seq]

description: Subspecies/admixture- Western


title: R2Li2 [BS-seq]

description: Indian origin


title: C4H1 [BS-seq]

description: Subspecies/admixture- Western

value: heart


title: C4H2 [BS-seq]

description: Subspecies/admixture- Western


title: R2K2 [BS-seq]

description: Indian origin


title: R2H2 [BS-seq]

description: Indian origin


title: R2H1 [BS-seq]

description: Indian origin


title: R2K1 [BS-seq]

description: Indian origin


title: R2Li1 [BS-seq]

description: Indian origin


title: C3Lu2 [BS-seq]

description: Subspecies/admixture- hybrid between Central and Western


title: C3Lu1 [BS-seq]


title: C3Li4 [BS-seq]


title: C3Li3 [BS-seq]


title: C3K2_17 [BS-seq]


title: C3K2_9 [BS-seq]


title: R1Li2 [BS-seq]

description: Indian origin


title: R1Lu2 [BS-seq]

description: Indian origin


title: R1Li1 [BS-seq]

description: Indian origin


title: C3K1_15 [BS-seq]


title: R1K1_1 [BS-seq]

description: Indian origin


title: R1K1_3 [BS-seq]

description: Indian origin


title: R1H2 [BS-seq]

description: Indian origin


title: C2Lu2 [BS-seq]

description: Subspecies/admixture- hybrid between Central and Nigerian


title: C3H1 [BS-seq]


title: C2Lu1 [BS-seq]


title: R1H1 [BS-seq]

description: Indian origin


title: R1K2 [BS-seq]

description: Indian origin


title: C3K1_3 [BS-seq]


title: C2Li2 [BS-seq]


title: C2Li1 [BS-seq]


title: R4Li

description: Indian origin


title: R1Lu3 [BS-seq]

description: Indian origin


title: C2K2 [BS-seq]


title: C2H2 [BS-seq]


title: R4K

description: Indian origin


title: R3Li

description: Indian origin


title: C1Lu3 [BS-seq]


title: C1Lu2 [BS-seq]


title: C1Lu4 [BS-seq]


title: C3H2 [BS-seq]


title: R3H

description: Indian origin


title: C2K1 [BS-seq]


title: R4H

description: Indian origin


title: R4Lu

description: Indian origin


title: C2H1 [BS-seq]


title: R1Lu

description: Indian origin


title: R2K

description: Indian origin


title: R2Li

description: Indian origin


title: R2Lu

description: Indian origin


title: R3K

description: Indian origin


title: R2H

description: Indian origin


title: R1K

description: Indian origin


title: R1H

description: Indian origin


title: C1K4 [BS-seq]


title: C1H3 [BS-seq]


title: C1Li1 [BS-seq]


title: C1K3 [BS-seq]


title: C4Lu

description: Subspecies/admixture- Western


title: C1Li2 [BS-seq]


title: C1H2 [BS-seq]


title: C1H1 [BS-seq]


title: R3Lu

description: Indian origin


title: C4Li

description: Subspecies/admixture- Western


title: C3Li


title: C4K

description: Subspecies/admixture- Western


title: C3H


title: C3K


title: R1Li

description: Indian origin


title: C1H4 [BS-seq]


title: C2Lu


title: Treg_ATAC_Spl_wCol_Nrp1n_2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Base calling was performed with Real-Time Analysis v2.4.11
ATAC-seq reads from two replicates per sample were filtered for quality using sickle v1.2 (default settings for PE reads), adapter-trimmed using cutadapt v1.8.3 (`-e 0.1, -m 20`), and mapped to mm9 using Bowtie v2.2.4, keeping only mate pairs that mapped to a single best location using samtools v1.3, and were non-duplicates using Picard v1.130.
To generate bigWig files, filtered and mapped reads were used to generate tag directories in HOMER v4.6 (`makeTagDirectory -tbp 1 -checkGC -illuminaPE`), followed by bedGraph files (HOMER  `makeUCSCfile -fsize 1e50 -norm 1e6`), which were then used to generate bigWig files using UCSC-tools (`bedGraphToBigWig`). For colon Treg samples, raw data files were generated from purified sub-populations of Nrp1(+) and Nrp1(-) Tregs. For each replicate, a combined Treg sample was derived by randomly sampling from Nrp1+ and Nrp1- .bam files and combining reads in the proportions in which these Tregs are found in colonic lamina propria (~50% Nrp1+/50% Nrp1- for the age of mice used in this study). This combined .bam file was then used to generate a processed bigWig file in the same pipeline outlined above. This process was repeated for splenic Treg samples corresponding to the Nrp1(+) and Nrp1(-) populations, except this time the proportions in the final file were 90% Nrp1(+), 10% Nrp1(-), based on flow-cytometric analysis of splenic CD4+FOXP3+ Tregs from the mice used in our study.
The data in the BED file represent the mm9 chromosomal coordinates of the complete set of 75,363 Treg open chromatin regions (OCRs) obtained by merging the individual peak/OCR files from all Treg ATAC-seq samples, as detailed in the methods of the manuscript DiSpirito, Zemmour et al. (pending).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, BED

source_name: Spleen

extract_protocol:
10,000 cells were sorted into collection buffer (PBS, 0.5% BSA, 2mM EDTA), pelleted and lysed in hypotonic buffer (10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% NP-40). Nuclei were pelleted by centrifugation for 30 min. at 500g, 4oC.
ATAC-seq adapted from Buenrostro et al., 2013 and Lara-Astiaso et al., 2014. Nuclear pellets were re-suspended in 5uL of transposition mix (1uL Tagment DNA Enzyme, 2.5uL Tagment DNA Buffer from Nextera DNA Sample Prep Kit, 1.5uL H2O), and incubated at 37C for 60min. Two sequential PCR reactions were performed. After the first PCR, libraries were selected for small fragments (< 600bp) using SPRI beads followed by a second round of PCR with the same conditions, and a final SPRI bead purification to capture all fragments for the final library.

tag: mouse id

value: spleen


title: Treg_ATAC_Spl_wCol_Nrp1p_2


title: C2K


title: Treg_ATAC_Spl_wCol_Nrp1n_1


title: Treg_ATAC_Spl_wCol_Nrp1p_1


title: C2Li


title: C1Li


title: Treg_ATAC_Spl_wVAT_2


title: Treg_ATAC_Spl_wMus_2


title: Treg_ATAC_Spl_wVAT_1


title: C1K


title: C2H


title: C3Lu


title: C4H

description: Subspecies/admixture- Western


title: Pam3CSK4 IFN-g rep2

city: Shanghai

first: Jiawen

last: Qian

address: 130 Dong'an Road

department: Immunology

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
used Tophat v2.1.0 to map the cleaned reads to the mouse mm10 reference genome with two mismatches.
Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM, count

source_name: adult microglia

growth_protocol: Adult microglia were prepared from 6-8 weeks old mice. Microglia were plated onto 24-well plates at a density of 1×10^5 cells per well with DMEM/F12 supplemented with 10% heat-inactivated FBS, 2 mM glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 5 ng/ml recombination TGF-β1 (Miltenyi, Germany), and 10 ng/ml Recombinant Mouse M-CSF Protein (R&D, USA). Half of the medium was changed every 3 days, for a total of 10-14 days. Cultures were incubated at 37 °C in a humidified atmosphere of 5% CO2/95%.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100. Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary microglia treated with or without Pam3CSK4 (100 ng/ml) for 24 h and followed with IFN-γ (20 ng/ml) for 24 h.

value: cerebrum

tag: treatment

value: Pam3CSK5 & IFN-gamma

tag: age

value: 6-8 weeks


title: Pam3CSK4 IFN-g rep1

value: Pam3CSK4 & IFN-gamma


title: IFN-g rep3

value: IFN-gamma


title: Pam3CSK4 IFN-g rep3

value: Pam3CSK6 & IFN-gamma


title: Treg_ATAC_Colon_Nrp1n_2

source_name: Colonic lamina propria

value: colon


title: Treg_ATAC_Colon_Nrp1n_1


title: C1H


title: Treg_ATAC_Colon_Nrp1p_2


title: IFN-g rep2


title: IFN-g rep1


title: Treg_ATAC_Colon_Nrp1p_1


title: Pam3CSK4 rep2


title: Treg_ATAC_Muscle_2

source_name: Hindlimb skeletal muscle

value: muscle


title: C1Lu

value: lung


title: Treg_ATAC_Spl_wMus_1


title: Control rep3


title: Treg_ATAC_VAT_2

source_name: Epididymal adipose tissue

value: adipose


title: Control rep1


title: Treg_ATAC_VAT_1


title: Pam3CSK4 rep1


title: Treg_ATAC_Muscle_1


title: NF24

city: Neuherberg-Munich

first: Pawel

last: Smialowski

address: Ingolstaedter Landstrasse 1

department: Institute of Stem Cell Research

institute: Helmholtz Zentrum Muenchen German Research Center for Environmental Health

description:
RiboZero
Total_FPKM.csv
3 replicates

data_processing:
Aligned using STAR 2.4.2a
Processed using rsem 1.3.0 and annotation release 103
Genome_build: Xt9.1

organism: Xenopus tropicalis

source_name: Animal Caps

growth_protocol: Embryos were grown as described by Showell, C. and Conlon, F.L. (2009)

extract_protocol:
total RNA was extracted using TRIzol (ambion) cleaned-up using Rneasy mini-Kit (qiagen) following manufacturer´s instructions. rRNA was depleted using using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) from Illumina using the manufacturer’s instructions
paired end libraries were prepared using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer´s instructions
Indexes and adaptors come from NEBNext Multiplex Oligos for Illumina both primer sets 1 and 2.

treatment_protocol: animal caps were manually dissected as described by Sive, H.L., Grainger, R.M. and Harland, R.M. (2000)

tag: Stage

value: tailbud

value: prospective epidermis

tag: bioreplicates

value: 3 biological replicates


title: NF16

description:
RiboZero
Total_FPKM.csv
3 replicates

value: neurula


title: B5

data_processing:
library strategy: Drop-Seq
Data were analyzed using Cell Ranger™ v2.0 pipelines and were visualized by Loupe™ Cell Browser v1.0. Both are available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: It includes mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.

source_name: pLN-SPF

extract_protocol:
For stromal cell isolation, skin-draining pLNs (inguinal and axillary) or mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase P (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche) as described previously (Fletcher et al., 2011, https://doi.org/10.3389/fimmu.2011.00035). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). CD45- cells were enriched by MACS separation after direct magnetic labeling of CD45+ cells using  anti-CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort CD45‑CD24‑ cells by FACS (Aria II)) for single-cell mRNA‑seq analysis.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.

tag: antibody

tag: index id

tag: index seq

value: AATAATGG,CCAGGGCA,TGCCTCAT,GTGTCATC


title: WT rep2

city: dallas

first: Zhiguang

last: Huang

state: Texas

address: 5323 Harry Hines Boulevard

institute: UTSW

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8

source_name: liver

growth_protocol: Wild type and Acss2-/- male mice were fed on chow diet and grew to 22 weeks old

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fasted for 48 hours

value: liver

tag: genotype

value: wild type


title: NF10.5

description:
RiboZero
Total_FPKM.csv
3 replicates

value: gastrula

tag: tissue


title: WT rep3

tag: strain


title: Acss2-KO rep3


title: 10x Reprogramming Foxa1-Hnf4a-Mettl7a1

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description:
10x Genomics Single Cell Expression Experiment
mettl.gfp.dge

data_processing:
The Cell Ranger v2.1.0 pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) was used to process data generated using the 10x Chromium platform. Cell Ranger processes, filters, and aligns reads generated with the Chromium single-cell RNA sequencing platform. This pipeline was used in conjunction with a custom reference genome. The custom reference genome was created by concatenating the sequences corresponding to the Hnf4a-t2a-Foxa1 transgene and the GFP-CellTag transgene as new chromosomes to the mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: 10x Digital Gene Expression matrix, gene list, and barcode list

source_name: E13.5 Mouse Embryonic Fibroblasts

growth_protocol: Mouse embryonic fibroblasts were converted to iHeps/iEPs as in Sekiya and Suzuki (2011) 10 . Briefly, fibroblasts were prepared from E13.5 embryos and serially transduced with polyethylene glycol concentrated Hnf4a-t2a-Foxa1, followed by culture on gelatin for 2 weeks in hepato-medium (DMEM:F-12, supplemented with 10% FBS, 1 mg/ml insulin (Sigma), dexamethasone (Sigma-Aldrich), 10 mM nicotinamide (Sigma-Aldrich), 2 mM L-glutamine, 50 mM b-mercaptoethanol (Life Technologies), and penicillin/streptomycin, containing 20 ng/ml hepatocyte growth factor (Sigma- Aldrich), and 20 ng/ml epidermal growth factor (Sigma-Aldrich), after which the emerging iEPs were cultured on collagen.

extract_protocol: Library was constructed according to manufacturers protocol (10x Genomics, Chomium single-cell)

tag: cell type

value: Mouse induced endoderm progenitors


title: Acss2-KO rep2


title: 10x Reprogramming Foxa1-Hnf4a


title: 10x Reprogramming timecouse 2, day 28

description:
10x Genomics Single Cell Expression Experiment
reprogramming.timecourse.dge


title: H78ΔrpoN mutant rep3

first: Xianqing

address: DongChuan RD, Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Base-calling software:BGISEQ-500.
Data filtering software: SOAPnuke.
Clean reads were aligned to the Reference genes using Bowtie2 and the Reference genome usiong HISAT.
Gene expression was quantified as Fragments Per Kilobase per Megabase of library size (FPKM) using RSEM.
Genome_build: Pseudomonas protegens H78  (Genbank Accession No. CP013184)
Supplementary_files_format_and_content: Excel file include FPKM values for each sample and differential expression analysis of all genes in the rpoN-deleted mutant relative to the wild-type H78 strain...

organism: Pseudomonas protegens

source_name: Pseudomonas protegens H78ΔrpoN mutant

growth_protocol: Pseudomonas protegens H78 and its rpoN-deleted mutant (ΔrpoN), which were grown to the late exponential phase (OD600 = 4.0 to 5.0) in the KMB media at 28 °C

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit (Cat.4106), purified by the Qiagen RNeasy micro kit (Cat.74004) and the Qiagen RNase-Free DNase Set (Cat.79254)
According to standard BGISEQ-500 RNA sequencing protocols, mRNA was enriched by removing rRNA and further fragmented to be used for synthesizing the first and second strands of cDNAs and constructing the sequencing library.

tag: growth phase

value: the late exponential phase

value: rpoN-deleted mutant


title: WT rep1


title: H78ΔrpoN mutant rep2


title: PDBL15

city: Lyon

first: Pascal

last: BERNARD

address: 46 allée d'Italie

department: LBMC

country: France

institute: CNRS

description: Ribodepletion

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Supplementary_files_format_and_content: S. pombe log fold expression for genes and read-through transcripts

organism: Schizosaccharomyces pombe

source_name: 5 x Total RNA samples in triplicates = 15 RNA samples. treated with turbo DNase (Ambion) RINe score (Tape station) > 7

extract_protocol: Total RNA-seq libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold rRNA Removal Kit (Yeast) (MRZY1324, Illumina, Paris, France). Briefly, starting with 2 microgrammes of total RNA, the first step involved the removal of cytoplasmic and mitochondrial ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single -A- nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Then surplus PCR primers were removed by purification using AMPure XP beads (Beckman Coulter). Final cDNA libraries were checked for quality and quantified using Fragment analyzer Automated CE System from Advanced Analytical Technologies, Inc.

tag: replicate


title: Acss2-KO rep1


title: H78ΔrpoN mutant rep1


title: 10x Reprogramming timecouse 2, day 21


title: H78 WT rep3

source_name: Pseudomonas protegens H78

value: wild-type


title: 10x Reprogramming timecouse 2, day 12


title: 10x Reprogramming timecouse 2, day 15


title: H78 WT rep2


title: PDBL12

description: Ribodepletion


title: PDBL14

description: Ribodepletion


title: H78 WT rep1


title: 10x Reprogramming timecouse 2, day 3


title: PDBL10

description: Ribodepletion


title: 10x Reprogramming timecouse 2, day 6


title: PDBL11

description: Ribodepletion

value: wt


title: PDBL9

description: Ribodepletion


title: PDBL8

description: Ribodepletion


title: TeSR-E8

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: YOW-iPS, cultured by TeSR-E8 method, undifferentiated

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Analyzed samples The human iPS cell line, YOW-iPS (Takayama et al., 2014), generated from primary human hepatocytes, was maintained by one of four different culture methods) on a feeder layer of mitomycin C-treated MEF (Merck Millipore) with ReproStem medium (ReproCELL) supplemented with 10 ng/ml fibroblast growth factor (FGF) 2 (Katayama Kogyo Kagaku), or the “Repro” method) on iMatrix-511 (Nippi)-coated plates with StemFit AK02N medium (Ajinomoto), or the “AK02N” method) on Vitronectin N (Cellular Dynamics International)-coated plates with E8 medium (Cellular Dynamics International), or the “E8” method) on Vitronectin XF (STEMCELL Technologies)-coated plates with TeSR-E8 medium (STEMCELL Technologies), or the “TeSR-E8” method. In every method, we performed maintenance of human iPS cells according to the manufacturer’s instructions.

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: We maintained human iPS cells for more than one month using each of the four methods.

tag: medium

tag: coating matrix

value: Vitronectin XF


title: OE3

city: Nanjing

first: qifeng

last: he

state: JIANGSU

address: zhongshan Road

department: general surgery

institute: nanjing university

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 mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments  Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: excel files include FPKM values for each Sample ...

source_name: CD8+ T cell

extract_protocol:
CD8+ T cells from healthy donors's PBMC were isolated, dealed with decribed above, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: see methods above

value: 26 years old

value: peripheral blood mononuclear cells

value: NC CD8+ T cell


title: PDBL13

description: Ribodepletion


title: PDBL7

description: Ribodepletion


title: AK02N

source_name: YOW-iPS, cultured by AK02N method, undifferentiated

value: StemFit AK02N


title: OE2


title: E8

source_name: YOW-iPS, cultured by E8 method, undifferentiated

value: Essential 8

value: Vitronectin N


title: 10x Reprogramming timecouse 1, day 28


title: OE1


title: 10x Reprogramming timecouse 1, day 21


title: 10x Reprogramming timecouse 2, day 9


title: 10x Reprogramming timecouse 1, day 15


title: DMSO_H295R_24hr

city: Fukuoka

first: Kenji

last: Ohe

state: Fukuoka

address: 8-19-1, Jyonan-ku, nanakuma

department: Faculty of Pharmaceutical Sciences

institute: Fukuoka University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: cell line

value: DMSO


title: CX-4945_5μM_H295R_24hr


title: 10x Reprogramming timecouse 2, day 0

value: Mouse embryonic fibroblasts


title: NC3

value: CD8+ T cell  TOX overexpressed


title: PDBL6

description: Ribodepletion


title: PDBL5

description: Ribodepletion


title: NC2


title: PDBL4

description: Ribodepletion


title: Repro

description: Repro

source_name: YOW-iPS, cultured by Repro method, undifferentiated

value: Repro Stem

value: MEF


title: 10x Reprogramming timecouse 1, day 12

value: Mouse induced endoderm progenitors


title: 10x Reprogramming timecouse 1, day 9


title: NC1


title: PDBL3

description: Ribodepletion


title: 10x Reprogramming timecouse 1, day 6


title: PDBL2

description: Ribodepletion


title: 10x Reprogramming timecouse 1, day 3


title: LipofectamineControl_9h

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 201 Schultz Laboratory

department: Molecular Biology

institute: Princeton University

description: Lipofectamine mock transfection 9 h

data_processing:
Barcodes splitting to deconvolute and assign reads to samples
Mapping using TopHat 2 set to map first stranded reads with default parameters
Exon counting using HTseq-count run in union mode
Genome_build: HG19
Supplementary_files_format_and_content: Excel sheet with exon counts

source_name: Lung carcinoma epithelium

growth_protocol: Grown in RMPI supplemented with 10% FBS

extract_protocol:
At the endpoint, media was aspirated and cells were lysed in 300 uL RLT buffer (RNeasy extraction kit, Qiagen) and total RNA was extracted. RNA integrity was verified by an RNA 6000 Nano Chip, using BioAnalyzer and 2100 Expert software (Agilent Technologies).
The mRNA was enriched by oligo-dT pulldown from total RNA, followed by fragmentation, adapter ligation, PCR amplification, and finally sequencing on Illumina HiSeq 2000 platform.

treatment_protocol: A 6-well plate of A549 cells were transfected with 1 ug/mL poly I:C using Lipofectamine 2000 as per manufracturer's instructions. Treatment duration = 9 h.

value: Lung carcinoma epithelium

value: Adherent


title: PDBL1

description: Ribodepletion


title: T5.sst-rma-gene-full-Signal(normalized)

city: Changsha

first: Junliang

last: ma

state: Hunan

address: No. 582 Xianjiahu Road, Yuelu District

department: The 2nd Department of Thoracic Surgery

institute: Hunan Cancer Hospital

description: lncRNA and mRNA expression of ESCC tumor tissue

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit  (AM1561) following the manufacturer's instructions

treatment_protocol: After the specimens were removed, the ESCC tumor tissues and their adjacent normal tissues with a diameter of about 3.0 mm were harvested. Specimens were frozen in liquid nitrogen and then stored at -80 ℃ refrigerator.

tag: tissues

value: ESCC tumor tissue

tag: gender

value: male


title: 10x Reprogramming timecouse 1, day 0


title: TF screen in EGM media gDNA

status: Public on Sep 24 2018

city: La Jolla

first: Yan

last: Wu

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description:
up-tf_dropout_counts.tsv
egm

data_processing:
Align mRNA fastq files to genome and generate gene expression matrices with 10X genomics cellranger 2.0.0 with default parameters
Convert genotype barcode fastq files to unaligned bam, tag each read with cell and molecule barcodes, and assign one of more genotypes to each cell
Process gDNA fastq files with MageCK with default parameters to generate fitness counts matrix
R1 is the barcode and R2 is biological. For R1, bases 1 - 16 correspond to the cell barcode and bases 17 -26 correspond to the unique molecular index (UMI).
Genome_build: hg38
Supplementary_files_format_and_content: Files ending in ".counts.tsv.gz" are counts matrices in tab separated value format.  Column headers are cell barcodes.
Supplementary_files_format_and_content: Files ending in "pheno_dict.csv" are genotype to cell dictionaries. Each line begins with the name of the genotype, followed by the cell barcodes mapped to that genotype separated by commas
Supplementary_files_format_and_content: File up-tf_functional_gene_modules.gmt corresponds to annotated gene clusters that we computed and are essential to our higher level analyses.
Supplementary_files_format_and_content: The Series-level supplementary files correspond to the aggregated data across biological samples.

source_name: H1 stem cells

growth_protocol: H1 hESC cells were maintained under feeder-free conditions in mTesR1 medium, in growth-factor reduced Matrigel coated tissue coated plates. Cellls were dissociated and passaged using Versene

extract_protocol:
Cells were dissociated to single cell suspensions using Accutase, resuspended in PBS-BSA and loaded onto the 10X Genomics Chromium system as per manufacturer's instructions. Remaining cells were pelleted, lysed, and genomic DNA was extracted for fitness effect quantification
Single cell libraries were constructed with the Single Cell 3' Reagent Kit v2 (10X genomics). TF barcodes were amplified from full length cDNA for genotype deconvolution using primers

treatment_protocol: H1 cells were seeded into 10 cm dishes and transduced with lentivirus added to fresh media mTeSR containing polybrene. On Day 1, medium was replaced with appropriate fresh medium. Hygromycin selection was started on Day 2

tag: culture media

value: EGM

tag: cell sorting

tag: estimated moi

value: Low


title: TF screen iDMEM media gDNA

description:
up-tf_dropout_counts.tsv
dmem

value: DMEM


title: T3.sst-rma-gene-full-Signal(normalized)

tag: age


title: TF screen in hPSC media gDNA sample 4

description:
up-tf_dropout_counts.tsv
low1b

value: mTESR


title: TF screen in hPSC media gDNA sample 3

description:
up-tf_dropout_counts.tsv
low1a


title: TF screen in hPSC media gDNA sample 1

description:
up-tf_dropout_counts.tsv
high1

value: High


title: TF screen in hPSC media gDNA sample 2

description:
up-tf_dropout_counts.tsv
high2


title: T4.sst-rma-gene-full-Signal(normalized)


title: Neuron Combinatorial Screen in hPSC media scRNA-seq with NoHygro vector sample 2

molecule: cytoplasmic RNA


title: PolyIC_9h

description: Lipofectamine-based transfection of 1 ug/mL poly-IC 9 h


title: cMyc mutants screen and KLF family screen in hPSC media scRNA-seq


title: Neuron Combinatorial Screen in hPSC media scRNA-seq sample 1


title: Neuron Combinatorial Screen in hPSC media scRNA-seq sample 2


title: TF screen in multilineage media scRNA-seq sample 2


title: Neuron Combinatorial Screen in hPSC media scRNA-seq with NoHygro vector sample 1


title: T2.sst-rma-gene-full-Signal(normalized)


title: N5.sst-rma-gene-full-Signal(normalized)

description: lncRNA and mRNA expression of normal esophageal tissue

value: normal esophageal tissue


title: T1.sst-rma-gene-full-Signal(normalized)


title: N4.sst-rma-gene-full-Signal(normalized)


title: N2.sst-rma-gene-full-Signal(normalized)


title: N1.sst-rma-gene-full-Signal(normalized)


title: TF screen in endothelial media scRNA-seq sample 1


title: TF screen in stem cell media scRNA-seq sample 3


title: TF screen in stem cell media scRNA-seq sample 2


title: TF screen in endothelial media scRNA-seq sample 2


title: TF screen in multilineage media scRNA-seq sample 1


title: subjectSLE71_week12

city: Cambridge

first: Emma

middle: Elisabeth

last: Davenport

state: Cambridgeshire

address: Hinxton

institute: Wellcome Sanger Institute

data_processing:
We aligned reads to the reference genome using Subread
We quantified gene expression using featureCounts
We included genes with at least 10 reads (CPM>0.38) in at least 32 samples (minimum number of subjects with both unexposed and exposed RNA-seq assays in a drug group) prior to normalization.
Following quality control, we removed 4 samples as outliers (SLE103_W0,  SLE106_W0,  SLE100_W12,  SLE36_W24)
We normalized 20,253 transcripts using the trimmed mean of M-values method and the edgeR R package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with normalized expression levels presented as log2(cpm +1) for each sample

source_name: Whole blood

extract_protocol:
We extracted total RNA from blood samples using the PAXgene Blood RNA kit (Qiagen). We processed an aliquot of 500-1000 ng of each RNA with a GlobinClear-Human kit, (ThermoFisher Scientific) to remove globin mRNA.
RNA samples were converted to cDNA libraries using TruSeq RNA Sample Prep Kit v2 (Illumina)

value: Whole blood

tag: timepoint

tag: ifn status

tag: drug dose

tag: drug exposure

tag: subject age

tag: subject sex

value: Female

tag: recruitment site


title: subjectSLE2_week12

tag: tissue


title: subjectSLE154_early_withdrawal

value: Male


title: subjectSLE152_week24


title: subjectSLE117_week24


title: subjectSLE107_week12

value: Placebo


title: subjectSLE4_week24


title: subjectSLE92_week12


title: subjectSLE131_week24


title: subjectSLE106_week24


title: subjectSLE168_early_withdrawal


title: subjectSLE66_week24


title: subjectSLE71_early_withdrawal


title: subjectSLE33_week12


title: subjectSLE28_week12


title: N3.sst-rma-gene-full-Signal(normalized)


title: subjectSLE167_week24


title: subjectSLE8_week12


title: subjectSLE169_week24


title: subjectSLE179_week0


title: subjectSLE143_week12


title: subjectSLE152_week12


title: subjectSLE175_week0


title: subjectSLE180_week12


title: subjectSLE170_week0


title: subjectSLE29_week12


title: subjectSLE13_week24


title: subjectSLE91_week12


title: subjectSLE166_week24


title: subjectSLE177_week12


title: subjectSLE171_week24


title: subjectSLE174_week24


title: subjectSLE73_week24


title: Control rep2

source_name: adult microglia

tag: strain

value: cerebrum

tag: treatment

value: 6-8 weeks


title: subjectSLE170_week12


title: subjectSLE36_week12


title: subjectSLE103_week24


title: subjectSLE105_week12


title: subjectSLE177_week0


title: subjectSLE101_early_withdrawal


title: subjectSLE175_week12


title: subjectSLE36_week24


title: subjectSLE164_week0


title: subjectSLE173_week12


title: subjectSLE45_week12


title: subjectSLE52_week24


title: subjectSLE73_week12


title: subjectSLE174_week0


title: subjectSLE91_week24


title: subjectSLE176_week0


title: subjectSLE72_week12


title: subjectSLE174_week12


title: subjectSLE171_week0


title: subjectSLE68_week24


title: subjectSLE178_week0


title: subjectSLE164_week24


title: subjectSLE46_week12


title: subjectSLE65_week12


title: subjectSLE173_week24


title: subjectSLE69_week12


title: subjectSLE45_week24


title: subjectSLE100_week12


title: subjectSLE172_week0


title: subjectSLE103_week12


title: subjectSLE52_week12


title: subjectSLE169_week12


title: subjectSLE101_week12


title: subjectSLE46_early_withdrawal


title: subjectSLE171_week12


title: subjectSLE68_week12


title: subjectSLE151_week12


title: subjectSLE10_week12


title: subjectSLE169_week0


title: subjectSLE168_week0


title: subjectSLE26_week12


title: subjectSLE26_week24


title: subjectSLE69_week24


title: subjectSLE166_week0


title: subjectSLE65_week24


title: subjectSLE105_week24


title: subjectSLE167_week12


title: subjectSLE10_week24


title: subjectSLE13_week12


title: subjectSLE39_early_withdrawal


title: subjectSLE166_week12


title: subjectSLE62_week24


title: subjectSLE63_early_withdrawal


title: subjectSLE140_week0


title: subjectSLE41_week24


title: subjectSLE58_week12


title: subjectSLE170_week24


title: subjectSLE116_week0


title: subjectSLE5_week12


title: subjectSLE98_week12


title: subjectSLE8_week24


title: subjectSLE89_week12


title: subjectSLE88_week24


title: subjectSLE16_week24


title: subjectSLE136_week12


title: subjectSLE5_early_withdrawal


title: subjectSLE20_week24


title: subjectSLE165_week12


title: subjectSLE16_week12


title: subjectSLE100_week24


title: subjectSLE173_week0


title: subjectSLE31_week12


title: subjectSLE20_week12


title: subjectSLE15_week12


title: subjectSLE165_week24


title: subjectSLE31_week24


title: subjectSLE18_week24


title: subjectSLE60_week24


title: subjectSLE17_week24


title: subjectSLE1_week12


title: subjectSLE75_early_withdrawal


title: subjectSLE12_week12


title: subjectSLE3_week12


title: subjectSLE72_week24


title: subjectSLE163_week0


title: subjectSLE4_week12


title: subjectSLE25_week12


title: subjectSLE87_early_withdrawal


title: subjectSLE161_week0


title: subjectSLE96_early_withdrawal


title: subjectSLE106_week12


title: subjectSLE58_week24


title: subjectSLE128_week12


title: subjectSLE109_week24


title: subjectSLE17_week12


title: subjectSLE86_week12


title: subjectSLE160_week0


title: subjectSLE41_week12


title: subjectSLE9_week12


title: subjectSLE89_early_withdrawal


title: subjectSLE107_week24


title: subjectSLE164_week12


title: subjectSLE136_early_withdrawal


title: subjectSLE111_week24


title: subjectSLE162_week0


title: subjectSLE161_week24


title: subjectSLE111_week12


title: subjectSLE9_week24


title: subjectSLE12_week24


title: subjectSLE11_week24


title: subjectSLE158_week0


title: subjectSLE23_week12


title: subjectSLE84_week24


title: subjectSLE156_week0


title: subjectSLE95_week24


title: subjectSLE155_early_withdrawal


title: subjectSLE159_week24


title: subjectSLE149_week24


title: subjectSLE159_week12


title: subjectSLE150_week0


title: subjectSLE84_week12


title: subjectSLE147_week12


title: subjectSLE23_week24


title: subjectSLE128_week24


title: subjectSLE160_week24


title: subjectSLE144_week12


title: subjectSLE124_week12


title: subjectSLE158_week12


title: subjectSLE114_week24


title: subjectSLE159_week0


title: subjectSLE153_early_withdrawal


title: subjectSLE124_week0


title: subjectSLE74_week12


title: subjectSLE157_week12


title: subjectSLE109_week12


title: subjectSLE64_week24


title: subjectSLE132_week0


title: subjectSLE157_week24


title: subjectSLE98_week24


title: subjectSLE157_week0


title: subjectSLE95_week12


title: subjectSLE112_week12


title: subjectSLE158_week24


title: subjectSLE123_week0


title: subjectSLE76_week12


title: subjectSLE67_week12


title: subjectSLE163_early_withdrawal


title: subjectSLE132_week24


title: subjectSLE145_early_withdrawal


title: subjectSLE154_week0


title: subjectSLE155_week0


title: subjectSLE144_week24


title: subjectSLE153_week0


title: subjectSLE152_week0


title: subjectSLE74_week24


title: subjectSLE147_week0


title: subjectSLE151_week0


title: subjectSLE149_week0


title: subjectSLE150_week24


title: subjectSLE151_early_withdrawal


title: subjectSLE147_week24


title: subjectSLE67_week24


title: subjectSLE76_week24


title: subjectSLE146_early_withdrawal


title: subjectSLE148_week0


title: subjectSLE146_week0


title: subjectSLE29_week24


title: subjectSLE145_week0


title: subjectSLE64_week12


title: subjectSLE42_week12


title: subjectSLE156_week12


title: subjectSLE88_week12


title: subjectSLE135_week24


title: subjectSLE143_week24


title: subjectSLE33_early_withdrawal


title: subjectSLE53_week24


title: subjectSLE81_week12


title: subjectSLE141_week12


title: subjectSLE92_week24


title: subjectSLE32_week24


title: subjectSLE40_week24


title: subjectSLE97_week24


title: subjectSLE53_week12


title: subjectSLE51_week12


title: subjectSLE49_week24


title: subjectSLE60_week12


title: subjectSLE149_week12


title: subjectSLE30_week12


title: subjectSLE134_week12


title: subjectSLE38_week24


title: subjectSLE144_week0


title: subjectSLE115_early_withdrawal


title: subjectSLE80_week12


title: subjectSLE42_early_withdrawal


title: subjectSLE22_early_withdrawal


title: subjectSLE21_week24


title: subjectSLE137_week24


title: subjectSLE80_week24


title: subjectSLE44_week12


title: subjectSLE142_week12


title: subjectSLE50_week12


title: subjectSLE142_week24


title: subjectSLE82_week12


title: subjectSLE142_week0


title: subjectSLE102_week24


title: subjectSLE83_week12


title: subjectSLE35_week24


title: subjectSLE141_week0


title: subjectSLE35_week12


title: subjectSLE56_week12


title: subjectSLE94_week24


title: subjectSLE79_week24


title: subjectSLE59_week12


title: subjectSLE37_week12


title: subjectSLE22_week12


title: subjectSLE57_week24


title: subjectSLE134_week24


title: subjectSLE102_week12


title: subjectSLE135_week0


title: subjectSLE54_week24


title: subjectSLE44_early_withdrawal


title: subjectSLE21_week12


title: subjectSLE40_week12


title: subjectSLE139_week0


title: subjectSLE37_week24


title: subjectSLE77_week12


title: subjectSLE94_week12


title: subjectSLE6_week24


title: subjectSLE50_week24


title: subjectSLE27_week12


title: subjectSLE54_week12


title: subjectSLE47_week24


title: subjectSLE77_week24


title: subjectSLE56_week24


title: subjectSLE140_week24


title: subjectSLE137_week12


title: subjectSLE48_week24


title: subjectSLE139_early_withdrawal


title: subjectSLE138_week0


title: subjectSLE25_week24


title: subjectSLE57_week12


title: subjectSLE3_week24


title: subjectSLE49_week12


title: subjectSLE137_week0


title: subjectSLE47_week12


title: subjectSLE48_week12


title: subjectSLE30_early_withdrawal


title: subjectSLE136_week0


title: subjectSLE82_week24


title: subjectSLE138_week12


title: subjectSLE83_week24


title: subjectSLE38_week12


title: subjectSLE138_week24


title: subjectSLE130_week0


title: subjectSLE70_week12


title: subjectSLE24_early_withdrawal


title: subjectSLE133_week24


title: subjectSLE125_week12


title: subjectSLE108_week12


title: subjectSLE66_week12


title: subjectSLE27_week24


title: subjectSLE110_week12


title: subjectSLE119_week0


title: subjectSLE133_week0


title: subjectSLE135_week12


title: subjectSLE126_week12


title: subjectSLE134_week0


title: subjectSLE130_week12


title: subjectSLE129_week24


title: subjectSLE126_week24


title: subjectSLE131_week12


title: subjectSLE133_week12


title: subjectSLE127_week12


title: subjectSLE132_week12


title: subjectSLE113_early_withdrawal


title: subjectSLE2_week24


title: subjectSLE39_week12


title: subjectSLE121_week24


title: subjectSLE122_week12


title: WT Mx-1Cre 2

city: Houston

first: Margarida

last: Almeida Santos

address: 1515 Holcombe Blvd Mail code 1000

department: Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
The reads were mapped to the mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M17 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the cpm (count per million fragments) value for each gene was calculated by R/Bioconductor package edgeR (version 3.8.6).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are cpm values (estimated by edgeR) for all the samples.

source_name: Bone marrow cells

extract_protocol:
Osteoclast progenitors (defined as B220/CD3 negative, Mac-1 negative, and CD115 positive cells) were sorted from freshly isolated bone marrow of WT Mx-1Cre and Ptip flox/flox Mx-1Cre mice. Cells were spun down and washed once with cold PBS, then RNA was isolated with a QIAGEN RNeasy kit (Cat# 74104) according to the manufacturer’s protocol.
RNA-Seq sequencing libraries were made from osteoclast progenitor cells following Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol.

tag: cell type

value: Osteoclast progenitors

tag: genotype

value: WT Mx-1Cre


title: subjectSLE55_week24


title: WT Mx-1Cre 1


title: subjectSLE131_week0


title: subjectSLE70_week24


title: Ptip flox/flox Mx-1Cre 2

value: Ptip flox/flox Mx-1Cre


title: subjectSLE127_week24


title: subjectSLE125_week0


title: Placental-Obese-BioRep9-TechRep3

type: genomic

city: Grand Forks

first: Kate

middle: J

last: Claycombe-Larson

state: ND

address: 2420 2nd Avenue North

department: ARS

institute: USDA

description: Obese frozen placental punch

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data was processed with the R packages wateRmelon, methylumi, minfi, and Limma. Probes containing SNPs, a detection p-value of greater than 0.001 in more than 1% of the samples, or a beadcount of less than 3 in 5% of samples were removed.  To correct for the differences in probe design, the BMIQ (Beta Mixture Quantile) normiization was used. The function “duplicateCorrelation” was used to account for samples that came from the same patient.

label: Cy3 and Cy5

source_name: Placental-Obese

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted from frozen tissue (Vanderbilt University Medical Center, Nashville, TN) using a DNeasy Blood and Tissue kit (Qiagen, Valencia, CA).

tag: gender

tag: sample type

value: Placental tissue punch

tag: weight

value: Obese


title: Placental-Obese-BioRep5-TechRep1

description: Obese frozen placental punch


title: Placental-Obese-BioRep5-TechRep4

description: Obese frozen placental punch


title: Placental-Obese-BioRep9-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep7-TechRep1

description: Obese frozen placental punch


title: Placental-Obese-BioRep8-TechRep3

description: Obese frozen placental punch


title: Placental-Obese-BioRep3-TechRep3

description: Obese frozen placental punch


title: subjectSLE129_week12


title: Placental-Obese-BioRep6-TechRep3

description: Obese frozen placental punch


title: Placental-Obese-BioRep5-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep5-TechRep3

description: Obese frozen placental punch


title: Placental-Obese-BioRep4-TechRep1

description: Obese frozen placental punch


title: Placental-Obese-BioRep3-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep6-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep8-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep6-TechRep1

description: Obese frozen placental punch


title: Placental-Obese-BioRep4-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep8-TechRep1

description: Obese frozen placental punch


title: subjectSLE120_week24


title: Placental-Obese-BioRep2-TechRep3

description: Obese frozen placental punch


title: Ptip flox/flox Mx-1Cre 1


title: subjectSLE130_week24


title: Placental-Obese-BioRep7-TechRep3

description: Obese frozen placental punch


title: Placental-Obese-BioRep2-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep9-TechRep1

description: Obese frozen placental punch


title: Placental-Obese-BioRep3-TechRep1

description: Obese frozen placental punch


title: subjectSLE117_week0


title: Placental-Obese-BioRep7-TechRep2

description: Obese frozen placental punch


title: Placental-Obese-BioRep4-TechRep3

description: Obese frozen placental punch


title: ctf4-4E H3K56ac eSPAN

city: New York

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
The sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To obtain the nucleosome occupancy, DNA fragments from 120 to 170 bp in size determined by the paired-reads were firstly selected for calculation. The length of DNA fragments were then adjusted to half of the nucleosome size (74bp) to increase the signal-to-noise ratio. Finally, the count of adjusted DNA fragments covering each base pair in the genome were used to calculate the nucleosome occupancy.
To identify BrdU-IP-ssSeq peaks, the sequence reads of both Watson and Crick strands were merged and used to call peaks using SICER software with false discovery rate (FDR) cut-off 0.01.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: To synchronize cells at G1, alpha factor was added at cell density OD600=0.4-0.5 to achieve a final concentration of five µg/mL for yeast strains.  After three hours arrest at 25°C, the cells were released to fresh YPD medium with or without 200 mM HU.  For the histone H3 Recombination-induced Tag Exchange (RITE) experiments, yeast cells were grown overnight in YPD in the presence of hygromycin B (200 μg/mL, Invitrogen). The cells were then diluted 1:10 into two fresh YPD flask (one with, the other without hygromycin B) and incubated for 32 hours (G0 state). The cells were centrifuged by 3000 rpm for 10 minutes. The cells cultured with hygromycin B were transferred to another flask containing depleted medium without hygromycin B. Recombination was induced by the addition of 1 μM β-estradiol (E-8875, Sigma-Aldrich) and the cells were cultured for additional 16 hours. Subsequently, these cells were diluted 1:25 in fresh YPD media containing 200 mM HU and 400ul/ml BrdU. After incubation at 25 C for 90 minutes, samples were collected for ChIP and eSPAN.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously except that Mnase digestion was used for chromatin fragmentation in order to map nucleosomes. Briefly, the samples were incubated with 1% fresh-made formaldehyde at 25 °C for 20 min, and then quenched with 0.125M glycine for five min.  The cells wer harvested and lysed with glass beads in ChIP lysis buffer (50 mM HEPES, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate). The resulting cell and chromatin pellet was washed with NP buffer (1.6 M sorbitol, 2 mM CaCl2, 5mM MgCl, 50 mM NaCl, 14 mM β-mercaptoethanol, 10 mM Tris-HCl (pH 7.4), 0.075% NP-40, 5 mM spermidine).  Proper amounts of Mnase was added to ensure that majority of chromatin are mono- and di-nucleosomes with incubation at 37 °C for 20 min . The reacation was terminated by adding 5ul 0.5M EDTA. Further, ¼ volume 5X ChIP lysis buffer was added into dilute thedigested chromatin. The lysates was incubated in ice for 30 minutes. After clarification of lysates by centrifugation, soluble chromatin (mainly mononucleosomes) was immunoprecipitated with a specific antibody including anti-H3K4me3 antibody (ab8580), anti-H3K56ac antibody (6), anti-HA antibody (12CA5) or anti-T7 (A190-117A BETHYL)). ChIP DNA was recovered using Chelex-100. The ChIP or total DNA was denatured at 100°C for five min and was immediately transferred to ice bath for five minutes.  The DNA was diluted at least ten times with BrdU IP solution (PBS, 0.0625% Triton X-100(v/v), 6.7 g/mL Escherichia. coli tRNA, 0.67 ul/mL BrdU antibody (BD Bioscience)).  After the samples were incubated at 4°C for two hour, 20 uL protein G beads (GE Healthcare) were added.  After incubation at 4°C for another hour, the protein G beads was washed extensively. DNA were eluted using 100 uL 1XTE buffer plus 1% SDS and incubation at 65 °C for 15 min. Eluted DNA was purified using a Qiagen Mini-elute kit.
We used the ssDNA library preparation kit to prepare library (Cat no. 10096 Swift Bioscience). The ssDNA libraries were sequenced using the paired-end method by different sequencing platform over the years including Hi-seq 2000 or 2500 machine at Mayo Clinic or Columbia University.

tag: media

value: YPD+HU

tag: cell cycle stage

value: S

value: ctf4-4E mutant

tag: strains genetic background

tag: chip antibody

value: Anti-H3K56ac and Anti-BrdU Antibody


title: subjectSLE15_week24

tag: timepoint

tag: ifn status

tag: drug dose


title: subjectSLE123_week24

value: Low

tag: drug exposure

tag: subject age

tag: subject sex


title: subjectSLE61_week12

tag: tissue

value: High

tag: recruitment site


title: subjectSLE110_week24

value: Whole blood


title: subjectSLE120_week0

value: Female


title: subjectSLE127_week0


title: ctf4-4E BrdU-IP-ssSeq

value: Anti-BrdU (BD BioScience, 347580)


title: ctf4-4E H3K56ac ChIP-ssSeq

value: Anti-H3K56ac antibody


title: subjectSLE119_week24

value: Placebo


title: subjectSLE126_week0

value: Male


title: subjectSLE128_week0


title: subjectSLE125_week24


title: subjectSLE129_week0


title: Placental-Obese-BioRep2-TechRep1

description: Obese frozen placental punch


title: ctf4-4E H3K4me3 ChIP-ssSeq

value: Anti-H3K4me3 Antibody (ab8580)


title: subjectSLE124_week24


title: subjectSLE123_week12


title: subjectSLE99_early_withdrawal


title: pol1-4A H3K4me3 eSPAN repeat 2

value: pol1-4A mutant

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: ctf4-4E input MNase-ssSeq


title: Placental-Obese-BioRep1-TechRep4

description: Obese frozen placental punch

value: Placental tissue punch


title: subjectSLE122_week0


title: ctf4-4E H3K4me3 eSPAN


title: Placental-Obese-BioRep1-TechRep3

description: Obese frozen placental punch

value: Obese


title: subjectSLE62_week12


title: pol1-4A H3K56ac eSPAN repeat 2

value: YPD+HU


title: subjectSLE116_week12


title: subjectSLE108_week24


title: subjectSLE118_week24


title: subjectSLE121_week0


title: subjectSLE34_early_withdrawal


title: pol1-4A H3K4me3 eSPAN repeat 1

value: S


title: pol1-4A H3K4me3 ChIP-ssSeq repeat 2


title: pol1-4A H3K56ac eSPAN repeat 1


title: subjectSLE119_week12


title: subjectSLE55_week12


title: subjectSLE118_week12


title: subjectSLE117_week12


title: subjectSLE120_week12


title: pol1-4A H3K4me3 ChIP-ssSeq repeat 1


title: pol1-4A H3K56ac ChIP-ssSeq repeat 1


title: subjectSLE116_week24


title: pol1-4A H3K56ac ChIP-ssSeq repeat 2


title: Placental-Obese-BioRep1-TechRep2

description: Obese frozen placental punch


title: subjectSLE6_week12


title: pol1-4A BrdU-IP-ssSeq repeat 2


title: subjectSLE96_week12


title: Placental-Lean-BioRep3-TechRep5

description: Lean frozen placental punch

source_name: Placental-Lean

value: Lean


title: subjectSLE43_week24


title: subjectSLE115_week0


title: Placental-Lean-BioRep3-TechRep3

description: Lean frozen placental punch


title: Placental-Lean-BioRep3-TechRep4

description: Lean frozen placental punch


title: pol1-4A BrdU-IP-ssSeq repeat 1


title: subjectSLE114_week0


title: subjectSLE112_week0


title: subjectSLE113_week0


title: pol1-4A input MNase-ssSeq repeat 1


title: Placental-Lean-BioRep3-TechRep1

description: Lean frozen placental punch


title: subjectSLE111_week0


title: Placental-Lean-BioRep3-TechRep2

description: Lean frozen placental punch


title: subjectSLE110_week0


title: subjectSLE109_week0


title: subjectSLE108_week0


title: subjectSLE106_week0


title: subjectSLE107_week0


title: Placental-Obese-BioRep1-TechRep1

description: Obese frozen placental punch


title: ctf4D H3K4me3 eSPAN repeat 2

value: ctf4 deletion


title: subjectSLE105_week0

value: Low


title: subjectSLE93_week0


title: subjectSLE103_week0


title: subjectSLE102_week0

value: High


title: subjectSLE101_week0

value: Whole blood


title: ctf4D H3K4me3 ChIP-ssSeq repeat 2


title: ctf4D H3K56ac eSPAN repeat 1

value: Anti-H3K56ac and Anti-BrdU Antibody


title: ctf4D H3K4me3 ChIP-ssSeq repeat 1


title: Placental-Lean-BioRep2-TechRep3

description: Lean frozen placental punch

value: Female


title: subjectSLE100_week0


title: Placental-Lean-BioRep1-TechRep1

description: Lean frozen placental punch


title: ctf4D H3K56ac eSPAN repeat 2


title: subjectSLE99_week0


title: Placental-Lean-BioRep2-TechRep1

description: Lean frozen placental punch


title: sample 29, primary tumor from ERpos BC

city: Amherst

first: Kathleen

last: Arcaro

state: Massachusetts

address: 240 Thatcher Road LSL1 N529, University of Massachusetts

department: Veterinary and Animal Science

institute: University of Massachusetts- Amherst

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan reader and standard Illumina protocols

data_processing: Illumina GenomeStudio version 1.9.0 methylation module was used to analyze the data, raw data were filtered using a detection p-value < 0.05.

source_name: genomic DNA from FFPE slide

label_protocol: Standard Illumina protocol

extract_protocol: DNA was purified from tumor tissue obtained from 10 μm sections of FFPE blocks. Briefly, a pathologist measured and outlined the breast tumor on an H&E stained slide to estimate the number of sections needed to purify a minimum of 500 ng of DNA. For samples exceeding 4 mm x 4 mm, a single section was sufficient. Tumor cells were collected from the sections by placing an unstained slide on top of the H&E stained slide and carefully removing cells within the parameters defined by H&E slide. Cells collected from multiple sections were combined in a single tube and DNA was purified using the BiOstic FFPE tissue DNA isolation kit (Mo Bio, Carlsbad, CA).

tag: group

value: no breast cancer recurrence after a 7-year follow up period

tag: Sex

value: female

value: breast tumor

tag: disease state

value: cancer

tag: estrogen receptor status

value: positive

tag: tumor status

value: primary


title: sample 24, primary tumor from ERpos BC


title: sample 28, primary tumor from ERpos BC


title: sample 27, primary tumor from ERpos BC


title: subjectSLE96_week0


title: sample 23, second tumor from ERneg BC

value: negative

value: second


title: subjectSLE97_week0

value: Placebo


title: Placental-Lean-BioRep2-TechRep2

description: Lean frozen placental punch

tag: gender

tag: sample type

value: Placental tissue punch

tag: weight


title: subjectSLE104_week0


title: subjectSLE93_early_withdrawal


title: sample 22, second tumor from ERneg BC


title: subjectSLE92_week0


title: ctf4D BrdU-IP-ssSeq repeat 1

tag: media

value: YPD+HU

tag: cell cycle stage

value: S

tag: genotype

tag: strains genetic background

tag: chip antibody

value: Anti-BrdU (BD BioScience, 347580)


title: sample 22, primary tumor from ERpos BC


title: sample 23, primary tumor from ERpos BC


title: sample 26, primary tumor from ERpos BC


title: ctf4D H3K56ac ChIP-ssSeq repeat 2

value: ctf4 deletion

value: Anti-H3K56ac antibody


title: ctf4D H3K56ac ChIP-ssSeq repeat 1


title: sample 25, primary tumor from ERpos BC


title: subjectSLE94_week0

value: Whole blood

tag: timepoint

tag: ifn status

value: High

tag: drug dose

tag: drug exposure

tag: subject age


title: ctf4D BrdU-IP-ssSeq repeat 2


title: subjectSLE91_week0

tag: tissue

tag: subject sex

value: Female

tag: recruitment site


title: subjectSLE95_week0

value: Low


title: subjectSLE90_week0


title: ctf4D input MNase-ssSeq repeat 2


title: subjectSLE89_week0


title: subjectSLE88_week0


title: ctf4D input MNase-ssSeq repeat 1


title: subjectSLE87_week0


title: subjectSLE85_week0


title: subjectSLE86_week0


title: sample 21, primary tumor from ERpos BC

tag: Sex

value: female

value: breast tumor

tag: disease state

tag: estrogen receptor status

tag: tumor status


title: subjectSLE84_week0


title: mcm2-3a H3K56ac eSPAN repeat 3

tag: media

value: mcm2-3a mutant

value: Anti-H3K56ac and Anti-BrdU Antibody


title: sample 21, second tumor from ERneg BC

value: cancer

value: negative


title: sample 20, second tumor from ERneg BC

value: second


title: subjectSLE81_week0

value: Placebo

value: Male


title: mcm2-3a H3K56ac eSPAN repeat 2

value: YPD+HU

tag: cell cycle stage

value: S


title: mcm2-3a H3K56ac ChIP-ssSeq repeat 3

tag: genotype


title: subjectSLE82_week0


title: ctf4D H3K4me3 eSPAN repeat 1

value: ctf4 deletion

tag: strains genetic background

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: subjectSLE80_week0

value: Whole blood


title: mcm2-3a H3K56ac ChIP-ssSeq repeat 2

tag: chip antibody

value: Anti-H3K56ac antibody


title: subjectSLE98_week0

tag: timepoint

value: High

value: Female


title: pol1-4A input MNase-ssSeq repeat 2

value: pol1-4A mutant


title: mcm2-3a BrdU-IP-ssSeq repeat 4

value: Anti-BrdU (BD BioScience, 347580)


title: subjectSLE83_week0

tag: ifn status


title: subjectSLE78_week0

tag: drug dose


title: subjectSLE77_week0

value: Low

tag: drug exposure


title: subjectSLE76_week0

tag: subject age


title: mcm2-3a BrdU-IP-ssSeq repeat 3

value: mcm2-3a mutant


title: subjectSLE79_week0

tag: tissue


title: mcm2-3a input MNase-ssSeq repeat 4


title: subjectSLE73_week0

tag: subject sex


title: sample 20, primary tumor from ERpos BC

value: female

value: breast tumor

value: cancer

value: positive

value: primary


title: subjectSLE74_week0

value: Placebo

tag: recruitment site


title: subjectSLE72_week0


title: mcm2-3a input MNase-ssSeq repeat 3

value: YPD+HU

value: S


title: subjectSLE75_week0


title: sample 19, primary tumor from ERpos BC

tag: Sex


title: subjectSLE70_week0


title: subjectSLE71_week0


title: sample 18, second tumor from ERneg BC

tag: disease state

value: negative

value: second


title: WT H3K4me3 eSPAN repeat 4

value: wild type

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: sample 19, second tumor from ERneg BC

tag: estrogen receptor status


title: sample 18, primary tumor from ERpos BC

tag: tumor status