title: Mouse No.43 Tumor No.1

first: Hong

last: Wang

address: 164 Frelinghuysen

institute: Rutgers the State Univesrity of New Jersey

description: Total RNA was labelled and hybridized to the microarray chip

hyb_protocol: Biotinylated cRNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the surface of MEEBO microarray slides enclosed in custom hybridization chambers.  The slides were hybridized for 16-18 hours under constant rotation in a Model 400 hybridization oven (Scigene, Sunnyvale, CA). After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen).

scan_protocol: After hybridization and washing, the microarray slides scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. Spot intensities were transformed by taking the base 2 logarithm of each value. The spot intensities were then normalized by subtracting the 70th percentile of the spot intensities of probes against mouse constitutive exons and adding back a scaling factor (grand mean of 70th percentile). After removing data for low quality spots, control sequences, and non-mouse probes, 34,279 mouse probe intensities remained. The mouse probes intensities were filtered to identify all probes with intensity above a normalized threshold (log2 (5* standard deviation of raw local background) + mean of log2-transformed negative controls) in at least 20% of sample, to arrive at 19,327 probes complementary to coding mRNA above threshold in all samples from at least one treatment group.

source_name: Colon tumor

label_protocol: Biotin-labeled complementary RNA (cRNA) was prepared from DNase treated total RNA. In briefly, an oligonucleotide containing a 5'-T7-promoter sequence and a 3' T24VN sequence was used to prime reverse transcription of RNA catalyzed by Superscript II (Invitrogen, Carlsbad, CA). Double-stranded cDNA was prepared from the 1st strand product and purified on a PCR purification column (Qiagen, Valencia, CA). The double-stranded cDNA was then used as a template for in vitro transcription with T7 RNA polymerase using a high yield transcription kit (Ambion, Austin, TX) and including biotin-16-UTP (Ambion) in the reaction mixture.

extract_protocol: Mouse colon tumors and adjacent normal epitlelium tissues were dissected under the dissection microscope and then used for extracting RNA using the Qiagen Rneasy Mini kit.

treatment_protocol: The CYP1A-humanized mice on AIN93M diet were treated with two doses of PhIP (100 mg/kg body weight) by govoge at the age of 6 weeks and then treated with 1.5% DSS in the drink water for one week.  Then the mice were maintained for 8 weeks without any other treatment.

value: Tumor

tag: histology

value: Tubular adenoma

tag: Sex

value: Male

value: 16 weeks

tag: genetic mutations (ctnnb1)

value: dominant active mutant


title: Jos6025(4x)(18)

status: Public on Sep 12 2019

type: RNA

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

country: USA

institute: Joslin Diabetes Center

description: primary muscle cells_standard media_undernourished_primary muscle cells_standard_undernourished_4x

hyb_protocol: 15ug cRNA was used to make 300ul hyb cocktail, of which 200ul were injected into GeneChip Mouse Gene  2.0 ST arrays and hybridized for 16 hours at 45C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with reagents from Affymetrix.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 system from Affymetrix.

data_processing: Data were normalized using RMA (Expression Console from Affymetrix)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: primary muscle cells from quadruceps,standard media,undernourished

label_protocol: Biotin labeling via WT PLUS Protocol

growth_protocol: Pregnant mice were housed individually with ad libitum access to standard rodent chow (T.2018, Harlan Teklad, Indianapolis, IN, USA). On day 12.5 of pregnancy, dams were randomly assigned to either a control or undernutrition group. In the undernutrition group, food was restricted to 50% that of gestational day -matched controls for the remainder of pregnancy. After delivery, mothers were given ad libitum access to chow and 24 hours after birth, litters were equalized to eight. We studied mice from 2 groups: in utero undernourished offpring (U) and control offspring (C). . Isolated primary muscle cells were grown on Matrigel coated flasks in low glucose (5.5 mmol/L) Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 20% FBS, 1X antibiotic-antimycotic, 2.5μg/ml gentamycin and 2.5ng/ml basic fibroblast growth factor.

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

treatment_protocol: On day 12.5 of pregnancy, dams were randomly assigned to either a control or undernutrition group. In the undernutrition group, food was restricted to 50% that of gestational day -matched controls for the remainder of pregnancy. Primary muscle cells were collected from offspring.  When cells reached approximately 90% confluency, they were differentiated in low glucose DMEM supplemented with 2% FBS, 1X antibiotic-antimycotic, and 2.5μg/ml gentamycin. Other cells were cultured overnight in substrate limited medium (glucose and glutamine free DMEM supplemented with 0.5mM glucose, 1mM glutamine, 0.5mM carnitine and 1% (v/v) FBS; pH 7.4).

tag: tissue

value: primary muscle cells from quadruceps

tag: strain

value: ICR


title: Mouse No.43 Normal

city: Piscataway

state: NJ

department: Chemical Biology

source_name: Colon epithelium

value: Normal

value: Normal colon epithelium

tag: age

value: Wild type


title: Mouse No.42 Tumor No.2

value: Female


title: Mouse No.42 Tumor No.1


title: Jos6024(4T)(17)

description: primary muscle cells_limited media_undernourished_primary muscle cells_limited_undernourished_4t

source_name: primary muscle cells from quadruceps,limited media,undernourished


title: Mouse No.41 Tumor No.1


title: NTC19

type: SRA

first: Jessica

middle: Sarah

last: Elman

state: MA

address: 150 Harrison Ave

department: DMCB

institute: Tufts University

description:
processed data file:
JE_FUBP_isoform.matrix.results.DEhigherthresh
JE_FUBP_genes.matrix.results.Dehigherthresh
A3SS.MATS.JCEC.txt
A5SS.MATS.JCEC.txt
MXE.MATS.JCEC.txt
SE.MATS.JCEC.txt
RI.MATS.JCEC.txt

library_source: transcriptomic

data_processing:
STAR version 2.6 for alignment
rMATS 4.0.1 for alternative splice analysis
RSEM (using bowtie2 for alignment)
EBSeq for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: JE_FUBP_*.matrix.results.DEhigherthresh  = text files with isoform or gene expression
Supplementary_files_format_and_content: *.MATS.JCEC.txt = tab-delimited text file with a3ss, a5ss, mxe, se, ri splice events, as indicated in the file names.
Supplementary_files_format_and_content: more details in the readme.txt

organism: Homo sapiens

source_name: MCF10F cells

growth_protocol: Cells were grown at 37°C with 5% CO2 and cultured in DMEM/F12 supplemented with 5% horse serum, 100ng/ml cholera toxin, 5μg/ml insulin, 0.5μg/ml hydrocortisone, 50ng/ml EGF, and 1% antibiotic/antimycotic (Corning, Corning, NY).

extract_protocol:
Total RNA was extracted from MCF10F cells using the RNeasy Maxi Kit (Qiagen).
Library was prepared with the TruSeq Stranded mRNA kit and samples were sequenced by the Illumina HiSeq 2500 system using the Rapid PE150 flow cell.

tag: cell line

tag: cell type

value: mammary epithelial cells

tag: genotype/variation

value: non-targeting control


title: CK_3

city: luoyang

first: Xiaochan

last: Gao

state: henan

address: kaiyuan street

country: China

institute: henan university of science and technology

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
De novo assembly of the transcriptome was performed with Trinity 2.4.0.
Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND [3] with a threshold of Evalue
Salmon  was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR . Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Supplementary_files_format_and_content: xls include TPM values for each Sample

organism: Andrias davidianus

source_name: spleen

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0
Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen)
Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature.
The paired-end libraries was 300 bp ( ± 50 bp)

tag: time

value: 2 weeks

tag: treatment

value: control


title: CK_2


title: WT_A

city: New York

first: Lauren

last: Bayer Horowitz

state: NY

address: 540 1st Ave

department: Cell Biology

institute: NYU School of Medicine

description:
wild type BAG cells replicate 1
WT-A

data_processing:
fastq files were aligned to the Caenorhabditis elegans genome and transcriptome (Wormbase WS243) using the STAR software package (Dobin et al., 2013).
Gene expression quantification was performed on the resulting BAM files using HTSeq (Anders et al., 2014)
Differential expression analysis was done using the DeSeq2 software package (Love et al., 2014) in R.
Tiled-data files (TDF) were generated from the genomic alignments (BAM files) using Integrative Genomics Viewer (Thorvaldsdottir et al., 2013) and used to generate read coverage histograms.
Genome_build: version 243 of the Caenorhabditis elegans reference genome from Wormbase, WS243
Supplementary_files_format_and_content: comma-separated file of the normalized read counts in the different cell populations sequenced;  TDF files for the different cell-populations sequenced.

organism: Caenorhabditis elegans

source_name: C. elegans fluorescent BAG cells

growth_protocol: Embryonic cell cultures were prepared as previously described (Christensen et al., 2002, Zhang et al., 2002) from wild-type and pmk-3(wz31) mutant animals expressing the BAG-specific and pmk-3 independent marker wzIs113[Pgcy-9::GFP].In brief, embryos were isolated from synchronized populations of hypochlorite treated hermaphrodites, and dissociated into single cells by chitinase treatment. Cells were resuspended in L-15 medium supplemented with 10% FBS (Sigma) and antibiotics, and passed through a 5 um syringe filter (Millipore). Cells were plated onto poly-D-lysine coated single-well chambered cover glasses (Lab-Tek II) and incubated overnight at 25degC.

extract_protocol:
GFP-labeled BAG neurons were isolated approximately 24 hours after dissociation using Fluorescence Activated Cell Sorting (FACS); sorted cells were confirmed to be >90% GFP positive by direct inspection on a fluorescent microscope. Non-fluorescent, ‘non-BAG’, cells were also collected. Dead cells were marked with propidium-iodide and excluded from sorted cells. Sorting was performed on a FACSAria Ilu SORP cell sorter using a 70 um nozzle. Cells were sorted directly into RNA Extraction Buffer (10,000 cells/100 uL buffer), and RNA was purified using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher). RNA integrity and concentration were evaluated using an Agilent Bioanalyzer. RNA samples had an RNA Integrity score of at least 8, indicating that all samples were of high quality.
cDNA libraries were prepared from RNA (1-2 ng) using the Ovation RNA-Seq System V2 (NuGEN), multiplexed, and sequenced as 100 base pair paired end reads using the HiSeq 2500 (Illumina).

tag: genotype

tag: developmental stage

value: embryonic


title: Mouse No.42 Normal


title: Jos6029(8X)(22)

description: primary muscle cells_standard media_undernourished_primary muscle cells_standard_undernourished_8x


title: CK_1


title: BI_3

value: Infection


title: Control_B

description:
wild type non-BAG cells replicate 2
Control-B

source_name: C. elegans non-fluorescent embryonic cells


title: BI_2


title: M1_POOL2: Monocyte_M1_rep2

type: genomic

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: Bisulfite-converted DNA

hyb_protocol: Illumina’s Infinium HD Assay Methylation Protocol

scan_protocol: HiScan Illumina Inc.

data_processing:
Raw data were decoded by GenomeStudio Illumina Inc. And normalization was done (1) forcePositive background correction, (2) log2 transformation, (3) quantile adjusted for color balance and (4) quantile normalization
Signal intensity and detection p-value as calculated by GenomeStudio Illumina Inc.

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Not provided

growth_protocol: Monocytes were cultured in RPMI medium (Life Technologies) supplemented with 10% FCS (ThermoFisher Scientific).

extract_protocol: Total DNA was extracted with a Genomic DNA Mini Kit (ATP Biotech)

treatment_protocol: Monocytes were incubated with GM-CSF (1000 U/ml, PeproTech) (M1 samples) or M-CSF (10 ng/ml, PeproTech) (M2 samples) for 7 days.

value: monocyte


title: MONOS_POOL1: Monocyte_CD14+_rep1

description: Bisulfite-converted DNA


title: Jos6028(8T)(21)

description: primary muscle cells_limited media_undernourished_primary muscle cells_limited_undernourished_8t


title: M2_POOL1: Monocyte_M2_rep1

description: Bisulfite-converted DNA


title: Control_A

description:
wild type non-BAG cells replicate 1
Control-A


title: BI_1


title: Mouse No.42 Tumor No.3

value: Tumor

value: Tubular adenoma


title: M2_POOL2: Monocyte_M2_rep2

description: Bisulfite-converted DNA


title: Mouse No.41 Tumor No.3

value: Male

value: 16 weeks


title: M1_POOL1: Monocyte_M1_rep1

description: Bisulfite-converted DNA


title: Myceliphothora thermophila DXyr1_Arabinoxylan 2 h R2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

description: Myceliphothora thermophila Xyr1 mutant grown on Arabinoxylan for 2 h

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Myceliophthora thermophila v2.0 ( https://mycocosm.jgi.doe.gov/Spoth2/Spoth2.home.html) genome using BWA/Bowtie2 (Langmead B et al., Genome Biology, 2009) .
“Fragments per kilobase of exon model per million mapped reads” (RPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Myceliophthora thermophila v2.0 ( https://mycocosm.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Thermothelomyces thermophilus

source_name: Mycelium sample

growth_protocol: All Myceliophthora thermophila strains described in this study were grown on Malt Extract Agar (MEA) plates at 37 °C for 7 days to obtain conidia. For growth phenotypic profiling, the WT and ΔMtxyr1 strain were grown on minimal medium agar plates (pH set to 6.0) containing AspA+N (70 mM NaNO3, 7 mM KCl, 11 mM KH2PO4), 2 mM MgSO4, trace elements (174 µM EDTA, 76 µM ZnSO4·7H2O, 178 µM H3BO3, 25 µM MnSO4·H2O, 18 µM FeSO4.7H2O, 7.1 µM CoCl2·6H2O, 6.4 µM CuSO4·5H2O and 6.2 µM Na2MoO4·2H2O), 1.6% agar-agar (Merck Company, Darmstadt, Germany), 10 mM of uridine (if necessary) and 25 mM of D-glucose, D-xylose, L-arabinose or cellobiose or 1% of birchwood xylan, wheat arabinoxylan, Avicel or cellulose. All sugar substrates were purchased from Sigma-Aldrich (St. Louis, MO, USA), except for cellobiose (Acros Organics, Belgium), wheat arabinoxylan (Megazyme, Wicklow, Ireland) and Avicel (Fluka Chemicals, Buchs, Switzerland). Strains were inoculated with 2 µl containing 500 spores and grown for 5 days at 37 °C. For RNA-seq analysis, the WT and ΔMtxyr1 strain were pre-grown in complete medium (pH 6.0) containing AspA+NH4, 2 mM MgSO4, trace elements, 0.1% casamino acids, 4 μg/L biotin and 2% D-fructose. Strains were inoculated with 1·106 spores per mL and incubated at 37 °C at 200 rpm in a rotary shaker. After 36h of incubation, aliquots of the mycelium wereas transferred to shake flasks with minimal medium and as a carbon source 1% of D-glucose, D-xylose, L-arabinose or wheat arabinoxylan, respectively. Minimal medium (pH 6.0) contained AspA+NH4, 2 mM MgSO4, trace elements, 0.1% casamino acids, 4 μg/L biotin and was buffered by anwith extra addition of 70 mM KH2PO4. Mycelial samples were harvested after 2 h of incubation in all monosaccharide cultures and after 2 and 8h of incubation in case of the wheat arabinoxylan culture. The mycelial samples were dried between tissue paper and directly frozen in liquid nitrogen for RNA extraction.

extract_protocol:
Total RNA was extracted from mycelium ground in a Tissue Lyser II (Qiagen, Venlo, the Netherlands) using TRIzol reagent (Invitrogen, Breda, the Netherlands) and purified with NucleoSpin® RNA II Clean-up kit (Macherey-Nagel) with rDNase treatment. The RNA quantity and quality was checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA). RNA samples were single-end sequenced at BGI Tech Solutions Co., Ltd. (Hong Kong, China) using Illumina HiSeqTM 2000 platform (http://illumina.com).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Xyr1 mutant

tag: sampling time

value: Arabinoxylan 2 h


title: Myceliphothora thermophila DXyr1_Arabinoxylan 8 h R1

description: Myceliphothora thermophila Xyr1 mutant grown on Arabinoxylan for 8 h

value: Arabinoxylan 8 h


title: Myceliphothora thermophila DXyr1_Arabinoxylan 2 h R1


title: MONOS_POOL2: Monocyte_CD14+_rep2

description: Bisulfite-converted DNA


title: CD34+_a: CD34+_rep1

description: Bisulfite-converted DNA

value: hematopoietic progenitor


title: CD34+_b: CD34+_rep2

description: Bisulfite-converted DNA


title: HeLa_treated_rep2

city: New Delhi

first: Rohini

last: Muthuswami

address: Room# 333, School of Life Sciences, JNU

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

data_processing:
Quality of trimmed raw reads obtained from the sequencing company was checked by fastqc
Trimmed reads were quasi aligned to hg19 on salmon 0.11.2 taking UCSC knowngene and ensembl.v29 GTF files as reference transcrptome.
Salmon generated transcript quantification file were normalised, converted to gene level quantification to import on DESeq2 (version 1.22.2) using tximport (version 1.10.1) package on R (version 3.5.2)
Differential gene expression of normalised counts was done on R by DESeq2 package
RNA-seq data was validated by qRT-PCR
Genome_build: hg19

molecule: polyA RNA

source_name: HeLa

growth_protocol: Cell lines used in this study were purchased from NCCS, Pune, India and maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin-amphotericin cocktail at 37°C in the presence of 5% CO 2

extract_protocol: RNA-seq library was prepared using 100 ng purified poly(A) mRNA using NEBNext Ultra II RNA Library Prep Kit with certain optimization in the user protocol provided by the manufacturer.

treatment_protocol: HeLa cells were seeded on 100mm culture plate a day prior to ADAADi treatment. On the Next day cells were treated with 5mM of ADAADi for 48 hours.

value: Cervical cancer cells

value: 5mM ADAADi

value: HeLa


title: HeLa_control_rep2


title: HeLa_treated_rep1


title: HeLa_control_rep1


title: Myceliphothora thermophila DXyr1_Arabinose 2 h R2

description: Myceliphothora thermophila Xyr1 mutant grown on Arabinose for 2 h

value: Arabinose 2 h


title: Myceliphothora thermophila DXyr1_Arabinoxylan 8 h R2


title: Jos6009(10X)(2)

description: primary muscle cells_standard media_control_primary muscle cells_standard_control_10x

source_name: primary muscle cells from quadruceps,standard media,control

value: primary muscle cells from quadruceps

value: ICR


title: Jos6015(15X)(8)

description: primary muscle cells_standard media_control_primary muscle cells_standard_control_15x


title: Mouse No.41 Normal

value: Normal

value: Normal colon epithelium

value: Wild type


title: Jos6014(15T)(7)

description: primary muscle cells_limited media_control_primary muscle cells_limited_control_15t

source_name: primary muscle cells from quadruceps,limited media,control


title: Input_Chip-Seq_Rep1

library_source: genomic

data_processing:
Raw reads were trimmed by trimmomatic (version-0.36.5) to remove adaptor sequence and base quality was checked by FASTQC
Trimmed reads were aligned to human genome (hg38) by BOWTIE2 with default settings
Aligned files were marked for duplicates by PicardMarkduplicates and filtered on bit wise flags by SAM tools on Galaxy platform. Only paired end reads that are mapped in proper pair were selected for peak calling
Biological replicates of SMARCAL1 and BRG1 were merged in a single BAM file before peak calling
Peak calling was performed by MACS2 (Version 2.1.1.20160309.0) with default settings
Genome_build: hg38

extract_protocol: ChIP-seq library was prepared as per the instructions of user manual of NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Catalog # E7370) with certain optimization and initial 100 ng of DNA purified after ChIP.

tag: chip antibody


title: Jos6031(9X)(24)

description: primary muscle cells_standard media_undernourished_primary muscle cells_standard_undernourished_9x


title: Jos6011(11X)(4)

description: primary muscle cells_standard media_control_primary muscle cells_standard_control_11x


title: SMARCAL1_Chip-Seq_Rep2

description:
SMARCAL1_ChiP-seq_narrowpeaks.bed
SMARCAL1_ChiP-seq_bigwig

value: Custom synthesised polyclonal antibody (Merk, india)


title: Myceliphothora thermophila DXyr1_Xylose 2 h R2

description: Myceliphothora thermophila Xyr1 mutant grown on Xylose for 2 h

value: Xylose 2 h


title: Myceliphothora thermophila DXyr1_Arabinose 2 h R1


title: Jos6030(9T)(23)

description: primary muscle cells_limited media_undernourished_primary muscle cells_limited_undernourished_9T


title: Myceliphothora thermophila DXyr1_Xylose 2h R1


title: SMARCAL1_Chip-Seq_Rep1


title: Jos6010(11T)(3)

description: primary muscle cells_limited media_control_primary muscle cells_limited_control_11t


title: PM_A

description:
pmk-3 mutant BAG cells replicate 1
PM-A

value: wzIs113[Pgcy-9::GFP]; pmk-3(wz31)

value: embryonic


title: WT_B

description:
wild type BAG cells replicate 2
WT-B


title: Myceliphothora thermophila wt_Arabinoxylan 8 h R2

description: Myceliphothora thermophila wild type grown on Arabinoxylan for 8 h

value: wild type


title: Myceliphothora thermophila DXyr1_Glucose 2 h R1

description: Myceliphothora thermophila Xyr1 mutant grown on Glucose for 2 h

value: Xyr1 mutant

value: Glucose 2 h


title: Jos6008(10T)(1)

description: primary muscle cells_limited media_control_primary muscle cells_limited_control_10t


title: Jos6016(16T)(9)

description: primary muscle cells_limited media_control_primary muscle cells_limited_control_16t


title: Blood3

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.0.
Genome_build: GRCh38 / mm10 (Ensembl 84)
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: PBMC

extract_protocol:
FACS
10X Genomics Single cell 3' gene expression V2

tag: disease status

value: fibrotic

tag: population

value: PBMC

tag: cause of liver disease

value: NAFLD

value: Female


title: Jos6017(16X)(10)

description: primary muscle cells_standard media_control_primary muscle cells_standard_control_16x


title: Myceliphothora thermophila DXyr1_Glucose 2h R2


title: Jos6023(24x)(16)

description: primary muscle cells_standard media_control_primary muscle cells_standard_control_24x


title: BRG1_ChiP-Seq_Rep1

description:
BRG1_ChiP-seq_narrowpeaks.bed
BRG1_ChiP-seq_bigwig

value: Cervical cancer cells

value: HeLa

value: BRG1 (Abcam Catalog# B8184)


title: BRG1_ChiP-Seq_Rep2


title: Blood4

description: 10X Genomics Single cell 3' gene expression V2

tag: Sex

value: Male


title: Jos6026(5T)(19)

description: primary muscle cells_limited media_control_primary muscle cells_limited_control_5T

value: primary muscle cells from quadruceps

value: ICR


title: Mouse No.41 Tumor No.2

description: Total RNA was labelled and hybridized to the microarray chip

value: Tumor

tag: histology

value: Tubular adenoma

value: 16 weeks

tag: genetic mutations (ctnnb1)

value: dominant active mutant


title: Myceliphothora thermophila wt_Arabinoxylan 2 h R2

description: Myceliphothora thermophila wild type grown on Arabinoxylan for 2 h

tag: strain

value: wild type

value: Arabinoxylan 2 h


title: Myceliphothora thermophila wt_Arabinoxylan 8 h R1

value: Arabinoxylan 8 h


title: Myceliphothora thermophila wt_Arabinoxylan 2 h R1


title: Blood1

value: fibrotic


title: Jos6022(24T)(15)

description: primary muscle cells_limited media_control_primary muscle cells_limited_control_24t

tag: tissue


title: Cirrhotic5_Cd45+

source_name: Liver

extract_protocol:
Enzymatic digestion and FACS
10X Genomics Single cell 3' gene expression V2

value: Leucocytes

value: PBC

tag: cell subtype


title: Blood2

value: PBMC

value: Hereditary Haemochromatosis


title: Cirrhotic4_Cd45+

value: NAFLD


title: Myceliphothora thermophila wt_Arabinose 2 h R1

description: Myceliphothora thermophila wild type grown on Arabinose for 2 h

value: Arabinose 2 h


title: Myceliphothora thermophila wt_Arabinose 2 h R2


title: Cirrhotic3_Cd45-

value: Other NPC

value: Alcohol

value: Male


title: Myceliphothora thermophila wt_Xylose 2 h R2

description: Myceliphothora thermophila wild type grown on Xylose for 2 h

value: Xylose 2 h


title: Jos6027(5X)(20)

description: primary muscle cells_standard media_control_primary muscle cells_standard_control_5x

value: primary muscle cells from quadruceps

value: ICR


title: mRNA_Monocytes_CCR2+_TN2 [tag_706_]

city: San Francisco

first: Zena

last: Werb

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: UCSF

description:
Monocytes_CCpos_TN2_tag_706_
mRNA
processed data file: Monocytes_TN2_vs_Monocytes_TN1.csv

data_processing:
For each sample, both pair-ended Fastq files were aligned to reference transcriptome (Mus_musculus.GRCm38) and counts and transcripts per million values were calculated using Kallisto50 quant, version 0.42.2.1.
Differential expression (DE) analysis was done using AltAnalyze version 2.0 (Emig et al. 2010; Salomonis et al. 2010) by counting the kallisto aligned reads for each sample in Ensembl genes and using AltAnalyze quantile normalization. DE analysis from Altanalyze and used for downstream analysis are presented as: FOR NEURTROPHILS = avg-Ne_TN1; avg-Ne_TN2 ; log_fold-Ne_TN2_vs_Ne_TN1; fold-Ne_TN2_vs_Ne_TN1 ; rawp-Ne_TN2_vs_Ne_TN1;adjp-Ne_TN2_vs_Ne_TN1. FOR CCR2+ MONOCYTES = Ensembl_gene Definition; Symbol; avg-Mo_TN1; avg-Mo_TN2; log_fold-Mo_TN2_vs_Mo_TN1; fold-Mo_TN2_vs_Mo_TN1; rawp-Mo_TN2_vs_Mo_TN1; adjp-Mo_TN2_vs_Mo_TN1.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Kallisto output with aligned read counts are presented in *.tsv format with ensembl annotations, Differential expression from Altanalzye are presented in *.csv format including Ensembl_gene Definition; Symbol; avg-expression group1; avg-expression group2; log_fold-group_2_v_group_1; fold-group_2_v_group_1;  rawp;  adjp.

source_name: CCR2+ Monocytes

extract_protocol:
RNA sequencing was performed on RNA extracted from FACS-sorted monocytes CCR2+ and neutrophils from lungs of mice bearing tumors HCl-001 and HCl-002 reaching end point, followed by purification using an RNeasy Micro Kit (Qiagen).
cDNA synthesis and whole, transcriptome amplification was performed using the Smart-seq2 protocol.
Sequencing libraries were prepared using Illumina XT Library Preparation Kit and sequenced by HiSeq 2500 sequencer.

value: NOD/scid

tag: cell type

value: CCR2+ Monocytes

value: Purified from Lungs HCl-002

tag: tumor progression

value: Endpoint


title: mRNA_Monocytes_CCR2+_TN2 [tag_367]

description:
Monocytes_CCpos_TN2_367
mRNA
processed data file: Monocytes_TN2_vs_Monocytes_TN1.csv


title: mRNA_Monocytes_CCR2+_TN2 [tag_1341]

description:
Monocytes_CCpos_TN2_tag_1341
mRNA
processed data file: Monocytes_TN2_vs_Monocytes_TN1.csv


title: mRNA_Monocytes_CCR2+_TN1 [tag_482]

description:
Monocytes_CCpos_TN1_tag_482
mRNA
processed data file: Monocytes_TN2_vs_Monocytes_TN1.csv

value: Purified from Lungs HCl-001


title: mRNA_Monocytes_CCR2+_TN1 [tag_191]

description:
Monocytes_CCpos_TN1_tag_191
mRNA
processed data file: Monocytes_TN2_vs_Monocytes_TN1.csv


title: mRNA_Neutrophils_TN2 [tag_706]

description:
Neutrophils_TN2_tag_706
mRNA
processed data file: Neutrophils_TN2_vs_Neutrophils_TN1.csv

source_name: Neutrophils

value: Neutrophils


title: mRNA_Neutrophils_TN2 [tag_1341]

description:
Neutrophils_TN2_tag_1341
mRNA
processed data file: Neutrophils_TN2_vs_Neutrophils_TN1.csv


title: Cirrhotic3_CD45+

value: fibrotic

value: Leucocytes


title: mRNA_Neutrophils_TN2 [tag_367]

description:
Neutrophils_TN2_tag_367
mRNA
processed data file: Neutrophils_TN2_vs_Neutrophils_TN1.csv


title: Cirrhotic2_CD45-


title: Myceliphothora thermophila wt_Glucose 2 h R2

description: Myceliphothora thermophila wild type grown on Glucose for 2 h

value: wild type

value: Glucose 2 h


title: mRNA_Neutrophils_TN1 [tag_482]

description:
Neutrophils_TN1_tag_482
mRNA
processed data file: Neutrophils_TN2_vs_Neutrophils_TN1.csv


title: mRNA_Neutrophils_TN1 [tag_191]

description:
Neutrophils_TN1_tag_191
mRNA
processed data file: Neutrophils_TN2_vs_Neutrophils_TN1.csv


title: Myceliphothora thermophila wt_Glucose 2 h R1


title: Cirrhotic2_Cd45+

description: 10X Genomics Single cell 3' gene expression V2


title: Cirrhotic1_Cd45-B

value: NAFLD

value: Female


title: F48F

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

institute: Shandong university

data_processing:
we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.Then we assembled those clean reads into Unigenes, followed with Unigene functional annotation, SSR detection and calculate the Unigene expression levels and SNPs of each sample. Finally, we identify DEGs (differential expressed genes) between samples and do clustering analysis and functional annotations
Genome_build: hg38
Supplementary_files_format_and_content: FPKMs

source_name: cell

growth_protocol: Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated, evaluated the quality, reverse-transcribed to cDNA,
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.

treatment_protocol: Cells were treated  with F. nucleatum at a multiplicity of infection (MOI) of F. nucleatum : cell =10:1, and cultured at 2h, 6h, 12h, 24h and 48h

value: human gingival fibroblasts

tag: individual

value: donor 5

tag: culture time

value: F. nucleatum


title: MUT_pancreas_rep2

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay St.

department: Development and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

description: Mesenchymal cells were isolated by flow-cytometry from microdissected tissues

data_processing:
bcl2fastq v2.17
Reads were trimmed for adapter sequences and low quality bases using trimmomatic v0.32 with the following command: java -Xmx16g -jar trimmomatic-0.32.jar PE -threads 16 file_R1.fastq.gz file_R2.fastq.gz file.1.fastq.gz file.1.U.fastq.gz file.2.fastq.gz file.2.U.fastq.gz ILLUMINACLIP:trimmomatic/0.32/adapters/NexteraPE-PE.fa:2:30:10:15:true LEADING:5 TRAILING:5 SLIDINGWINDOW:5:20 MINLEN:36
Trimmed reads with both mates surviving were aligned to mm10 using STAR v2.5.1b with the following command: star/2.5.1b/bin/Linux_x86_64_static/STAR --genomeDir mmus/star_index/ --runThreadN 16 --readFilesIn file.1.fastq.gz file.2.fastq.gz --outFileNamePrefix file --readFilesCommand zcat  --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 8000000000 --twopassMode Basic;
Gene level counts were obtained using featureCounts v1.5.0 with the following command: subread-1.5.0-Linux-x86_64/bin/featureCounts -a genomes/mmus/gtf/gencode.vM4.annotation.gtf -o file.txt -g gene_name -p -s 0 -C –donotsort file.sortedName.bam
Genome_build: mm10 (GRCm38.68). Genome used for STAR alignment generated with the following command (scaffold contigs were omitted)  star/2.5.1b/bin/Linux_x86_64_static/STAR  --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles ../Mus_musculus.GRCm38.68.dna.chromosomes.fa --sjdbGTFfile ../gtf/gencode.vM4.annotation.gtf --runThreadN 16 --sjdbOverhang 100
Genome_build: transcriptome annotation: gencode.vM4
Supplementary_files_format_and_content: Counts – gene level counts generated by featureCounts (see data processing above)

source_name: pancreatic mesynchyme

extract_protocol:
RNeasy kit (Qiagen, 74134)
clontech/nextera XT (non-stranded)

value: mixed 129S

tag: genotype


title: Virus 4

city: Godollo

first: Peter

last: Gyula

state: Pest

address: Szent-Gyorgyi Albert u. 4.

department: Department of Plant Biotechnology

country: Hungary

institute: Hungarian University of Agricultural and Life Sciences

data_processing:
The sequences were trimmed and quality-filtered by the sequencing facility (UD-GenoMed Ltd, Debrecen, Hungary)
Sequences were mapped to the Nicotiana benthamiana Niben101 transcriptome using kallisto v0.44.0 (Pimentel et al., 2017) with the following parameters: -b 100 --single -l 200 -s 20 –bias.
The differential expression analysis using the kallisto-quantified data was performed with sleuth v0.28.0 (Pimentel et al., 2017). We considered a transcript expression differentially expressed if its modelled expression fold-change (beta) was at least 2-fold, its mean abundance (counts) was at least 10, and if its Q-value was less than 0.01.
The normalized expression table and the Wald-test table were exported from sleuth, merged, and annotated using the Niben101 annotation table.
Genome_build: Nicotiana benthamiana v1.0.1
Supplementary_files_format_and_content: The normalized expression values of the Niben101 transcripts (values are transcript per million, TPM) in the mock and virus-infected samples (4-4 replicates) are in the ‘kallisto_table_w_Wald_test_annotated.txt.gz’ file.

organism: Nicotiana benthamiana

source_name: shoot apical meristem region

growth_protocol: Nicotiana benthamiana plants were grown in environmental test chambers (MLR-350; Sanyo, Tokyo, Japan) at 21°C under long day conditions in the soil for four weeks.

extract_protocol:
Meristem samples (45 meristem for each replicate) were collected four days after inoculation under a stereomicroscope and directly frozen in liquid nitrogen. RNA extraction was performed as described previously (Burgyán et al., 2000).
The libraries were constructed using the TruSeq RNA Library Prep Kit v2 (unstranded), according to the manufacturer's instructions.

treatment_protocol: Four-week-old plants were infected with purified CymRSV virions (Dalmay et al., 1993). RNA was prepared from the SAM region as described previously (Burgyán et al., 2000).

value: shoot apical meristem region

tag: infection

value: Virus

tag: replicate


title: Cirrhotic1_Cd45-A

value: Other NPC


title: F48C

tag: treatment

value: control


title: Myceliphothora thermophila wt_Xylose 2 h R1

tag: sampling time

value: Xylose 2 h


title: WT_stomach_rep2

source_name: stomach mesenchyme

tag: developmental stage


title: Virus 3


title: F24F


title: HEK293-Mock-BiolRep2-TechRep2

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

description:
HEK293 cells, mock transfected, Technical Replicate 2 of Biological Replicate 2
M_2.2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Array data were processed using the methylkey pipeline which was developed in-house. Cross-reactive probes, probes overlapping genetic variants at targeted CpG sites, probes with genetic variants overlapping the body of the probe, and XY chromosome probes were removed. Pre-processing and normalization were done using the minfi Bioconductor package. PCA analysis followed by Wilcoxon Rank Sum Tests were conducted to identify possible confounding variables. SVA was performed to correct for potential batch effects. β-values were converted to M-values, and a linear regression model with adjustments for Sentrix ID was used to identify differentially methylated probes (DMPs) using the Bioconductor limma package

label: Cy5 and Cy3

source_name: HEK293, mock transfected

label_protocol: Standard Illumina Protocol

growth_protocol: Human embryonic kidney cell line HEK293 (ATCC, CRL-1573) was maintained in Dulbecco's Modified Eagle Medium (Sigma Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (Sigma Aldrich), 4 mM L-glutamine (Sigma Aldrich), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma Aldrich).  Cells were incubated at 37°C in a humidified 5% CO2-containing atmosphere.

extract_protocol: DNA was isolated from harvested cells using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).

treatment_protocol: The dSpCas9-DNMT3A N-terminal fusion was used to target IL6ST with four sgRNAs and dSpCas9-TET1 N-terminal fusion was used to target MGAT3 with five gRNAs. For each locus, two types of constructs were used: i) construct having both the fusion protein and the selection marker (PuroR) under the same strong, constitutive CAG promoter; ii) the fusion construct under the weak EFS promoter, while maintaining efficient selection of transfected cells with PuroR under the strong SV40 promoter. Transfection of HEK293 cells in a 6-well plate was performed as for all other experiments using 800 ng of plasmids co-expressing dSpCas9-TET1 or dSpCas9-DNMT3A and gRNAs, in biological and technical duplicates. Cells were harvested 8th day after transfection.

tag: fusion protein

value: Mock transfected

tag: promoter

value: Not applicable


title: HEK293-dSpCas9-CAG-DNMT3A-IL6ST-BiolRep2-TechRep2

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by strong promoter (CAG), and gRNA targeting IL6ST1, Technical Replicate 2 of Biological Replicate 2
D_2.2

source_name: HEK293, dSpCas9-CAG-DNMT3A

value: CAG


title: WT_pancreas_rep2


title: Virus 2


title: F24C


title: Healthy5_Cd45+

tag: disease status

value: healthy

tag: population

value: Leucocytes

tag: cause of liver disease

tag: Sex

value: Male


title: Healthy4_Cd45-

tag: cell subtype


title: MUT_pancreas_rep1

tag: strain


title: HEK293-dSpCas9-CAG-DNMT3A-IL6ST-BiolRep2-TechRep1

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by strong promoter (CAG), and gRNA targeting IL6ST1, Technical Replicate 1 of Biological Replicate 2
D_2.1


title: WT_intestine_rep2

source_name: intestinal mesenchyme


title: Mock 4

treatment_protocol: Four-week-old plants were infected with inoculation buffer. RNA was prepared from the SAM region as described previously (Burgyán et al., 2000).

tag: tissue

value: Mock


title: Virus 1


title: Healthy4_Cd45+

value: Female


title: F6F

tag: cell type

value: human gingival fibroblasts

tag: individual


title: WT_stomach_rep1

tag: genotype


title: Mock 3

tag: infection


title: HEK293-dSpCas9-EFS-DNMT3A-IL6ST-BiolRep2-TechRep2

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by weak promoter (EFS), and gRNA targeting IL6ST1, Technical Replicate 2 of Biological Replicate 2
D_S_2.2

source_name: HEK293, dSpCas9-EFS-DNMT3A

value: EFS


title: F6C

value: donor 5

tag: culture time


title: WT_pancreas_rep1

value: mixed 129S


title: Mock 2

value: shoot apical meristem region

tag: replicate


title: HEK293-dSpCas9-EFS-TET1-MGAT3-BiolRep2-TechRep2

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by weak promoter (EFS), and gRNA targeting MGAT3, Technical Replicate 2 of Biological Replicate 2
T_S_2.2

source_name: HEK293, dSpCas9-EFS-TET1


title: F2F

tag: treatment

value: F. nucleatum


title: Healthy3_Cd45-B

value: Other NPC


title: Cirrhotic1_Cd45+

value: fibrotic

value: NAFLD


title: Healthy3_Cd45-A


title: F12C

value: control


title: HEK293-dSpCas9-CAG-TET1-MGAT3-BiolRep2-TechRep2

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by strong promoter (CAG), and gRNA targeting MGAT3, Technical Replicate 2 of Biological Replicate 2
T_2.2

source_name: HEK293, dSpCas9-CAG-TET1


title: Mock 1


title: PDAC-3

city: Duarte

first: Juan

last: Du

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

description: normalized-counts.txt

data_processing:
Basecalls performed using bcl2fastq v2.18.0.12
Sequenced reads were aligned to the mouse mm10 reference genome with TopHat2 (v 2.0.14)
Gene expression level was quantified by HTSeq (v 0.6.1), and normalized by DESeq2 (v 1.14.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample

source_name: Microdissected pancreatic cancer cells

extract_protocol:
Total RNA was extracted from samples using the PicoPure RNA isolation kit (ThermoFisher) following manufacturer’s instructions, including on column DNAse treatment using RNase-Free DNase I (Qiagen).
RNA sequencing libraries were prepared with Kapa RNA HyperPrep kit with RiboEase (Kapa Biosystems, Cat KR1351) according to the manufacturer's protocol. Sequencing run was performed in the single read mode of 51cycle of read1 and 7 cycles of index read using Illumina HiSeq 2500 with HiSeq SBS V4 Kits. Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling.

treatment_protocol: For total pancreatic RNA, pancreata were resected, washed in ice cold PBS and submerged in RNAlater (Qiagen). For LCM enriched samples, pancreata and tumors were resected, embedded in OCT compound (Tissue-Tek) and frozen using liquid nitrogen cooled isopentane. 10 µM sections of samples were mounted on PEN membrane slides (Leica), fixed by immersion in 70% ethanol, stained with hematxoylin Q.S. (Vector Laboratories) and dehydrated with graded ethanol solutions. Slides were then immediately subjected to LCM using the Leica LMD 7000 platform.

value: Microdissected pancreatic cancer cells

value: KPT


title: Healthy3_Cd45+

value: healthy


title: Healthy2_Cd45-


title: F0


title: TC2

city: Beijing

first: Ying

last: Zhang

address: Haidian District, Yuanmingyuan West Road 2

institute: China Agricultural University

data_processing:
Illumina Hiseq 2500 used for basecalling.
ChIP-seq reads were aligned to the Gallus gallus genome assembly using Bowtie2.
The protein-DNA binding peak regions were identified using Model-Based Analysis of ChIP-seq data (MACS 1.4.2).
Differential binding region screen using edgeR package.
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: bed files

organism: Gallus gallus

source_name: Chorioallantoic membrane (CAM) of embryos

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: breed

value: Tibetan

tag: age

value: 11-day of embryo

value: Chorioallantoic membrane

tag: chip antibody

value: H1alpha67 (abcam, ab463)


title: TC1


title: HEK293-dSpCas9-CAG-TET1-MGAT3-BiolRep1-TechRep2

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by strong promoter (CAG), and gRNA targeting MGAT3, Technical Replicate 2 of Biological Replicate 1
T_1.2

tag: fusion protein

tag: promoter

value: CAG


title: E48F

value: human gingival fibroblasts

value: donor 4


title: WT_intestine_rep1

value: mixed 129S

tag: developmental stage


title: PDAC-1

description: normalized-counts.txt


title: PDAC-2

description: normalized-counts.txt


title: CH2

value: Chahua


title: Healthy1_Cd45-B

tag: disease status

tag: population

tag: cause of liver disease

tag: Sex

value: Male


title: HEK293-dSpCas9-EFS-DNMT3A-IL6ST-BiolRep2-TechRep1

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by weak promoter (EFS), and gRNA targeting IL6ST1, Technical Replicate 1 of Biological Replicate 2
D_S_2.1

value: EFS


title: HEK293-dSpCas9-EFS-TET1-MGAT3-BiolRep2-TechRep1

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by weak promoter (EFS), and gRNA targeting MGAT3, Technical Replicate 1 of Biological Replicate 2
T_S_2.1


title: CH1

tag: tissue


title: E24F

tag: cell type

tag: individual

value: F. nucleatum


title: HEK293-dSpCas9-EFS-TET1-MGAT3-BiolRep1-TechRep2

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by weak promoter (EFS), and gRNA targeting MGAT3, Technical Replicate 2 of Biological Replicate 1
T_S_1.2


title: ADM-2

description: normalized-counts.txt

source_name: Microdissected metaplastic epithelium

value: Microdissected metaplastic epithelium

tag: genotype


title: Healthy1_Cd45-A

value: Other NPC

tag: cell subtype


title: E24C

tag: culture time

value: control


title: HEK293-dSpCas9-CAG-TET1-MGAT3-BiolRep2-TechRep1

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by strong promoter (CAG), and gRNA targeting MGAT3, Technical Replicate 1 of Biological Replicate 2
T_2.1


title: HSF1_wt_ABE_3

city: Urbana

first: Alan

last: Luu

state: Illinois

address: 1110 W Green St.

department: Physics

institute: University of Illinois at Urbana Champaign

description:
Sequenced HSF1 exons 10, 11, 12, 13. Exon 11 targeted with base editor ABE.
ABE_exon_skip.xlsx

data_processing:
Reads demultiplexed by occurrence of primer at beginning of sequence
Reads quality trimmed to phred quality 20 using cutadapt
RNA reads aligned using Tophat2.
Transcript isoforms quantified by checking for occurrence of canonical and exon-skipped junctions
DNA reads aligned using Bowtie2
Variants called in 120 bp windows around protospacers using samtools mpileup
Global error rate estimated by averaging the fraction of alternative allele depths across all positions of control samples
Variants deemed statistically significant using binomial test with null hypothesis proportion equal to higher of global or local error rate
Genome_build: GRCh38
Supplementary_files_format_and_content: ABE_exon_skip.xlsx is an xlsx file containing counts and percentages of each type of isoform
Supplementary_files_format_and_content: ABE_base_edit.xlsx is an xlsx file containing statistically significant variants, whether the target is an on or off-target, and proportion and significance of alternative alleles

source_name: HEK293T Cells

growth_protocol: 293T cells were cultured according to ATCC recommendations (ATCC CRL-3216)

extract_protocol:
RNA was harvested from cell pellets using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer's instructions. cDNA synthesis was performed using the qScript cDNA Synthesis Kit (Quanta Biosciences) from 500-1000 ng of RNA with cycling conditions performed as directed by the supplier. PCR amplicons of cDNA were generated using primers flanking the targeted exon, to enable us to detect transcripts that were missing the exon. PCR amplicons were generated using KAPA2G Robust PCR kits from Kapa Biosystems. The 25 uL reactions used 50 ng of cDNA, Buffer A (5 uL), Enhancer (5 uL), dNTPs (0.5 uL), 10M forward primer (1.25 uL), 10M reverse primer (1.25 uL), KAPA2G Robust DNA Polymerase (0.5 U) and water (up to 25 uL). We used cycling parameters as recommended by the manufacturer. RNA was harvested from cell pellets using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer's instructions. cDNA synthesis was performed using the qScript cDNA Synthesis Kit (Quanta Biosciences) from 500-1000 ng of RNA with cycling conditions performed as directed by the supplier. PCR amplicons of cDNA were generated using primers flanking the targeted exon, to enable us to detect transcripts that were missing the exon. PCR amplicons were generated using KAPA2G Robust PCR kits from Kapa Biosystems. The 25 uL reactions used 50 ng of cDNA, Buffer A (5 uL), Enhancer (5 uL), dNTPs (0.5 uL), 10M forward primer (1.25 uL), 10M reverse primer (1.25 uL), KAPA2G Robust DNA Polymerase (0.5 U) and water (up to 25 uL). We used cycling parameters as recommended by the manufacturer.
Indexed amplicon libraries were prepared using a Nextera XT DNA Library Prep from Illumina following manufacturer's instructions.

treatment_protocol: 293T cells were transfected with 1 µg of plasmid using Lipofectamine 2000 (Invitrogen) in a 24-well according to manufacturer's instructions.

tag: tissue type

value: Human Embryonic Kidney Cells

tag: passages


title: Healthy1_Cd45+

source_name: Liver

value: healthy

value: Leucocytes


title: HEK293-dSpCas9-CAG-DNMT3A-IL6ST-BiolRep1-TechRep2

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by strong promoter (CAG), and gRNA targeting IL6ST1, Technical Replicate 2 of Biological Replicate 1
D_1.2


title: ADM-1

description: normalized-counts.txt

value: KPT


title: ADM-3

description: normalized-counts.txt


title: HEK293-Mock-BiolRep2-TechRep1

description:
HEK293 cells, mock transfected, Technical Replicate 1 of Biological Replicate 2
M_2.1

value: Mock transfected

value: Not applicable


title: HSF1_wt_ABE_2


title: E12F

tag: treatment


title: HSF1_wt_ABE_1


title: E12C


title: HP-3

description: normalized-counts.txt

source_name: Total pancreatic RNA

value: Total pancreatic RNA

value: KP


title: HP-2

description: normalized-counts.txt


title: HEK293-Mock-BiolRep1-TechRep2

description:
HEK293 cells, mock transfected, Technical Replicate 2 of Biological Replicate 1
M_1.2


title: HSF1_Split_WT_ABE_3

description:
Sequenced HSF1 exons 10, 11, 12, 13. Exon 11 targeted with split ABE base editor.
ABE_exon_skip.xlsx


title: HEK293-Mock-BiolRep1-TechRep1

description:
HEK293 cells, mock transfected, Technical Replicate 1 of Biological Replicate 1
M_1.1


title: HP-1

description: normalized-counts.txt


title: E6C

value: human gingival fibroblasts

value: donor 4


title: Healthy2_Cd45+

description: 10X Genomics Single cell 3' gene expression V2


title: E6F


title: E48C


title: HSF1_Split_WT_ABE_1

treatment_protocol:
293T cells were cultured according to ATCC recommendations (ATCC CRL-3216)
293T cells were transfected with 1 µg of plasmid using Lipofectamine 2000 (Invitrogen) in a 24-well according to manufacturer's instructions.


title: HSF1_Split_WT_ABE_2


title: HSF1_GFP_3

description:
Sequenced HSF1 exons 10, 11, 12, 13. No base editor applied.
ABE_exon_skip.xlsx


title: F2C

value: donor 5


title: E2C


title: HSF1_GFP_2


title: VCAP_siNTC_R2 (RNA-Seq)

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

data_processing:
Raw reads were aligned to hg19 (genecode v24lift37) using STAR (v2.4.2a)
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Genome_build: GRCh37
Supplementary_files_format_and_content: tab file for gene level read count

source_name: VCAP

growth_protocol: VCaP cells are cultured routinely in 10% FBS containing DMEM and passed every 5-6 days

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
TruSeq® Strnd Total RNA LT (Illumina) was used for RNA-Seq library construction.

treatment_protocol: VCaP cells were transfected with siRNA against non-targeting control (siNTC), or ZBTB7A (siZBTB7A) in 10% FBS containing DMEM.

tag: cell line

value: prostate cancer cell line VCAP

value: siNTC


title: HEK293-dSpCas9-EFS-DNMT3A-IL6ST-BiolRep1-TechRep1

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by weak promoter (EFS), and gRNA targeting IL6ST1, Technical Replicate 1 of Biological Replicate 1
D_S_1.1

tag: fusion protein

value: EFS


title: VCAP_siNTC_R1 (RNA-Seq)


title: VCAP_siZBTB7A_R2 (RNA-Seq)


title: E0

source_name: cell


title: VCAP_siZBTB7A_R1 (RNA-Seq)


title: HEK293-dSpCas9-EFS-DNMT3A-IL6ST-BiolRep1-TechRep2

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by weak promoter (EFS), and gRNA targeting IL6ST1, Technical Replicate 2 of Biological Replicate 1
D_S_1.2

tag: promoter


title: D48F

value: donor 3

value: F. nucleatum


title: VCAP_FBS_ZBTB7A (ChIP-seq)

description:
VCAP_FBS_ZBTB7A.narrowPeak
VCAP_FBS_ZBTB7A.bw

data_processing:
Raw reads were aligned to hg19 using bwa (version 0.7.2-r351)
sam files are converted to bam with samtools (version 0.1.18 (r982:295))
MACS2 (version 2.0.10.20131216) was used to call peak on the bam files
bedGraph files containing signal per million reads produced from MACS2 was converted to bigwig files with ucsctool kit (315)
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig and narrowPeak files containing normalized signal and peak intervals

growth_protocol: VCaP cells are cultured routinely in 10% FBS containing DMEM and passed every 5-6 days.

extract_protocol:
ChIP DNA was collected according to the ChIP protocol in the paper’s methods section.
ThruPLEX® DNA-seq 48D Kit (Rubicon Genomics) was used for ChIP-Seq library construction.

treatment_protocol: VCaP cells were treated with vehicle or 10 nM DHT for 4 hours in 5% CSS containing phenol red free RPMI 1640.

tag: culture condition

value: FBS

tag: chip antibody

value: Human/Mouse ZBTB7A/Pokemon Antibody (R&D Systems, catalog# MAB3496, lot# CDOR0109121)


title: CTNNA1_wt_ABE_6

description:
Sequenced CTNNA1 exons 6, 7, 8. Exon 7 targeted with base editor ABE
ABE_exon_skip.xlsx

value: Human Embryonic Kidney Cells


title: CTNNA1_wt_ABE_5


title: HEK293-dSpCas9-CAG-DNMT3A-IL6ST-BiolRep1-TechRep1

description:
HEK293 cells, transfected with dSpCas9-DNMT3A fusion protein driven by strong promoter (CAG), and gRNA targeting IL6ST1, Technical Replicate 1 of Biological Replicate 1
D_1.1

value: CAG


title: HEK293-dSpCas9-CAG-TET1-MGAT3-BiolRep1-TechRep1

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by strong promoter (CAG), and gRNA targeting MGAT3, Technical Replicate 1 of Biological Replicate 1
T_1.1


title: E2F


title: HEK293-dSpCas9-EFS-TET1-MGAT3-BiolRep1-TechRep1

description:
HEK293 cells, transfected with dSpCas9-TET1 fusion protein driven by weak promoter (EFS), and gRNA targeting MGAT3, Technical Replicate 1 of Biological Replicate 1
T_S_1.1


title: VCAP_DHT_ZBTB7A_L2 (ChIP-seq)

description:
VCAP_DHT4_ZBTB7A.narrowPeak
VCAP_DHT4_ZBTB7A.bw

value: DHT


title: D24F


title: D48C

value: control


title: HSF1_GFP_1


title: VCAP_DHT_ZBTB7A_L1 (ChIP-seq)


title: CTNNA1_wt_ABE_4


title: VCAP_CSS_ZBTB7A_L2 (ChIP-seq)

description:
VCAP_CSS_ZBTB7A.narrowPeak
VCAP_CSS_ZBTB7A.bw

value: CSS


title: D24C


title: D12F


title: VCAP_CSS_ZBTB7A_L1 (ChIP-seq)


title: D6F


title: CTNNA1_wt_ABE_2


title: CTNNA1_wt_ABE_1


title: CTNNA1_wt_ABE_3


title: D12C


title: D2C


title: D2F


title: CTNNA1_GFP_2

description:
Sequenced CTNNA1 exons 6, 7, 8. No base editor applied.
ABE_exon_skip.xlsx


title: CTNNA1_GFP_1


title: D6C


title: D0


title: CTNNA1_ABE_UGI_5

description:
Sequenced CTNNA1 exons 6, 7, 8. Exon 7 targeted with base editor ABE-UGI
ABE_exon_skip.xlsx


title: CTNNA1_ABE_UGI_6


title: CTNNA1_GFP_3


title: CTNNA1_ABE_UGI_4


title: C48F

value: donor 2


title: C48C


title: E17R2MU9

first: Qinggang

last: Li

state: Outside the United States or Canada

address: 28 Fuxing Road,Haidian District

institute: Chinese PLA General Hospital

description: Gene expression data from patient thalamencephalon

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

source_name: Robo2 homozygous kidneys

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

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

value: E17 kidney


title: E17R2MU2

description: Gene expression data from normal human thalamencephalon


title: CTNNA1_ABE_UGI_3


title: E17R2WT3

description: Gene expression data from normal human parietal lobe

source_name: wild-type kidneys


title: E17R2WT7


title: E17R2MU8


title: R2NB-5


title: C24F

value: human gingival fibroblasts


title: Rux_2GM [ATAC-seq]

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics). Adapters used for sequencing were removed with TrimGalore (Babraham Bioinformatics). In this step, peaks were called by MACS2 software using the correspondent control group to call the peaks of the experimental group.
Read alignment was performed with bowtie2 mapping against the Human Genome 38 reference (hg38). The alignment was performed with the command "bowtie2 -X 2000 --n 2", which supports paired-end read sequencing. Reads mapped to mitochondrial and unknown, random or sexual chromosomes were removed.
Duplicated reads were removed with Picard (http://broadinstitute.github.io/picard/) MarkDuplicates. Reads with low quality values (MAPQ < 10) were removed using samtools view. Results of the reads mapping were exported as input for the peak calling.
Biological replicates merged and peak calling was performed using Model-based analysis of ChIP-seq (MACS) 2 (Zhang et al., 2008) to identify open chromatin regions over background (control group) with an enrichment threshold of adjusted p-value < 0.01.
Genome_build: Human genome hg38 (GRCh38)
Supplementary_files_format_and_content: *.broadPeak: Peaks called from merged biological replicates by MACS2 are submitted as tab-delimited text files with ".broadPeak" extension.

source_name: Human peripheral blood monocytes

extract_protocol:
5,000 cells were resuspended in 50 μl of tagmentation mixture (25 μl TD buffer, 2.5 μl of TDE1, 0.5 μl 1% digitonin and 22 μl of water) (Nextera DNA Library Preparation Kit, Illumina) and incubated at 37°C for 30 minutes. After tagmentation, DNA was purified with MinElute PCR Purification kit.
Cells were lysed and tagmented following FAST ATACseq protocol (Corces et al. Nat Genet. 2016 October ; 48(10): 1193–1203) and tagmented DNA was amplified as previously described (Buenrostro et al. Nat Methods. 2013; 10:1213–1218). Final libraries were size selected using AMPure XT beads.

treatment_protocol: Monocytes were incubated with GM-CSF (1000 U/ml, PeproTech) or M-CSF (10 ng/ml, PeproTech) for 12h. Monocytes treated with GM-CSF were also treated with wortmannin (250 nM), trametinib (75 nM) or ruxolitinib (600 nM) (Selleck Chemicals).

value: Monocyte CD14+

tag: differentiation treatment

value: GM-CSF

tag: inhibitor treatment

value: Ruxolitinib


title: Tram_2GM [ATAC-seq]

value: Trametinib


title: CTNNA1_ABE_UGI_2


title: E17R2WT1


title: Wort_2GM [ATAC-seq]

value: Wortmannin


title: C24C


title: R2NB-4


title: CTNNA1_ABE_UGI_1


title: CTNNA1_ABE_GGGGS5_UGI_3

description:
Sequenced CTNNA1 exons 6, 7, 8. Exon 7 targeted with base editor ABE-GGGGS5-UGI
ABE_exon_skip.xlsx


title: CTNNA1_ABE_GGGGS5_UGI_2


title: C6F


title: R2NB-3


title: Mo2 [ATAC-seq]


title: Cont_2M [ATAC-seq]

value: M-CSF


title: Cont_2GM [ATAC-seq]


title: R2E17-6


title: C6C


title: Rux_1GM [ATAC-seq]


title: Wort_1GM [ATAC-seq]


title: Tram_1GM [ATAC-seq]


title: R2E17-3


title: C2C


title: CTNNA1_ABE_GGGGS5_6

description:
Sequenced CTNNA1 exons 6, 7, 8. Exon 7 targeted with base editor ABE-GGGGS5
ABE_exon_skip.xlsx


title: Cont_1GM [ATAC-seq]


title: CTNNA1_ABE_GGGGS5_4


title: C0


title: CTNNA1_ABE_GGGGS5_UGI_1


title: B48F

value: donor 1

value: F. nucleatum


title: Cont_1M [ATAC-seq]


title: CTNNA1_ABE_GGGGS5_3


title: B48C


title: CTNNA1_ABE_GGGGS5_2


title: ecig day 4.5, biological rep4

city: Chapel Hill

first: Kathleen

middle: M

last: Caron

state: NC

address: 111 Mason Farm Road, CB7545

department: Cell Biology and Physiology

institute: University of North Carolin

description:
gene expression data from day 4.5 pseudopregnant uterus, e-cigarette exposed
ecig_4

hyb_protocol: GeneChips were washed and stained in the  2 GeneChip Fluidics Station 450

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

data_processing: Data was analyzed using Partek Genomics Suite with Gene Expression Workflow followed by quantile normalization

source_name: mouse, day4.5 pseudopregnant

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocol.

growth_protocol: C57BL/6J mice were cared for according to the Institution of Animal Care and Use Committee at the University of North Carolina, with 12 hour light cycles and normal rodent chow.

extract_protocol: RNA was extracted using Trizol with two aqueous phase separations using chloroform and 1-Bromo-3-chloropropane, precipitated with ethanol, and cleaned up and eluted with Qiagen RNEasy mini prep kit.

treatment_protocol: Mice were exposed to E-Cigarette aerosol in a SCIREQ inExpose whole-body inhalation system (Montréal, QC, Canada) for 3 hours/day with 2 puffs/minute. Puff duration was approximately 2 seconds. Vapor was generated using a Joyetech eVic VTC Mini with a 0.15 Ω adjustable-temperature atomizer set to 245° C. The propylene glycol and vegetable glycerin mixture was made fresh in a 55:45 ratio with 24mg/mL nicotine. No flavorings or other adulterants were added. Sham mice were exposed to room air. C57BL/6J females were primed with E-Cigarette for 5 days a week, for 4 weeks before mating to vasectomized males. The presence of a copulatory plug was recorded as day 0.5 and pseudopregnant mice were exposed for each day of pregnancy until euthanasia on the morning of day 4.5

tag: strain

value: uterus

tag: time

value: day 4.5 pseudopregnancy

value: wildtype

value: ecig


title: Mo1 [ATAC-seq]

tag: cell type


title: C2F

tag: individual


title: CTNNA1_ABE_GGGGS5_5

value: Human Embryonic Kidney Cells


title: ecig day 4.5, biological rep3

description:
gene expression data from day 4.5 pseudopregnant uterus, e-cigarette exposed
ecig_3

tag: tissue

tag: genotype


title: CTNNA1_ABE_GGGGS5_1


title: sham day 4.5, biological rep4

description:
gene expression data from day 4.5 pseudopregnant uterus, sham exposed
sham_4

value: sham


title: ecig day 4.5, biological rep2

description:
gene expression data from day 4.5 pseudopregnant uterus, e-cigarette exposed
ecig_2


title: B24F

tag: culture time


title: sham day 4.5, biological rep3

description:
gene expression data from day 4.5 pseudopregnant uterus, sham exposed
sham_3


title: CTNNA1_ABE_EAAA5_3

description:
Sequenced CTNNA1 exons 6, 7, 8. Exon 7 targeted with base editor ABE-EAAA5
ABE_exon_skip.xlsx

tag: tissue type


title: Mouse_healthy

description: 10X Genomics Single cell 3' gene expression V2

tag: disease status

value: healthy

tag: population

value: Mononuclear Phagocytes

tag: cause of liver disease

tag: Sex

value: Male


title: sham day 4.5, biological rep1

description:
gene expression data from day 4.5 pseudopregnant uterus, sham exposed
sham_1

tag: treatment


title: CTNNA1_ABE_EAAA5_2

tag: passages


title: B24C

value: human gingival fibroblasts

value: control


title: sham day 4.5, biological rep2

description:
gene expression data from day 4.5 pseudopregnant uterus, sham exposed
sham_2


title: B12F


title: B12C


title: CHIP dBRF1 ZNF-FLAG rep 1 input

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

institute: University of Georgia

description:
CHIP dBRF1 ZNF-FLAG rep 1 input
brf1_Znf2_ChIP_Peaks_Rep1_L2.5_localsize_20000.txt

data_processing:
Reads were aligned with HISAT2
Visulization tracks were created with deepTools, normalized by FPKM
ATAC peaks were called with MACS
ChIP peaks were called with HOMER
Genome_build: GCF_000091045.1
Supplementary_files_format_and_content: peaks

organism: Cryptococcus neoformans

source_name: XL280 grown in V8

extract_protocol: Nuclei were isolated and Nextera sequencing adapters were integrated via pre-loaded Tn5

value: yeast cells

tag: antibody


title: CTNNA1_ABE_EAAA5_1


title: Mouse_fibrotic

value: fibrotic

value: Carbon tetracholride


title: CHIP dBRF1 ZNF-FLAG rep 1

description:
CHIP dBRF1 ZNF-FLAG rep 1
brf1_Znf2_ChIP_Peaks_Rep1_L2.5_localsize_20000.txt


title: CHIP dBRF1 ZNF-FLAG rep 2 input

description:
CHIP dBRF1 ZNF-FLAG rep 2 input
brf1_Znf2_ChIP_Rep2_L2.5_localsize_20000.txt


title: C12F

value: donor 2


title: B6C

value: donor 1


title: RT-76 v1

city: Boston

first: Julio

middle: C

last: Mantero

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip HG-U133A 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Processed using affy package for R, using RMA normalization. Brainarray custom CDF for HGU133A2 (version 21.0.0, ENTREZG) was utilized for this data set. Http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/entrezg.asp

source_name: human skin

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

extract_protocol: Skin bioeise placed in RNAlater at bedside were stored at -80 degrees C until processing. RNA was exrtacted by homogenization in RLT Buffe and purifying over Rneasy columns

treatment_protocol: Each subject was randomized to either treatment or placebo and treated for 42 days.

tag: timepoint

value: Pre

value: Drug


title: B6F

value: F. nucleatum


title: CTNNA1_ABE_Dual_3

description:
Sequenced CTNNA1 exons 6, 7, 8. Exon 7 targeted with base editor ABE-Dual
ABE_exon_skip.xlsx


title: CTNNA1_ABE_Dual_2


title: C12C


title: CTNNA1_ABE_Dual_1


title: RT-50 v3

value: Post


title: CHIP ZNF2 FLAG rep 2 input

description:
CHIP ZNF2 FLAG rep 2 input
WT_Znf2Peaks_Rep2_L2.5_localsize_20000.txt

value: filamentous cells


title: CHIP ZNF2 FLAG rep 2

description:
CHIP ZNF2 FLAG rep 2
WT_Znf2Peaks_Rep2_L2.5_localsize_20000.txt


title: CTNNA1_ABE_AP5_3

description:
Sequenced CTNNA1 exons 6, 7, 8. Exon 7 targeted with base editor ABE-AP5
ABE_exon_skip.xlsx

value: Human Embryonic Kidney Cells


title: B2C


title: CHIP dBRF1 ZNF-FLAG rep 2

description:
CHIP dBRF1 ZNF-FLAG rep 2
brf1_Znf2_ChIP_Rep2_L2.5_localsize_20000.txt


title: CHIP ZNF2-FLAG rep 1 input

description:
CHIP ZNF2-FLAG rep 1 input
WT_Znf2peaks_Rep1_L2.5_localsize_20000.txt


title: RT-20 v3


title: ecig day 4.5, biological rep1

description:
gene expression data from day 4.5 pseudopregnant uterus, e-cigarette exposed
ecig_1

value: uterus

value: day 4.5 pseudopregnancy

value: wildtype

value: ecig


title: RT-76 v3


title: RT-20 v1


title: B0

value: human gingival fibroblasts


title: CTNNA1_ABE_AP5_2


title: CTNNA1_ABE_AP5_1


title: RT-18 v3

value: Placebo


title: RT-18 v1


title: ChIP ZNF2-FLAG rep 1

description:
ChIP ZNF2-FLAG rep 1
WT_Znf2peaks_Rep1_L2.5_localsize_20000.txt


title: sample24: HighFe_HighCO2_Dark_3

city: Seattle

first: Ginger

last: Armbrust

state: WA

address: 616 NE Northlake Pl

department: Oceanography

institute: University of Washington

data_processing:
Sequence reads from Illumina were trimmed with Trimmomatic
trimmed sequences were mapped against the Thaps v3 genome (https://genome.jgi.doe.gov/Thaps3/Thaps3.home.html) using the sequence aligner bowtie2
Transcript abundances were quantified as the number of sequence reads that aligned to a given gene (read counts) using HTSeq
Normalization by library size was done using the R package edgeR
Genome_build: Thaps v3 genome https://genome.jgi.doe.gov/Thaps3/Thaps3.home.html
Supplementary_files_format_and_content: Each sampleXX file (txt file) contain the transcript abundance of the sequence reads that aligned to a given Thaps3 gene in sample XX (not normalized by library size)

organism: Thalassiosira pseudonana CCMP1335

source_name: Axenic Thalassiosira pseudonana (CCMP 1335) grown in batch culture

growth_protocol: Cells were grown in batch cultures using chelexed Aquil media with the addition of either 1000 nmol L-1 or 50 nmol L-1 iron (EDTA at 100 µmol L-1), at 20˚C under a 12:12 light:dark cycle at 50 µmol photons m-2 sec-1. The media was bubbled with air containing 400 or 800 ppm CO2 prior to cell inoculation. The combination of Fe addition and pH resulted in four concentration of available Fe: 1160, 233, 58 and 12 pM.

extract_protocol:
Samples for transcriptomes were collected over one day during the exponential growth phase at 6 hours into the light and 6 hours into the dark phase. Approximately 3 x 10E7 cells were gently filtered onto a 0.4 mm polycarbonate Millipore filter, flash frozen, and stored at -80˚C until analysis. Samples were extracted with the ToTALLY RNA Total RNA Isolation Kit
Library preparation and sequencing was performed at the Northwest Genomics Center (University of Washington) via Illumina NextSeq

tag: available iron

tag: co2 (ppm)

tag: time of day

value: Midnight


title: L25_1

description:
Sequenced CTNNA1 exons 6, 7, 8 (cDNA) and exon 7 splice acceptor (genomic DNA); HSF1 exons 10, 11, 12, 13 (cDNA) and exon 11 splice acceptor (genomic DNA); JUP exons 9, 10, 11 (cDNA) and exon 10 splice acceptor (genomic DNA); AHCY exons 7, 8, 9, 10 (cDNA) and exon 9 splice acceptor (genomic DNA). Base editor ABE-GGGGS5 targeted at exons with splice acceptor sequenced.
ABE_exon_skip.xlsx
ABE_base_edit.xlsx

extract_protocol:
Genomic DNA was isolated from cell pellets using a DNeasy Blood and Tissue Kit (Qiagen), PCR amplicons containing the targeted splice acceptor site were generated using KAPA2G Robust PCR kits from Kapa Biosystems. The 25 uL reactions used 50 ng of cDNA, Buffer A (5 uL), Enhancer (5 uL), dNTPs (0.5 uL), 10M forward primer (1.25 uL), 10M reverse primer (1.25 uL), KAPA2G Robust DNA Polymerase (0.5 U) and water (up to 25 uL). We used cycling parameters as recommended by the manufacturer.
Indexed amplicon libraries were prepared using a HyperPrep DNA Library Prep kit from Kapa Biosystems without shearing and following manufacturer's instructions.


title: L25_2


title: B2F

tag: cell type


title: ATAC SNF5 rep 1

description: ATAC SNF5 rep 1

value: yeast cells

tag: tag


title: RT-17 v3


title: RT-17 v1


title: ABE_UGI_2

description:
Sequenced CTNNA1 exons 6, 7, 8 (cDNA) and exon 7 splice acceptor (genomic DNA); HSF1 exons 10, 11, 12, 13 (cDNA) and exon 11 splice acceptor (genomic DNA); JUP exons 9, 10, 11 (cDNA) and exon 10 splice acceptor (genomic DNA); AHCY exons 7, 8, 9, 10 (cDNA) and exon 9 splice acceptor (genomic DNA). Base editor ABE-UGI targeted at exons with splice acceptor sequenced.
ABE_exon_skip.xlsx
ABE_base_edit.xlsx


title: sample23: HighFe_HighCO2_Dark_2

tag: strain

tag: tissue

value: Axenic Thalassiosira pseudonana (CCMP 1335) grown in batch culture


title: ATAC dZNF2 rep 2

description: ATAC dZNF2 rep 2


title: sample22: HighFe_HighCO2_Dark_1


title: sample21: HighFe_HighCO2_Light_3

value: Midday


title: RT-16 v1


title: RT-16 v3


title: ATAC dZNF2 rep 1

description: ATAC dZNF2 rep 1


title: ABE_2

description:
Sequenced CTNNA1 exons 6, 7, 8 (cDNA) and exon 7 splice acceptor (genomic DNA); HSF1 exons 10, 11, 12, 13 (cDNA) and exon 11 splice acceptor (genomic DNA); JUP exons 9, 10, 11 (cDNA) and exon 10 splice acceptor (genomic DNA); AHCY exons 7, 8, 9, 10 (cDNA) and exon 9 splice acceptor (genomic DNA). Base editor ABE targeted at exons with splice acceptor sequenced.
ABE_exon_skip.xlsx
ABE_base_edit.xlsx


title: ATAC dBRF1 + BRF1oe rep 2

description: ATAC dBRF1 + BRF1oe rep 2

value: dBRF1 + BRF1oe


title: ABE_UGI_1


title: ATAC SNF5 rep 2

description: ATAC SNF5 rep 2


title: sample19: HighFe_HighCO2_Light_1


title: sample18: LowFe_HighCO2_Dark_3

value: 12 pM


title: GFP_2

description:
Sequenced CTNNA1 exons 6, 7, 8 (cDNA) and exon 7 splice acceptor (genomic DNA); HSF1 exons 10, 11, 12, 13 (cDNA) and exon 11 splice acceptor (genomic DNA); JUP exons 9, 10, 11 (cDNA) and exon 10 splice acceptor (genomic DNA); AHCY exons 7, 8, 9, 10 (cDNA) and exon 9 splice acceptor (genomic DNA). No base editor applied.
ABE_exon_skip.xlsx
ABE_base_edit.xlsx


title: ATAC dBRF1 rep 2

description: ATAC dBRF1 rep 2


title: GFP_1


title: ATAC dBRF1 _ BRF1oe rep 1

description: ATAC dBRF1 _ BRF1oe rep 1

value: dBRF1 _ BRF1oe


title: sample17: LowFe_HighCO2_Dark_2


title: ATAC WT V8 rep 2

description: ATAC WT V8 rep 2

value: WT V8


title: ATAC dBRF1 rep 1

description: ATAC dBRF1 rep 1


title: RT-15 v3

value: Post


title: RT-15 v1

value: Pre


title: RT-12-v3

value: Drug


title: sample20: HighFe_HighCO2_Light_2


title: RT-14-v3


title: ATAC WT V8 rep 1

description: ATAC WT V8 rep 1

value: filamentous cells


title: ABE_1

value: Human Embryonic Kidney Cells


title: sample15: LowFe_HighCO2_Light_3


title: RT-12-v1/GC17 v06


title: sample13: LowFe_HighCO2_Light_1


title: sample14: LowFe_HighCO2_Light_2


title: ATAC WT YPD rep2

description: ATAC WT YPD rep2

source_name: XL280 grown in YPD

value: WT YPD


title: ATAC WT YPD rep 1

description: ATAC WT YPD rep 1


title: RT-14-v1


title: sample16: LowFe_HighCO2_Dark_1


title: sample12: LowFe_LowCO2_Light_3

value: 58 pM


title: RT09- v3


title: MDA-Panc28 shTAK1

city: Verona

first: Davide

last: Melisi

address: P.le LA Scuro 10

country: Italy

institute: University of Verona

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The Illumina Genome Studio software (Genome Studio V2011.1) was used to obtain probe intensity. Raw data were Loess normalized with the Lumi R package and further processed with Excel software.

source_name: Pancreatic cancer cell line

label_protocol: 500ng total RNA were reverse-transcribed and cRNA was synthesized and biotinylated using the IlluminaTotalPrep RNA Amplification Kit (AMIL1791, Ambion)

extract_protocol: Total RNA was extracted using Trizol reagent following manufacturer’s instruction

tag: cell line

value: Pancreatic cancer

tag: expression


title: JC53

city: Evry

first: Marco Antonio

last: Mendoza Parra

address: 2 Gaston Crémieux

institute: Genoscope

data_processing:
Samples were aligned to the reference genome (Rattus_norvegicus Rnor_6.0.94) with  Bowtie2(Langmead and Salzberg, 2012). Aligned sequenced reads per sample were associated to annotated genes with HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/count.html), followed by an inter-sample quantile normalization to correct for technical differences. Differential expression analysis (relative to the samples issued from non-injured and vehicle treated animals) has been performed with Deseq2 (Love et al., 2014). Differentially expressed genes assessed in various conditions (non-injured +C286; Injured +vehicle; Injured +C286) were stratified over three major states (induced, repressed or non-differentially expressed) such that a total of 26 hypothetical combinatorial co-expression events were inferred. Among them, only 8 appeared as biologically significant situations where the effect of the ligand C286 could be inferred. To support this hypothesis, all combinatorial co-expression events were analyzed for Gene Ontology (GO) enrichment (DAVID bioinformatics resources),(Huang da et al., 2009) demonstrating relevant enrichment GO terms preferentially in the case of the  selected biologically selected co-expression paths.
Genome_build: Rnor_6.0.94
Supplementary_files_format_and_content: raw and normalized counts

organism: Rattus norvegicus

extract_protocol:
After defined survival times, animals were killed by terminal anesthetization and transcardially perfused with 4% paraformaldehyde, for immunohistochemistry or ice-cold PBS, for mRNA extraction and Western blotting. The lumbar spinal cords were excised, rapidly removed and the tissue corresponding to L5 spinal cord was isolated.  For mRNA extraction and Western blotting, L5 spinal cords were bi-dissected into ipsi and contralateral side to the injury, and tissue was snap frozen in liquid nitrogen and kept at -80 degrees Celcius until further use. Frozen micro dissected spinal cord samples were lysed with Teflon-glass homogenizers and  QIAshredder columns (Qiagen). Total RNA was isolated with the Qiagen RNeasy® Mini kit.  The RNA was assessed for purity and quantity using the Nanodrop 1000 spectrophotometer  and assessed for quality on the Agilent Bioanalyzer 2100.
400 ng of intact high-quality total RNA (RIN>7.9) from each sample was then used  as input to generate libraries for RNA-sequencing using the NEBNext Ultra II Directional kit  (NEB, Cat.no: E7760S) following the manufacturer’s recommendations. This protocol involved an initial step of mRNA selection using a poly-A isolation module (NEB, Cat.no:  E7490) to select for mRNA with a mature polyA tail, followed by fragmentation prior to first  cDNA synthesis and barcoding second-strand cDNA synthesised with indices for Illumina  sequencing for final library amplification (10-cycles). The resulting libraries (342-421bp) were assessed on the Bioanalyzer 2100 for purity. The NEBNext Library Quant Kit for Illumina (NEB, Cat.no: E7630L) was used to calculate the quantity of each library.
The quantification data was used to pool the libraries in equal molarity prior to performing a QC run on the MiSeq (MiSeq Reagent Kit v3 (150-cycle); Cat no: MS-102-3001). Further deep sequencing was performed on the pooled library over 2 lanes using a HiSeq4000 (by GENEWIZ) to generate roughly 26 million reads per sample.

treatment_protocol: Rats were treated with vehicle or a novel selective RAR-Betaagonist, C286 (Goncalves et al.,  2019a) (synthesized by Sygnature Chemical Services, Nottingham, UK), given by oral gavage  (po) three times a week for four weeks at 3mg/kg. C286 has a high potency at RAR-Beta(similar potency to all-trans-retinoic acid) and behaves as a full agonist showing an EC50 of 1.94 nM at the mouse RAR-Betareceptor and a selectivity for RAR-Betaover RAR-alphaof 13.4, with selectivity for RAR-Betaover RAR-gammabeing 5.6-fold (Goncalves et al., 2019a).

tag: assay

value: Spinal cord injury assay

tag: agent

value: C286 (RAR-Beta agonist)


title: JC52


title: RT-06 v3


title: RT-09-v1/GC12 v06


title: JC51


title: MDA-Panc28 GFP Ctrl

value: shControl


title: RT-06 v1


title: sample10: LowFe_LowCO2_Light_1

value: Axenic Thalassiosira pseudonana (CCMP 1335) grown in batch culture


title: sample09: LowFe_LowCO2_Dark_3

value: Midnight


title: RT-05v1


title: sample07: LowFe_LowCO2_Dark_1


title: JC50

source_name: L5-SNL + vehicle

value: vehicle


title: sample11: LowFe_LowCO2_Light_2

value: Midday


title: RT-05 v3


title: JC49


title: RT-07 v3

value: Placebo


title: AsPC-1 shTAK1


title: S_15: Monocyte_M2_rep2

city: Derio

first: Ana

last: Aransay

address: Parque tecnologico de Bizkaia, Building 801-A

institute: CIC bioGUNE

description: Monocytes treated in vitro with M-CSF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

label: Biotin

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

extract_protocol: Total RNA was extracted using an RNAqueous-Micro kit (Ambion).

value: monocyte


title: Panc-1 shTAK1


title: S_14: Monocyte_M2_rep2

description: Monocytes treated in vitro with M-CSF


title: RT-03v1


title: Panc-1 GFP Ctrl


title: sample06: HighFe_LowCO2_Dark_3


title: JC48


title: AsPC-1 GFP Ctrl


title: RT-03 v3

value: Post


title: RT-02 v3


title: S_13: Monocyte_M2_rep1

description: Monocytes treated in vitro with M-CSF


title: sample05: HighFe_LowCO2_Dark_2


title: S_12: Monocyte_M1_rep2

description: Monocytes treated in vitro with GM-CSF


title: JC17

source_name: Non-injured + C286

value: Spinal cord injury assay (control)


title: JC18


title: sample04: HighFe_LowCO2_Dark_1


title: RT-02v1

value: Pre

value: Drug


title: sample03: HighFe_LowCO2_Light_3


title: JC16


title: S_11: Monocyte_M1_rep2

description: Monocytes treated in vitro with GM-CSF


title: RT-50 v1


title: sample02: HighFe_LowCO2_Light_2


title: S_10: Monocyte_M1_rep1

description: Monocytes treated in vitro with GM-CSF


title: sample01: HighFe_LowCO2_Light_1


title: JC12

source_name: Non-injured + vehicle


title: S_7: Monocyte_CD14+_rep1

description: Ex vivo isolated monocytes from peripheral blood


title: RT-01 v1


title: B10 cells from Cko mouse, anti-CD40 for 48 h

status: Public on Sep 11 2019

city: Taipei City

first: Ying-Hsiu

last: Wang

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical Center

description: Gene expression data from IL-10 negative B cells were isolated from splenic B cells stimulated with LPS for 48 h.

hyb_protocol: After converting linear RNA into 35-200 nt biotin-labeled fragments, samples were then subjected to Mouse Genome 430 2.0 Array.

scan_protocol: The array data were acquired with GeneChip® Scanner 3000.

data_processing: The data from Ctrl B10 and Cko B10 were analyzed by GeneSpring 14.

source_name: splenic B10 cells were sorted from Cko mouse and rhen stimulated with anti-CD40 for 48 h.

label_protocol: 1 ug of total RNA was subjected to reverse transcription and biotin-conjugated nucleotide incorporation by using GeneChip ® 3' IVT Express Kit (Affymetrix).

growth_protocol: Splenic B10 cells were cultured in the complete medium with RPMI 1640 containing 10% FBS, 1% penicillin/ streptomycin and 0.1% 2-mercaptoethanol at the density of 2 × 106 cells/ml

extract_protocol: Total RNA was extracted according to the manufacturer's instructions by RNeasy Plus Mini Kit (QIAGEN).

treatment_protocol: Splenic B10 cells were stimulated with 2 μg/ml anti-CD40 for 48 h.

tag: stimulation

value: Cko B10


title: B10 cells from Ctrl mouse, anti-CD40 for 48 h

description: Gene expression data from IL-10 positive B cells were isolated from splenic B cells stimulated with LPS for 48 h.

source_name: splenic B10 cells were sorted from Ctrl mouse and rhen stimulated with anti-CD40 for 48 h.

value: Ctrl B10


title: B10 cells from Ctrl mouse, 0 h

description: Gene expression data from IL-10 positive B cells were isolated from splenic B cells stimulated with anti-CD40 for 48 h.

source_name: splenic B10 cells were sorted from Ctrl mouse.

value: No


title: B10 cells from Cko mouse, 0 h

description: Gene expression data from IL-10 negative B cells were isolated from splenic B cells stimulated with anti-CD40 for 48 h.

source_name: splenic B10 cells were sorted from Cko mouse.


title: RT-07v1


title: RT-01 v3


title: JC13


title: RPI98

city: Shanghai

first: Zhang

last: Tiancheng

address: Xietu Road NO.2140

institute: Shanghai institute of Planned Parenthood Research

data_processing:
Used cutadapt to trim adapter sequence(TGGAATTCTCGGGTGCCAAGGC) and filt the low quality reads
The processed reads longer than 17nt were mapped to human miRNA database (miRBase version 22), allowing ±2 base to be template by the corresponding genomic sequence at the 3'end (http://www.mirbase.org/).
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: Testis Sperm

extract_protocol:
Total cellular RNA was extracted using TRIzol reagent (Takara)
Small RNA library was constructed using approximately 200 ng of total cellular RNA

value: Testis Sperm

tag: embryonic development stage

value: blastocyst stage

tag: ferilization rate (fr)

tag: experimental event rate (eer)

tag: high quality embryo rate (hqer)


title: RPI99


title: RPI94


title: RPI9


title: RPI95


title: RPI93


title: RPI92


title: RPI97


title: RPI96


title: RPI90


title: IL-10 positive B cells, LPS for 48 h, biological rep1

description:
Gene expression data from IL-10 positive B cells were isolated from splenic B cells stimulated with LPS for 48 h.
splenic B cells were stimulated with LPS for 48 h followed by isolation of IL-10 positive B cells and IL-10 negative B cells.

data_processing: The data from IL-10 positive and IL-10 negative were analyzed by GeneSpring 14.

source_name: IL-10 positive B cells, LPS for 48 h

growth_protocol: Splenic B cells were cultured in the complete medium with RPMI 1640 containing 10% FBS, 1% penicillin/ streptomycin and 0.1% 2-mercaptoethanol at the density of 2 × 106 cells/ml

treatment_protocol: Splenic B cells were stimulated with 2 μg/ml anti-CD40 or 10 μg/ml LPS for 48 h.

value: IL-10 positive B cells

value: LPS


title: IL-10 negative B cells, LPS for 48 h, biological rep2

description:
Gene expression data from IL-10 negative B cells were isolated from splenic B cells stimulated with LPS for 48 h.
splenic B cells were stimulated with LPS for 48 h followed by isolation of IL-10 positive B cells and IL-10 negative B cells.

source_name: IL-10 negative B cells, LPS for 48 h

value: IL-10 negative B cells


title: IL-10 negative B cells, anti-CD40 for 48 h, biological rep1

description:
Gene expression data from IL-10 negative B cells were isolated from splenic B cells stimulated with anti-CD40 for 48 h.
splenic B cells were stimulated with anti-CD40 for 48 h followed by isolation of IL-10 positive B cells and IL-10 negative B cells.


title: IL-10 positive B cells, LPS for 48 h, biological rep2


title: S_8: Monocyte_CD14+_rep2

treatment_protocol: Monocytes were incubated with GM-CSF (1000 U/ml, PeproTech) (M1 samples) or M-CSF (10 ng/ml, PeproTech) (M2 samples) for 7 days.


title: RPI89


title: RPI88


title: RPI86


title: RPI87


title: RPI84


title: RPI8


title: RPI85


title: IL-10 positive B cells, anti-CD40 for 48 h, biological rep2

description:
Gene expression data from IL-10 positive B cells were isolated from splenic B cells stimulated with anti-CD40 for 48 h.
splenic B cells were stimulated with anti-CD40 for 48 h followed by isolation of IL-10 positive B cells and IL-10 negative B cells.


title: IL-10 negative B cells, anti-CD40 for 48 h, biological rep2


title: IL-10 negative B cells, LPS for 48 h, biological rep1


title: RPI83


title: IL-10 positive B cells, anti-CD40 for 48 h, biological rep1


title: RPI82


title: RPI81


title: RPI80


title: RPI7


title: S_9: Monocyte_CD14+_rep2


title: RPI75


title: RPI74


title: RPI6


title: RPI73


title: RPI71


title: RPI72


title: RPI70


title: RPI69


title: RPI67


title: RPI65


title: RPI61


title: RPI60


title: RPI64


title: RPI5


title: RPI59


title: RPI66


title: RPI63


title: RPI62


title: RPI56


title: RPI57


title: RPI58


title: RPI78


title: RPI79


title: RPI77


title: RPI76


title: RPI52


title: RPI51


title: RPI48


title: RPI50


title: RPI49


title: RPI4


title: RPI47


title: RPI44


title: RPI38


title: RPI36


title: RPI45


title: RPI37


title: RPI43


title: RPI35


title: RPI46


title: RPI40


title: RPI41


title: RPI3


title: RPI32


title: RPI33


title: RPI34


title: RPI42


title: RPI31


title: RPI2


title: RPI30


title: sample08: LowFe_LowCO2_Dark_2

value: 58 pM

value: Midnight

value: Axenic Thalassiosira pseudonana (CCMP 1335) grown in batch culture


title: RPI55


title: RPI53


title: RPI29


title: RPI54


title: RPI27


title: RPI26


title: RPI28


title: RPI23


title: RPI20


title: RPI21


title: RPI19


title: RPI18


title: RPI17


title: RPI10


title: RPI13


title: RPI104


title: RPI107


title: RPI108


title: RPI110


title: RPI11


title: RPI12


title: RPI103


title: RPI106


title: RPI100


title: RPI101


title: Ortho_ERRBS_3

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Fastq format reads were trimmed using Trim Galore  v0.4.0 in rrbs mode
Trimmed reads were mapped to the hg19 genome using Bismark_v0.14.3.
Quantitation of methylation was performed using bismark_methylation_extractor.
Differential methylation was identified using methylKit v1.2.4
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing cytosine methylation positions and quantitation.

source_name: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)

extract_protocol:
Progenitor cells at each stage were sorted by a combination of cell surface markers for IL-3R, CD34 and CD36. Erythroblasts at each stage of terminal erythroid differentiation were sorted by a combination of cell surface markers for glycophorin A, band 3, and α4 integrin.  Genomic DNA was isolated using a Qiagen Gentra Puregene kit.
Enhanced Reduced Representation Bisulfite sequencing (ERRBS) was performed at the Weill Cornell Genomics Core.

tag: Stage

value: orthochromatic erythroblast

tag: surface markers to isolate cells by facs-based methods

value: GPA positive, Band3 high and alpha 4 integrin negative


title: Ortho_ERRBS_2

value: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)


title: Ortho_ERRBS_1


title: RPI25


title: Poly_ERRBS_3

value: polychromatic erythroblast

value: GPA positive, Band3 high and alpha 4 integrin medium


title: Poly_ERRBS_2


title: Poly_ERRBS_1


title: LBaso_ERRBS_3

value: late basophilic erythroblast

value: GPA positive, Band3 high and alpha 4 integrin high


title: RPI16


title: RPI1


title: RPI15


title: EBaso_ERRBS_3

value: early basophilic erythroblast

value: GPA positive, Band3 medium and alpha 4 integrin high


title: LBaso_ERRBS_2


title: LBaso_ERRBS_1


title: EBaso_ERRBS_2


title: ProE_ERRBS_3

value: proerythroblast

value: GPA low, Band3 negative and alpha 4 integrin high


title: ProE_ERRBS_1


title: CFUE_ERRBS_2

value: CFUE


title: ProE_ERRBS_2


title: RPI105

value: Testis Sperm

value: blastocyst stage


title: EBaso_ERRBS_1


title: CFUE_ERRBS_3


title: CFUE_ERRBS_1


title: HSPC_ERRBS_2

source_name: Human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)

value: HSPC


title: BFUE_ERRBS_3

value: BFUE


title: HSPC_ERRBS_3

value: Human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)


title: BFUE_ERRBS_1


title: BFUE_ERRBS_2


title: P136 [discovery]

city: New York

first: Weijia

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

description:
Standard mRNA library.
Total RNA was extracted from whole blood drawn from kidney transplant recipients at 3m post transplantation, and mRNA sequencing was performed on an Illumina HiSeq2000 sequencer.

data_processing:
The reads with good quality were firstly aligned to human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering for reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. The read counts were log2 transformed and normalized at an equal global median value in order to compare transcription level across samples, followed by quantile normalization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include quantile-normalized counts.

source_name: whole blood

extract_protocol:
Total RNA was extracted from whole blood of kidney transplant recipients 3 months post-transplantation.
The library was generated standard TruSeq mRNA library generation kit (Illumina Inc).

value: Whole blood

tag: acr at 3m

value: Yes


title: HSPC_ERRBS_1


title: P134 [discovery]


title: P106 [discovery]


title: P140 [discovery]


title: P120 [discovery]


title: P129 [discovery]


title: P100 [discovery]


title: P96 [discovery]


title: P103 [discovery]


title: P86 [discovery]


title: P91 [discovery]


title: P68 [discovery]


title: P146 [discovery]

value: No


title: P65 [discovery]


title: P55 [discovery]


title: P67 [discovery]


title: P132 [discovery]


title: P54 [discovery]


title: P53 [discovery]


title: P34 [discovery]


title: P141 [discovery]


title: P19 [discovery]


title: P41 [discovery]


title: P57 [discovery]


title: P13 [discovery]


title: P145 [discovery]


title: P130 [discovery]


title: P137 [discovery]


title: P125 [discovery]


title: P127 [discovery]


title: P109 [discovery]


title: P107 [discovery]


title: P102 [discovery]


title: P111 [discovery]


title: P98 [discovery]


title: P99 [discovery]


title: P124 [discovery]


title: P97 [discovery]


title: P95 [discovery]


title: P93 [discovery]


title: P101 [discovery]


title: P128 [discovery]


title: P87 [discovery]


title: P89 [discovery]


title: P38 [discovery]


title: P46 [discovery]


title: P43 [discovery]


title: P47 [discovery]


title: P44 [discovery]


title: P32 [discovery]


title: P42 [discovery]


title: P35 [discovery]


title: P33 [discovery]


title: P30 [discovery]


title: P62 [discovery]


title: P50 [discovery]


title: P69 [discovery]


title: P64 [discovery]


title: P49 [discovery]


title: P51 [discovery]


title: P59 [discovery]


title: P56 [discovery]


title: P61 [discovery]


title: P72 [discovery]


title: P85 [discovery]


title: P63 [discovery]


title: P70 [discovery]


title: P60 [discovery]


title: P52 [discovery]


title: P66 [discovery]


title: P27 [discovery]


title: P23 [discovery]


title: P25 [discovery]


title: P22 [discovery]


title: P31 [discovery]


title: P21 [discovery]


title: P20 [discovery]


title: P58 [discovery]


title: P12 [discovery]


title: P16 [discovery]


title: P8 [discovery]


title: P26 [discovery]


title: P6 [discovery]


title: P5 [discovery]


title: P3 [discovery]