title: ACCLAIM_856452_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19270

tag: tissue

tag: randomized treatment


title: Rpb3 in Q Replicate 1 IP

status: Public on Dec 27 2018

type: SRA

city: Seattle

first: Sarah

middle: G.

last: Swygert

state: WA

address: 1100 Fairview Avenue North MS A1-162

department: Basic Sciences Division

country: USA

institute: Fred Hutchinson Cancer Research Center

library_source: genomic

data_processing:
Reads were aligned to the sacCer3 reference genome using Bowtie2 in very sensitive mode.
Aligned reads were filtered and indexed using SAMtools.
Indexed reads were normalized to genome average and the genome average was set to 1 fold enrichment.
Genome_build: sacCer3 reference genome (release R64-2-1)
Supplementary_files_format_and_content: Files are .sgr (can be converted to txt) which describe read count normalized to genome average at each basepair in the genome.  Processed data files for IP samples must be divided by the processed data file for the corresponding input sample in order to be normalized to input.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Quiescent cells

growth_protocol: All strains were generated in prototrophic W303 backgrounds.  Log cells were grown to ~0.6-0.8 OD.  Q cells were purified from 7-day cultures via Percoll density gradient.

extract_protocol:
Approximately 300 OD units of cells were bead-beat until cell walls were disrupted.  Lysates were sonicated to shear chromatin to ~200-400 bp fragments and clarified.  Protein was immuniprecipitated using the indicated antibody.
Nugen Ovation Ultra-Low v2

treatment_protocol: Cells were fixed in formaldehyde for 20 minutes

tag: genotype

value: WT

tag: strain

tag: chip antibody

value: anti-Rpb3 antibody (Biolegend, catalog #665003)


title: Rpb3 in Log Replicate 2 Input

source_name: Log cells

value: none, input


title: Quiescent cells

description:
sacCer3.5000.bins.annot.bed.gz
sacCer3.1000.bins.annot.bed.gz
sacCer3.200.bins.annot.bed.gz

data_processing:
Library strategy: Micro-C XL
Reads were aligned to the sacCer3 reference genome using Bowtie2 in very sensitive mode.
Except for rDNA interaction analyses, all read pairs where both  reads mapped with MAPQ >= 6 were deduplicated, and filtered to exclude in-facing  read pairs with ends < 400 bp apart, which likely represent unligated fragments.
Read pairs were ICE normalized using the Cooler suite balance function with settings --ignore-diags 1 -- mad-max 9.
Genome_build: sacCer3 reference genome (release R64-2-1)
Supplementary_files_format_and_content: The files are txt files with 4 tab-delimited columns which are (only for nonzero values): bin 1, bin 2, raw, normalized.  In order to map bin numbers to genomic coordinates, bin annotation files included in bed format should be used.

growth_protocol: All strains were generated in prototrophic W303 backgrounds.  200 mL cultures of log cells were grown to 0.55 OD.  Q cells were purified from 25 mL 7-day cultures via Percoll density gradient.

extract_protocol:
Spheroplasts were incubated with a concentration of micrococcal nuclease titrated to each experiment designed to retain ~90% mononucleosome sized fragments in the insoluble chromatin fraction for 20 min at 37 degrees. DNA ends were repaired and biotin labeled, fragments were proximity ligated, crosslinking was reversed, and DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Purified DNA ends were readied for ligation, A-tailed, and Illumina Truseq adapters were ligated.  Proximity ligated DNA was pulled down with streptavidin beads, and library was amplified with Illumina Truseq primers.

treatment_protocol: Cells were fixed in 3% formaldehyde at 30 degrees for 10 minutes, cell walls were permeabilized at 30 degrees in 250 ug/mL zymolyase for 30 min (log) or 1 mg/mL zymolyase for 1.5 hours (quiescent), then spheroplasts were crosslinked in 3mM disuccinimidyl glutarate for 40 min at 30 degrees.

tag: culture condition

value: grown to quiescence and purified


title: Rpb3 in Log Replicate 1 Input


title: AB4141

city: Rehovot

first: Yaniv

last: Lubling

address: POB 26

country: Israel

institute: Weizmann Institute of Science

description: Amp batch AB4141

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
UMI counting was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651)
Note: UMI counts are supplied here, raw sequences are availiable at Europena Genome-phenome Archive (EGA).
Genome_build: hg19
Supplementary_files_format_and_content: T_cells_tcrb.txt: tab-delimited table with the TCRb clonal membership data of the T cells in this study.

molecule: polyA RNA

organism: Homo sapiens

source_name: Immune cells sorted from melanoma tumors

extract_protocol:
Cells were digested to form a single cell suspension and FACS sorted into capture plates
3' end mRNA libraries were prepared for sequencing using MARS-seq2.0 - improvements to MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantification

treatment_protocol: All samples were dissected from patients and digested into single cell suspension

tag: plate id

tag: amplification batch

tag: sample source

value: Tumor

tag: patient id

tag: facs gate


title: Rpb3 in Log Replicate 1 IP


title: ACCLAIM_903842_15_Treg

city: Bethesda

first: Tielin

last: Qin

state: MD

address: 7500 Old Georgetown Road, Suite 800

institute: Immune Tolerance Network

description:
RNAseq_Treg_norm_counts.csv
lib19264

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.4.1)
Read counts per Ensembl gene ID were computed in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38

molecule: total RNA

source_name: PBMC

extract_protocol:
500 cells were sorted directly into lysis buffer on a BD FACSAria Fusion flow cytometer. cDNA was constructed per instructions with the Takara SMART-Seq v4 Ultra Low Input RNA Kit.
Libraries were constructed for RNA-seq using standard Illumina protocols.

tag: cell type

value: Treg

value: PBMC

tag: participantid

tag: visitnumber

tag: barcode

value: Abatacept

tag: age

tag: Sex

value: Female

tag: race

value: White


title: Rpb3 in SMC4-off All Replicates Merged Input

source_name: Quiescent cells + doxycycline


title: AB4140

description: Amp batch AB4140


title: Rpb3 in SMC4-off All Replicates Merged IP


title: ACCLAIM_903842_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19261

tag: tissue

tag: randomized treatment


title: Rpb3 in SMC4-off Replicate 2 Input

tag: genotype

tag: strain


title: Rpb3 in SMC4-off Replicate 1 Input

tag: chip antibody


title: Rpb3 in SMC4-off Replicate 1 IP


title: Rpb3 in Log Replicate 2 IP


title: ACCLAIM_626637_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19255

value: Placebo


title: Rpb3 in Log All Replicates Merged Input


title: ACCLAIM_903842_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19258


title: AB4138

description: Amp batch AB4138

tag: plate id


title: AB4137

description: Amp batch AB4137

tag: amplification batch


title: Brn1 in Q All Replicates Merged Input


title: ACCLAIM_626637_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19252


title: Brn1 in Q Replicate 2 Input


title: ACCLAIM_864448_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19246

value: Male


title: AB4135

description: Amp batch AB4135

tag: sample source


title: Brn1 in Q Replicate 3 Input


title: Brn1 in Q All Replicates Merged IP

value: 9E10 purified anti-Myc (Covance, catalog #139049002)


title: Brn1 in Q Replicate 1 Input


title: ACCLAIM_864448_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19243


title: AB4134

description: Amp batch AB4134

tag: patient id


title: Brn1 in Q Replicate 2 IP


title: ACCLAIM_864448_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19240


title: AB4139

description: Amp batch AB4139

tag: facs gate


title: Brn1 in Log All Replicates Merged IP


title: Rpb3 in SMC4-off Replicate 2 IP


title: ACCLAIM_768526_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19237

tag: cell type


title: ACCLAIM_768526_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19234

tag: participantid


title: Brn1 in Q Replicate 3 IP


title: Brn1 in Log Replicate 3 IP


title: AB4131

description: Amp batch AB4131


title: Brn1 in Log Replicate 2 Input


title: AB4132

description: Amp batch AB4132


title: AB4136

description: Amp batch AB4136


title: Brn1 in Log Replicate 2 IP


title: ACCLAIM_119004_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19228

tag: visitnumber

value: Black or African American


title: AB4129

description: Amp batch AB4129


title: Brn1 in Log Replicate 1 Input


title: AB4130

description: Amp batch AB4130


title: Brn1 in Q Replicate 1 IP


title: L10015D rep3

city: Taian

last: Liu

state: Shandong Province

address: Daizong Street 61

department: College of Life Science

country: China

institute: Shandong Agricultural University

data_processing:
Illumina HiSeqTM 2000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 reference genome (RefGen_v3) whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Zea mays

source_name: Seeds

extract_protocol:
Seeds were removed, flash frozen on liquid nitrogen, and RNA was harvested using CTAB(hexadecyl trimethyl ammonium bromide).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: 15 days after of pollination, 15DAP

value: Seeds

value: transgenic line L100


title: ACCLAIM_119004_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19222

tag: barcode

tag: age


title: ACCLAIM_119004_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19225

tag: Sex

tag: race


title: AB4128

description: Amp batch AB4128


title: L10015D rep1

tag: tissue


title: Brn1 in Log Replicate 1 IP

tag: genotype


title: ACCLAIM_349885_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19219

tag: randomized treatment


title: L10015D rep2


title: AB4133

description: Amp batch AB4133

value: CD3 & CD45


title: L10010D rep2

value: 10 days after pollination, 10DA


title: Brn1 in Log All Replicates Merged Input

tag: strain

tag: chip antibody

value: none, input


title: L10010D rep3


title: Brn1 in Log Replicate 3 Input


title: ACCLAIM_349885_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19216


title: AB4127

description: Amp batch AB4127

tag: plate id

tag: amplification batch


title: L10010D rep1


title: CK15D rep3

value: Q319 wild type


title: AB4126

description: Amp batch AB4126

tag: sample source

value: Tumor

tag: patient id


title: ACCLAIM_937612_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19207

tag: cell type

value: Treg


title: CK15D rep1


title: CK10D rep3


title: CK15D rep2


title: ACCLAIM_937612_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19210

value: PBMC

tag: participantid


title: CK10D rep2


title: AB4125

description: Amp batch AB4125

tag: facs gate


title: ACCLAIM_937612_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19204

tag: visitnumber

value: Abatacept


title: AB4124

description: Amp batch AB4124


title: CK10D rep1

tag: Stage


title: ACCLAIM_750328_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19201

tag: barcode

tag: age

value: Female


title: L100 rep1

source_name: Leaves

growth_protocol: Maize are planted in the field

extract_protocol:
Leaves were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: the six-leaf stage

value: Leaves


title: L100 rep2


title: ACCLAIM_750328_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19198

value: Placebo

tag: Sex

tag: race


title: L100 rep3

tag: tissue

tag: genotype


title: AB4123

description: Amp batch AB4123


title: AB4122

description: Amp batch AB4122


title: ACCLAIM_415432_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19192

tag: randomized treatment

value: Male

value: White


title: CK rep2


title: AB4121

description: Amp batch AB4121


title: H3K9me3_input

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
ChIP-seq reads were aligned to the ce6 genome using bowtie2 software
peakcalls performed with macs2
Genome_build: ce6
Supplementary_files_format_and_content: MACS peaks file

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were grown on NGM (Nematode Growth Medium) plates seeded with OP50 at 22 °C or 25 °C

extract_protocol: ChIP DNAs were isolated with antibody from whole worm lystaes.

tag: strain

tag: antibody

value: input

tag: developmental stage


title: H3K9me3_ChIPSeq


title: ACCLAIM_415432_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19189


title: AB4032

description: Amp batch AB4032

tag: plate id

tag: amplification batch

tag: sample source


title: AB4031

description: Amp batch AB4031

tag: patient id


title: H3K4me3_input


title: CK rep1


title: H3K4me3_ChIPSeq


title: ACCLAIM_415432_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19186

tag: cell type

tag: participantid


title: AB4030

description: Amp batch AB4030

tag: facs gate


title: ACCLAIM_527582_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19183

tag: visitnumber

tag: barcode


title: AB4029

description: Amp batch AB4029


title: CK rep3

tag: Stage


title: AB4028

description: Amp batch AB4028


title: D4_CD31pos_EC

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
CellRanger Pipelines software were used for generate feature-barcode matrices.
Sequenced reads were aligned to the human reference genome (GRCh38) uisng STAR with the transcript annotation supplied
We provide normalized gene data.
The output of CellRanger was used as input for Seurat to perform data normalizing, PCA, dimensionality reduction, cell cluster, differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited text files include normalized gene values for each cell

source_name: H1 samples collected from day 4 of hematopoietic differentiation

growth_protocol: H1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 2 days. Finally, cells were feeded with Custom mTeSR1 medium supplemented with  40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) and SB-431542 (Sellleck) for 3 days.

extract_protocol:
Single CD31+ endothelial cells at day4 of hESC hematopoietic differentiation dissociated into a single cell suspension,
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: AB4027

description: Amp batch AB4027


title: AB3945

description: Amp batch AB3945


title: ACCLAIM_360231_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19168

tag: tissue

tag: age

tag: Sex

tag: race


title: ACCLAIM_360231_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19171

tag: randomized treatment


title: ACCLAIM_527582_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19180


title: ACCLAIM_360231_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19174


title: ACCLAIM_763271_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19165


title: AB3944

description: Amp batch AB3944


title: AB3946

description: Amp batch AB3946


title: ACCLAIM_763271_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19162


title: AB3943

description: Amp batch AB3943


title: ACCLAIM_987582_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19156


title: dilated_perivascular_adipose_tissue_42

type: RNA

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were imported in the R software version 3.4.0 and analyzed with the lumi R/Bioconductor package. Variance stabilizing transformation (VST) was applied and transformed data were then normalized by robust spline normalization (RSN). Probes with a detection P‐value <0.01 in at least 30% of the samples were retained.

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was extracted by adding 1 mL of TRIzol Reagent  to 50-100 mg of frozen adipose tissue samples. Tissues were homogenized through a 5 mm stainless steel bead in a Tissue Lyzer. After homogenization, samples underwent a second round of purification with chloroform and precipitated with isopropanol.  RNA resuspended in RNase-free water was further cleaned-up by the RNeasy MinElute Cleanup kit, following the manufacturer’s instructions and, then, treated with TURBO DNase as described by the manufacturer's protocol. Infinite M200 PRO multimode microplate reader (Tecan) and the 2100 Bioanalyzer (Agilent Technologies) were used to assess RNA yield/purity and RNA integrity, respectively.

treatment_protocol: Collected adipose tissue samples were directly snap-frozen in liquid nitrogen and stored at -80°C until processing

tag: subject id

tag: patient diagnosis

value: abdominal aortic aneurysm

value: periaortic adipose tissue

tag: age (years)

tag: country of origin

value: Italy


title: dilated_perivascular_adipose_tissue_41


title: subcutaneous_abdominal_fat_41

value: subcutaneous abdominal fat


title: omental-visceral_fat_38

value: omental-visceral fat


title: subcutaneous_abdominal_fat_40


title: non-dilated_perivascular_adipose_tissue_41


title: non-dilated_perivascular_adipose_tissue_42


title: subcutaneous_abdominal_fat_38


title: omental-visceral_fat_42


title: omental-visceral_fat_41


title: subcutaneous_abdominal_fat_42


title: non-dilated_perivascular_adipose_tissue_40


title: dilated_perivascular_adipose_tissue_40


title: non-dilated_perivascular_adipose_tissue_29


title: dilated_perivascular_adipose_tissue_29


title: ACCLAIM_987582_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19153


title: AB3941

description: Amp batch AB3941

tag: plate id

tag: amplification batch

tag: sample source

tag: patient id

value: Live


title: ACCLAIM_519740_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19147

tag: cell type

tag: participantid

tag: visitnumber

value: Black or African American


title: AB3939

description: Amp batch AB3939

value: Tumor

tag: facs gate

value: CD3 & CD45


title: AB3940

description: Amp batch AB3940


title: AB3942

description: Amp batch AB3942


title: omental-visceral_fat_40

tag: tissue


title: AB3938

description: Amp batch AB3938


title: ACCLAIM_987582_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19150

value: Treg

value: PBMC

tag: barcode

value: Abatacept

tag: age


title: ACCLAIM_519740_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19144

tag: Sex

value: Female

tag: race


title: ACCLAIM_509364_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19138

tag: randomized treatment


title: AB3937

description: Amp batch AB3937


title: non-dilated_perivascular_adipose_tissue_38

tag: subject id

tag: patient diagnosis


title: dilated_perivascular_adipose_tissue_52

tag: age (years)

tag: country of origin


title: ACCLAIM_509364_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19135


title: subcutaneous_abdominal_fat_52


title: AB3755

description: Amp batch AB3755

tag: plate id

tag: amplification batch


title: subcutaneous_abdominal_fat_29


title: AB3726

description: Amp batch AB3726

tag: sample source

tag: patient id

value: CD3 & CD45 (+ partly live cells)


title: dilated_perivascular_adipose_tissue_38

value: Male


title: ACCLAIM_509364_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19132

tag: cell type

tag: participantid

value: White


title: omental-visceral_fat_52


title: ACCLAIM_578949_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19129

tag: visitnumber

value: Placebo


title: non-dilated_perivascular_adipose_tissue_52

value: abdominal aortic aneurysm

tag: tissue


title: AB3725

description: Amp batch AB3725

tag: facs gate


title: omental-visceral_fat_29


title: omental-visceral_fat_26


title: ACCLAIM_578949_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19126

tag: barcode

tag: age


title: dilated_perivascular_adipose_tissue_26

value: periaortic adipose tissue

tag: Sex


title: non-dilated_perivascular_adipose_tissue_27

value: Italy


title: subcutaneous_abdominal_fat_26

value: subcutaneous abdominal fat


title: subcutaneous_abdominal_fat_27


title: omental-visceral_fat_27

value: omental-visceral fat


title: dilated_perivascular_adipose_tissue_27


title: subcutaneous_abdominal_fat_51_rep2


title: AB3719

description: Amp batch AB3719


title: ACCLAIM_526007_15_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19120

tag: randomized treatment

tag: race


title: non-dilated_perivascular_adipose_tissue_26

tag: subject id

tag: patient diagnosis


title: AB3718

description: Amp batch AB3718


title: ACCLAIM_264812_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19111


title: ACCLAIM_526007_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19114


title: AB3284

description: Amp batch AB3284

value: Live


title: AB3283

description: Amp batch AB3283


title: AB3281

description: Amp batch AB3281


title: subcutaneous_abdominal_fat_50_rep2

tag: age (years)

tag: country of origin


title: AB3282

description: Amp batch AB3282

tag: plate id

tag: amplification batch


title: subcutaneous_abdominal_fat_51_rep1


title: ACCLAIM_264812_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19108


title: ACCLAIM_323548_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19099


title: AB3280

description: Amp batch AB3280

tag: sample source

tag: patient id


title: ACCLAIM_526007_7_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19117

tag: cell type

tag: participantid


title: ACCLAIM_323548_0_Treg

description:
RNAseq_Treg_norm_counts.csv
lib19096

tag: tissue

tag: visitnumber


title: dilated_perivascular_adipose_tissue_49


title: dilated_perivascular_adipose_tissue_36


title: omental-visceral_fat_49


title: non-dilated_perivascular_adipose_tissue_36


title: subcutaneous_abdominal_fat_49


title: non-dilated_perivascular_adipose_tissue_49


title: subcutaneous_abdominal_fat_50_rep1


title: dilated_perivascular_adipose_tissue_24


title: AB3279

description: Amp batch AB3279

tag: facs gate


title: omental-visceral_fat_36


title: ACCLAIM_536297_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19358

value: Tfh

tag: barcode

tag: age


title: subcutaneous_abdominal_fat_24

tag: Sex


title: AB3278

description: Amp batch AB3278

value: Tumor


title: ACCLAIM_496198_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19352

tag: randomized treatment

tag: race


title: AB3277

description: Amp batch AB3277

value: CD3 & CD45


title: AB3276

description: Amp batch AB3276


title: ACCLAIM_496198_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19349


title: ACCLAIM_536297_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19361


title: AB3275

description: Amp batch AB3275


title: AB3274

description: Amp batch AB3274


title: AB3096

description: Amp batch AB3096


title: ACCLAIM_496198_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19346


title: ACCLAIM_312337_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19343


title: ACCLAIM_312337_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19340


title: AB3095

description: Amp batch AB3095


title: ACCLAIM_931903_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19334

value: Black or African American


title: AB3094

description: Amp batch AB3094


title: subcutaneous_abdominal_fat_18

tag: subject id

tag: patient diagnosis


title: non-dilated_perivascular_adipose_tissue_24

tag: age (years)

tag: country of origin


title: subcutaneous_abdominal_fat_13


title: subcutaneous_abdominal_fat_05


title: AB3093

description: Amp batch AB3093

tag: plate id

tag: amplification batch


title: subcutaneous_abdominal_fat_01


title: subcutaneous_abdominal_fat_23


title: AB3092

description: Amp batch AB3092

tag: sample source

tag: patient id


title: omental-visceral_fat_33


title: dilated_perivascular_adipose_tissue_39


title: ACCLAIM_815412_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19325

tag: cell type

value: PBMC

tag: participantid


title: ACCLAIM_931903_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19328

tag: tissue

tag: visitnumber

value: Abatacept


title: ACCLAIM_931903_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19331

tag: barcode

value: Female


title: non-dilated_perivascular_adipose_tissue_33


title: omental-visceral_fat_39


title: AB3091

description: Amp batch AB3091

tag: facs gate


title: subcutaneous_abdominal_fat_39

tag: Sex


title: dilated_perivascular_adipose_tissue_33


title: ACCLAIM_815412_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19322

tag: randomized treatment

tag: age


title: ACCLAIM_673379_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19316

tag: race


title: AB3089

description: Amp batch AB3089


title: ACCLAIM_673379_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19310


title: ACCLAIM_673379_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19313


title: EMVA060D

type: genomic

city: Toronto

middle: J.

last: Goodman

state: ON

address: PGCRL, 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the QIAamp DNA Mini Kit (Qiagen) as per manufacturer’s instructions.

value: Buccal

tag: sample well

value: M

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: AB3090

description: Amp batch AB3090

tag: plate id

tag: amplification batch


title: non-dilated_perivascular_adipose_tissue_39

tag: subject id

tag: patient diagnosis

value: Male

tag: age (years)

tag: country of origin


title: EMVA065L

tag: tissue


title: EMVA023D


title: EMVA053L

value: F


title: subcutaneous_abdominal_fat_33

value: abdominal aortic aneurysm


title: AB3087

description: Amp batch AB3087

tag: sample source

tag: patient id


title: ACCLAIM_139519_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19307

tag: cell type

tag: participantid

tag: visitnumber

tag: barcode

value: Placebo

tag: Sex

value: White


title: EMVA026L

tag: sample well

tag: age at sample collection (years)


title: subcutaneous_abdominal_fat_32

value: subcutaneous abdominal fat

value: Italy


title: omental-visceral_fat_43

value: omental-visceral fat


title: AB3086

description: Amp batch AB3086

tag: facs gate


title: EMVA07D

tag: plate id

tag: sentrix id

tag: sentrix position


title: ACCLAIM_139519_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19304

value: Tfh

tag: randomized treatment

tag: age

tag: race


title: EMVA080L

tag: tissue


title: AB3079

description: Amp batch AB3079

tag: amplification batch

tag: sample source

value: Tumor


title: EMVA031D


title: dilated_perivascular_adipose_tissue_44

tag: subject id

tag: patient diagnosis

value: periaortic adipose tissue

tag: age (years)

tag: country of origin


title: ACCLAIM_911284_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19295

tag: cell type

tag: participantid

tag: visitnumber

tag: barcode

tag: Sex

value: Black or African American


title: EMVA064D

tag: sample well

tag: plate id

tag: age at sample collection (years)

tag: sentrix id


title: ACCLAIM_911284_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19298

value: PBMC

tag: randomized treatment

tag: age

tag: race


title: AB3078

description: Amp batch AB3078

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: subcutaneous_abdominal_fat_43

tag: subject id

tag: patient diagnosis

tag: tissue

tag: age (years)

tag: country of origin


title: AB2990

description: Amp batch AB2990


title: ACCLAIM_911284_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19292

tag: cell type

tag: participantid

tag: visitnumber

tag: barcode

value: Abatacept

tag: Sex


title: AB2989

description: Amp batch AB2989

tag: plate id


title: ACCLAIM_159059_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19289

tag: randomized treatment

tag: age

value: Female


title: EMVA034L

value: Buccal

tag: sample well

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: EMVA054L


title: subcutaneous_abdominal_fat_44

tag: subject id


title: EMVA071D

value: M


title: EMVA051D


title: AB2936

description: Amp batch AB2936

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: AB3088

description: Amp batch AB3088


title: ACCLAIM_159059_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19286

tag: cell type

tag: tissue

tag: race


title: AB2919

description: Amp batch AB2919


title: EMVA061D


title: dilated_perivascular_adipose_tissue_43

tag: patient diagnosis

value: Male

tag: age (years)

tag: country of origin


title: ACCLAIM_795063_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19277

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

tag: Sex


title: AB2918

description: Amp batch AB2918

tag: plate id


title: omental-visceral_fat_44

tag: subject id


title: AB2917

description: Amp batch AB2917

tag: amplification batch


title: EMVA056D

tag: sample well

value: F

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: ACCLAIM_795063_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19274

tag: cell type

tag: tissue

tag: age


title: non-dilated_perivascular_adipose_tissue_44

tag: patient diagnosis

value: abdominal aortic aneurysm

tag: age (years)


title: EMVA079L


title: ACCLAIM_795063_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19280

tag: participantid

tag: race


title: EMVA042D


title: non-dilated_perivascular_adipose_tissue_43

tag: country of origin


title: ACCLAIM_856452_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19271

tag: visitnumber

tag: barcode

tag: randomized treatment

value: Placebo


title: AB2916

description: Amp batch AB2916

tag: plate id

tag: sample source

tag: patient id

tag: facs gate


title: AB2915

description: Amp batch AB2915

tag: amplification batch


title: ACCLAIM_856452_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19268

tag: Sex

value: White


title: AB2914

description: Amp batch AB2914

value: CD3 & CD45


title: ACCLAIM_903842_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19262

tag: cell type


title: EMVA079L-rep

tag: tissue

tag: sample well

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: AB2913

description: Amp batch AB2913


title: ACCLAIM_903842_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19259

tag: participantid

tag: age

tag: race


title: subcutaneous_abdominal_fat_21

tag: subject id

tag: patient diagnosis

value: subcutaneous abdominal fat

tag: age (years)

tag: country of origin

value: Italy


title: ACCLAIM_903842_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19256

value: Tfh

tag: visitnumber

tag: barcode

tag: randomized treatment


title: EMVA05F

tag: plate id

tag: Sex


title: omental-visceral_fat_19

tag: tissue

value: omental-visceral fat


title: EMVA069D

tag: sample well


title: AB2912

description: Amp batch AB2912

tag: amplification batch

tag: sample source

value: Tumor

tag: patient id

tag: facs gate


title: AB2911

description: Amp batch AB2911


title: non-dilated_perivascular_adipose_tissue_05

value: periaortic adipose tissue


title: ACCLAIM_626637_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19253

tag: cell type

value: PBMC

tag: participantid

tag: age


title: EMVB083L

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: EMVA035L


title: EMVB011F


title: omental-visceral_fat_32

tag: subject id

tag: patient diagnosis

tag: age (years)

tag: country of origin


title: dilated_perivascular_adipose_tissue_20

tag: Sex


title: non-dilated_perivascular_adipose_tissue_21

tag: tissue


title: omental-visceral_fat_21


title: ACCLAIM_626637_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19250

tag: visitnumber

tag: barcode

tag: randomized treatment

tag: race


title: EMVB080F

tag: sample well

tag: plate id


title: AB2910

description: Amp batch AB2910

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: omental-visceral_fat_01


title: non-dilated_perivascular_adipose_tissue_32


title: non-dilated_perivascular_adipose_tissue_19


title: AB2908

description: Amp batch AB2908


title: ACCLAIM_864448_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19244

tag: cell type

tag: participantid

value: Abatacept

tag: age


title: AB2909

description: Amp batch AB2909


title: AB2907

description: Amp batch AB2907


title: ACCLAIM_864448_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19241


title: EMVB179F

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: EMVB039D

tag: tissue

tag: Sex


title: EMVB008F


title: AB2905

description: Amp batch AB2905


title: non-dilated_perivascular_adipose_tissue_51

tag: subject id

tag: patient diagnosis

tag: age (years)

tag: country of origin


title: ACCLAIM_864448_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19238

tag: visitnumber

tag: barcode

tag: randomized treatment

tag: race


title: ACCLAIM_768526_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19232

value: Female


title: EMVB155F

value: Buccal

tag: sample well

tag: plate id


title: dilated_perivascular_adipose_tissue_01


title: non-dilated_perivascular_adipose_tissue_50


title: EMVC097D


title: ACCLAIM_119004_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19226

tag: cell type

tag: participantid

value: Black or African American


title: AB2906

description: Amp batch AB2906

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: dilated_perivascular_adipose_tissue_50

tag: tissue

tag: Sex

value: Male


title: ACCLAIM_119004_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19223

tag: age


title: EMVB072D

value: M

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: EMVB041L


title: AB2904

description: Amp batch AB2904


title: AB2903

description: Amp batch AB2903


title: ACCLAIM_119004_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19220

tag: visitnumber

tag: barcode


title: EMVB018L

value: F


title: omental-visceral_fat_50

tag: subject id

tag: patient diagnosis

value: abdominal aortic aneurysm

tag: age (years)

tag: country of origin


title: EMVB120L

tag: sample well

tag: plate id


title: AB2902

description: Amp batch AB2902

tag: amplification batch

tag: sample source


title: AB2901

description: Amp batch AB2901

tag: patient id

tag: facs gate


title: ACCLAIM_349885_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19217

tag: cell type

tag: tissue

tag: participantid

tag: randomized treatment

value: Placebo

tag: Sex

tag: race

value: White


title: omental-visceral_fat_13


title: EMVB131F

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: non-dilated_perivascular_adipose_tissue_13

tag: subject id

tag: patient diagnosis

tag: age (years)


title: dilated_perivascular_adipose_tissue_13

tag: country of origin


title: AB2900

description: Amp batch AB2900

tag: plate id

tag: amplification batch


title: ACCLAIM_349885_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19214

tag: visitnumber

tag: barcode

tag: age


title: AB2899

description: Amp batch AB2899

tag: sample source

tag: patient id

tag: facs gate

value: CD3 & CD45


title: EMVC069F

tag: tissue

tag: sample well

tag: Sex


title: EMVC060F

tag: age at sample collection (years)

tag: sentrix id


title: ACCLAIM_937612_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19208

tag: cell type

tag: participantid

tag: randomized treatment

tag: race


title: dilated_perivascular_adipose_tissue_51

tag: subject id

tag: patient diagnosis

tag: age (years)

tag: country of origin

value: Italy


title: subcutaneous_abdominal_fat_20

value: subcutaneous abdominal fat


title: AB2898

description: Amp batch AB2898

tag: plate id

tag: amplification batch


title: ACCLAIM_937612_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19205

value: Tfh

tag: visitnumber

tag: barcode

tag: age


title: ACCLAIM_937612_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19202

tag: tissue


title: AB2574

description: Amp batch AB2574

tag: sample source

value: Tumor

tag: patient id

tag: facs gate


title: AB2570

description: Amp batch AB2570


title: ACCLAIM_750328_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19199

tag: cell type

tag: Sex


title: omental-visceral_fat_05

value: omental-visceral fat


title: B052D-rep

value: PBMC

tag: sample well

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: AB2553

description: Amp batch AB2553


title: ACCLAIM_750328_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19196

tag: participantid

tag: randomized treatment

tag: race


title: EMVB105F

tag: plate id


title: AB2549

description: Amp batch AB2549

tag: amplification batch


title: ACCLAIM_415432_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19190

tag: visitnumber

tag: barcode

value: Abatacept


title: AB2543

description: Amp batch AB2543


title: non-dilated_perivascular_adipose_tissue_20

tag: subject id

tag: patient diagnosis

tag: tissue

value: periaortic adipose tissue

tag: age (years)

tag: country of origin


title: ACCLAIM_415432_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19187

tag: cell type

tag: age

tag: Sex


title: subcutaneous_abdominal_fat_19


title: A031D

tag: sample well

tag: age at sample collection (years)

tag: sentrix id


title: B195D

tag: sentrix position


title: non-dilated_perivascular_adipose_tissue_01


title: ACCLAIM_415432_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19184

tag: participantid

tag: randomized treatment

tag: race


title: B155F-rep

tag: plate id


title: B105F


title: AB2542

description: Amp batch AB2542

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: omental-visceral_fat_51

tag: subject id

tag: patient diagnosis

tag: tissue

tag: age (years)


title: dilated_perivascular_adipose_tissue_21

tag: Sex

tag: country of origin


title: ACCLAIM_527582_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19181

tag: cell type

tag: visitnumber

tag: barcode

tag: age

value: Female


title: AB2541

description: Amp batch AB2541


title: AB2521

description: Amp batch AB2521


title: omental-visceral_fat_20


title: dilated_perivascular_adipose_tissue_19


title: AB2520

description: Amp batch AB2520


title: B120L

tag: sample well

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: dilated_perivascular_adipose_tissue_05


title: ACCLAIM_360231_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19172

tag: participantid

tag: randomized treatment

tag: race


title: A060D

tag: plate id


title: AB2519

description: Amp batch AB2519

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: ACCLAIM_360231_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19169

tag: tissue

tag: Sex


title: C024H


title: AB2518

description: Amp batch AB2518


title: B130F


title: omental-visceral_fat_18

tag: subject id

tag: patient diagnosis

tag: age (years)

tag: country of origin


title: AB2517

description: Amp batch AB2517


title: ACCLAIM_360231_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19166

tag: cell type

tag: visitnumber

tag: barcode

tag: age


title: dilated_perivascular_adipose_tissue_32


title: ACCLAIM_768526_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19235

tag: participantid

tag: randomized treatment


title: ACCLAIM_763271_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19163

tag: race


title: omental-visceral_fat_09


title: C059L

tag: sample well

tag: plate id

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: non-dilated_perivascular_adipose_tissue_09

tag: tissue

tag: Sex


title: A054L


title: A042D


title: B210F


title: AB2516

description: Amp batch AB2516

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: ACCLAIM_763271_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19160

tag: cell type

tag: visitnumber


title: AB2515

description: Amp batch AB2515


title: ACCLAIM_987582_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19154

tag: barcode

tag: age


title: B155F


title: non-dilated_perivascular_adipose_tissue_18

tag: subject id

tag: patient diagnosis

tag: age (years)

tag: country of origin


title: AB2514

description: Amp batch AB2514

tag: plate id


title: B160F

tag: sample well

tag: age at sample collection (years)

tag: sentrix id


title: omental-visceral_fat_23

tag: tissue

tag: Sex


title: ACCLAIM_987582_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19151

tag: participantid

tag: randomized treatment

tag: race


title: ACCLAIM_987582_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19148

tag: cell type


title: AB2513

description: Amp batch AB2513

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: B144F

tag: sentrix position


title: non-dilated_perivascular_adipose_tissue_23

tag: subject id

tag: patient diagnosis

tag: age (years)


title: AB2512

description: Amp batch AB2512

tag: plate id


title: AB2511

description: Amp batch AB2511


title: dilated_perivascular_adipose_tissue_23

tag: country of origin


title: AB2510

description: Amp batch AB2510


title: ACCLAIM_519740_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19142

tag: visitnumber

tag: barcode

tag: age

value: Black or African American


title: C069F

tag: tissue

tag: sample well

tag: Sex

tag: age at sample collection (years)

tag: sentrix id


title: ACCLAIM_519740_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19145

tag: cell type

tag: participantid

tag: randomized treatment

tag: race


title: B218D

tag: sentrix position


title: omental-visceral_fat_04

tag: subject id

tag: patient diagnosis

value: Male


title: ACCLAIM_509364_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19133


title: AB2508

description: Amp batch AB2508

tag: plate id

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: ACCLAIM_509364_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19136

tag: tissue

tag: visitnumber

tag: barcode

tag: age


title: non-dilated_perivascular_adipose_tissue_04

tag: Sex

tag: age (years)

tag: country of origin


title: B131F

tag: sample well

tag: age at sample collection (years)

tag: sentrix id


title: B204D

value: M

tag: sentrix position


title: ACCLAIM_527582_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19178

tag: cell type

tag: participantid

tag: randomized treatment

tag: race


title: subcutaneous_abdominal_fat_04

tag: subject id

tag: patient diagnosis


title: dilated_perivascular_adipose_tissue_04

tag: tissue


title: AB2507

description: Amp batch AB2507

tag: plate id

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: ACCLAIM_578949_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19127

tag: visitnumber

tag: barcode

tag: age

tag: Sex


title: AB2506

description: Amp batch AB2506


title: subcutaneous_abdominal_fat_03

tag: age (years)

tag: country of origin


title: A035L

tag: sample well

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: ACCLAIM_509364_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19130

tag: cell type

tag: participantid

tag: randomized treatment

tag: race


title: ACCLAIM_578949_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19124

tag: tissue


title: ACCLAIM_526007_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19118


title: C083F

tag: plate id

value: F


title: AB2505

description: Amp batch AB2505

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: omental-visceral_fat_03

tag: subject id

tag: patient diagnosis

value: abdominal aortic aneurysm

tag: Sex


title: AB2504

description: Amp batch AB2504


title: ACCLAIM_526007_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19115

tag: visitnumber

tag: barcode

tag: age


title: non-dilated_perivascular_adipose_tissue_03

tag: age (years)

tag: country of origin


title: AB2503

description: Amp batch AB2503


title: dilated_perivascular_adipose_tissue_03


title: omental-visceral_fat_02


title: A079L-rep

tag: sample well

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: ACCLAIM_526007_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19112

tag: cell type

tag: tissue

tag: participantid

tag: randomized treatment

tag: race


title: AB2502

description: Amp batch AB2502

tag: plate id

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: ACCLAIM_264812_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19106

tag: visitnumber

tag: barcode

value: Placebo

tag: age

tag: Sex


title: AB2501

description: Amp batch AB2501


title: C058D

tag: sample well

tag: age at sample collection (years)


title: ACCLAIM_323548_15_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19100

value: White


title: A056D

tag: sentrix id

tag: sentrix position


title: B175D

tag: tissue


title: C006D


title: B003L


title: AB2500

description: Amp batch AB2500


title: B062L


title: ACCLAIM_323548_7_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19097

tag: cell type

tag: participantid


title: subcutaneous_abdominal_fat_02

tag: subject id

tag: patient diagnosis

tag: age (years)

tag: country of origin


title: dilated_perivascular_adipose_tissue_18


title: ACCLAIM_323548_0_Tfh

description:
RNAseq_Tfh_norm_counts.csv
lib19094

tag: randomized treatment

tag: race


title: B083L

tag: plate id


title: dilated_perivascular_adipose_tissue_02


title: AB2499

description: Amp batch AB2499

tag: amplification batch

tag: sample source

tag: patient id

tag: facs gate


title: AB2509

description: Amp batch AB2509


title: non-dilated_perivascular_adipose_tissue_02

tag: Sex


title: A051D

tag: sample well

tag: age at sample collection (years)

tag: sentrix id


title: AB2498

description: Amp batch AB2498


title: LIN-OE + ∆IMP1 RNA

city: Piscataway

first: Premal

last: Shah

state: NJ

address: 145 Bevier Road, Rm 326

department: Genetics

institute: Rutgers University

data_processing:
RNA-seq and footprinting reads were mapped to the human transcriptome using the riboviz pipeline (Carja et al., BMC Bioinformatics 2017). Sequencing adapters were trimmed from reads using Cutadapt 1.10 (--trim-n -O 1 –minimum-length 5).
The reads from different samples were separated based on the barcodes in their 3’ linkers using fastx_barcode_splitter (FASTX toolkit, Hannon lab) with utmost one mismatch allowed. UMI and barcodes were removed from reads in each sample using Cutadapt (--trim-n -m 10 -u 4 -u -10)
Trimmed reads that aligned to human/mouse rRNA were removed using Bowtie v1.1.2 . Remaining reads were mapped to a set of 19,192 principal transcripts for each gene in the APPRIS database (using HISAT2 v2.1.0). Only reads that mapped uniquely were used for all downstream analyses. For genes with multiple principal transcripts, the first one in the list was chosen.
All analyses of ribosome profiling datasets were performed in R. We restricted analyses to genes with at least one dataset (RNA-seq or footprinting across conditions) with 64 mapped reads and genes with 0 read counts in any dataset were ignored unless the mean read counts across all 8 datasets was above 64.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample

source_name: SW480 cell lines

extract_protocol:
Ribosome profiling libraries from 3 pooled cell culture plates were prepared using a standard protocol (McGlincy and Ingolia, Methods 2017), with minor modifications.
Separate 5’ and 3’ linkers were ligated to the RNA-fragment instead of 3’ linker followed by circularization (Subtelny et al, Nature 2014). 5’ linkers contained 4 random nt unique molecular identifier (UMI) similar to a 5 nt UMI in 3’ linkers. During size-selection, we restricted the footprint lengths to 18-34 nts. Matched RNA-seq libraries were prepared using RNA that was randomly fragmentation by incubating for 15 min at 95C with in 1 mM EDTA, 6 mM Na2CO3, 44 mM NaHCO3, pH 9.3. RNA-seq fragments were restricted to 18-50 nts. Ribosomal rRNA were removed from pooled RNA-seq and footprinting samples using RiboZero (Epicenter MRZH116). cDNA for the pooled library were PCR amplified for 15 cycles.

tag: cell line

tag: genotype/variation

value: LIN28B OE+IMP1-/- knockout


title: B029D

tag: tissue

tag: sentrix position


title: dilated_perivascular_adipose_tissue_09

tag: subject id

tag: patient diagnosis

tag: age (years)

value: Italy


title: B026D


title: AB2497

description: Amp batch AB2497


title: LIN-OE + ∆IMP1 RPF

description: Ribosome-protected fragments

data_processing:
Library strategy: Ribo-Seq
RNA-seq and footprinting reads were mapped to the human transcriptome using the riboviz pipeline (Carja et al., BMC Bioinformatics 2017). Sequencing adapters were trimmed from reads using Cutadapt 1.10 (--trim-n -O 1 –minimum-length 5).
The reads from different samples were separated based on the barcodes in their 3’ linkers using fastx_barcode_splitter (FASTX toolkit, Hannon lab) with utmost one mismatch allowed. UMI and barcodes were removed from reads in each sample using Cutadapt (--trim-n -m 10 -u 4 -u -10)
Trimmed reads that aligned to human/mouse rRNA were removed using Bowtie v1.1.2 . Remaining reads were mapped to a set of 19,192 principal transcripts for each gene in the APPRIS database (using HISAT2 v2.1.0). Only reads that mapped uniquely were used for all downstream analyses. For genes with multiple principal transcripts, the first one in the list was chosen.
All analyses of ribosome profiling datasets were performed in R. We restricted analyses to genes with at least one dataset (RNA-seq or footprinting across conditions) with 64 mapped reads and genes with 0 read counts in any dataset were ignored unless the mean read counts across all 8 datasets was above 64.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample


title: LIN-OE RNA

value: LIN28B OE


title: AB2496

description: Amp batch AB2496


title: AB2495

description: Amp batch AB2495


title: LIN-OE RPF

description: Ribosome-protected fragments


title: G_Input

city: Amsterdam

first: Abhishek

last: Singh

address: Plesmanlaan

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (Ensembl release 55: Homosapiens GRCh 37.55) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Genome_build: GRCh 37.55

source_name: primary prostate cancer

growth_protocol: fresh frozen material

extract_protocol:
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

treatment_protocol: Surgical resections from Prostate, breast and endometrium tumors.

tag: case/control

value: DSG


title: AB2493

description: Amp batch AB2493

tag: plate id

value: Tumor


title: B027F


title: AB2494

description: Amp batch AB2494

tag: amplification batch


title: B177H-rep


title: AB2492

description: Amp batch AB2492

tag: sample source


title: A005F


title: H_F12

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

hyb_protocol: Two hundred nanograms from the set RNA samples were labelled using Illumina TotalPrep-96 RNA Amplication kit lot #00408854 (Ambion) as per amplication protocol. 22 were selected for hybridization and 750 nanograms of cRNA generated from these samples were used to hybridize onto two human HT-12 v4 beadchips. The beadchips were incubated at 58C with rotation speed 5 for 18 hours. The beadchips were washed and stained as per illumina protocol and scanned on iScan. The datafiles were quantified in GenomeStudio Version 2011.1. All samples passed Illumina's sample dependant and independant QC metrics.

scan_protocol: standard Illumina protocol

data_processing:
Data was checked for overall quality using R (v2.15.3) with the Bioconductor framework and the LUMI package installed. All samples passed qc and were included in subsequent analysis
Data was imported in GeneSpring v13.1.1 for analysis. During import, the data was normalized using a standard (for Illumina arrays) quantile normalization followed by a “per probe” median centred normalization.
All data analysis and visualization were performed on log2 transformed data.
Data was filtered to remove the confounding effect probes that show no signal may have on subsequent analysis. Only probes that were above the 20th percentile of the distribution of intensities in 80% of any of the 1 of 2 groups were allowed to pass through this filtering. The final set contained 33788 probes.

label: biotin

source_name: Neck skin

label_protocol: standard Illumina protocol

extract_protocol: Samples were pulvarized after freezing in liquid nitrogen and RNA extraction was performed using Qiagen Rneasy.

value: fibrotic tissue


title: H_F11


title: E_Input_FA

source_name: Primary endometrium cancer

tag: patient id

value: FA


title: E_Input_DSG


title: H_F10


title: H_F9


title: AB2491

description: Amp batch AB2491

tag: facs gate


title: H_F13


title: B_Input_FA

source_name: primary breast cancer


title: AB2108

description: Amp batch AB2108


title: B057D-rep

value: PBMC

tag: Sex


title: H_F7


title: B109F

tag: sample well


title: B_Input_DSG


title: AB2107

description: Amp batch AB2107


title: P_Input_FA


title: H_F6


title: AB2106

description: Amp batch AB2106


title: H_F8


title: P_Input_DSG


title: B041L

tag: age at sample collection (years)


title: AB2105

description: Amp batch AB2105


title: AB2104

description: Amp batch AB2104


title: LNCAP_Input

source_name: LNCAP cell line


title: H_F5


title: H_F3


title: AB2103

description: Amp batch AB2103


title: MCF7_Input


title: B187D

tag: sentrix id


title: H_F4


title: B011F


title: G2_H3K27ac_DSG

tag: chip antibody

value: H3K27ac (Active Motif; 39133)


title: H_F2


title: AB2102

description: Amp batch AB2102


title: C097D


title: B125F


title: G2_FOXA1_DSG

value: FOXA1 (Santa Cruz; sc-6554)


title: AB2101

description: Amp batch AB2101


title: H_F1


title: H_N8

value: normal tissue


title: G2_AR_DSG

value: AR (Santa Cruz; sc-816)


title: H_N9


title: A080L


title: B180F


title: G1_H3K27ac_DSG


title: AB2099

description: Amp batch AB2099


title: B007L


title: G1_FOXA1_DSG


title: A034L

value: M


title: G1_AR_DSG


title: AB2100

description: Amp batch AB2100


title: AB2098

description: Amp batch AB2098


title: AB2096

description: Amp batch AB2096


title: H_N6


title: H_N4


title: E3_H3K27ac_DSG


title: B030D

value: F


title: B008F


title: A065L


title: H_N7


title: H_N5


title: E3_H3K27ac_FA


title: AB2097

description: Amp batch AB2097


title: H_N2


title: H_N3


title: E3_ER_DSG

value: ER (Santa Cruz; sc-543)


title: B018L


title: mammary gland KO_r2 (RNA-seq)

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

description: mammary gland transplants 8-wk

data_processing:
TopHat 2.02 is used to align reads to reference genome.
Htseq-count is used to count the reads in each gene for each sample against the Ensembl NCBIM37.67 gtf file
Genome_build: mm9
Supplementary_files_format_and_content: read counts for each gene extracted by Htseq-count from the bam files aligned by TopHat

organism: Mus musculus

source_name: mammary gland

growth_protocol: Mice were maintained in standard conditions

extract_protocol:
RNA was extracted using the Arcturus® PicoPure® RNA Isolation Kit (Applied Biosystems)
NuGEN RNA-Seq and Illumina DNA Seq library preparation protocol were used to prepare the library

treatment_protocol: In all cases MECs were isolated from WT and miR205fl/fl cre+ outgrowth according to our lab protocol and FACS-purified into basal and luminal subpopulations using cell surface markers.

value: mammary gland

tag: age

value: 8-wk-old transplants

tag: genotype

value: miR205fl/flmTmGfl/fl cre+

tag: cell type

value: GFP+ basal cells (CD24+CD49fhigh) sorted from mammary epithelial cell (MECs)


title: A071D

tag: tissue

tag: sentrix position


title: E3_ER_FA


title: mammary gland WT_r2 (RNA-seq)

description: mammary gland transplants 8-wk

value: WTfl/flmTmGfl/fl cre+


title: H_N1


title: E2_H3K27ac_DSG

value: DSG


title: AB2093

description: Amp batch AB2093

value: Tumor


title: mammary gland KO_r1 (RNA-seq)

description: mammary gland transplants 8-wk


title: B121D


title: E2_H3K27ac_FA


title: B057D


title: AB1892

description: Amp batch AB1892


title: AB1891

description: Amp batch AB1891


title: Bulk_Neg_rep2 [314_CACAGT]

city: New York

first: Michael

last: Rendl

state: NY

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
314_CACAGT

data_processing:
(Bulk RNA-seq) All raw RNA sequencing reads were mapped to the mouse genome (mm10) with TopHat v2.0.3 coupled with the Bowtie2 aligner with default parameters. Transcriptomes were assembled and fragments per kilo-base per million reads (FPKM) for each gene were computed with Cufflinks v2.1.1 with default parameters.
(Single Cell RNA-seq) Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mm10 mouse genome release downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: mm10
Supplementary_files_format_and_content:
(Bulk RNA-seq) E15.0_bulkRNAseq.xlsx: Tab separated file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the sorted cell type (each sorted cell type has two biological replicates). The first column lists the official gene symbol.
(Single Cell RNA-seq) E15.0_Mesenchymal cells_scRNAseq.csv: Tab separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples (including 16 blank wells/plate, called ERCC). Column name indicates the cell type determined from index sorting,  sample number,followed by the cell number of the library, all separated by underscores (i.e. Cell Type_Sample_Cell Number). The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Bulk_Neg [Bulk RNA-seq]

extract_protocol:
Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8.8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN).
From 100ng amplified cDNA sequencing libraries were generated with 16 unique barcoded adapters (8 samples x 2 replicates) using the Ovation Ultralow DR Library System (NuGEN).

tag: strain

tag: developemental stage

value: backskin

value: negative population


title: E2_ER_DSG

tag: case/control


title: AB1890

description: Amp batch AB1890

tag: plate id

tag: amplification batch


title: mammary gland WT_r1 (RNA-seq)

description: mammary gland transplants 8-wk


title: A079L

value: PBMC


title: B072D


title: Bulk_Neg_rep1 [298_AAGCCT]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
298_AAGCCT


title: B102F


title: B084L


title: E1_H3K27ac_DSG

value: H3K27ac (Active Motif; 39133)

tag: patient id


title: Bulk_Sch_rep2 [312_CGTAGA]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
312_CGTAGA

source_name: Bulk_Sch [Bulk RNA-seq]

value: Schwann cells


title: Natural SSA High 10Ca

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

data_processing:
Reads were trimmed using cutadapt version 1.15 to remove the "QuantSEQ FWD" adaptor sequence
The trimmed reads were mapped against the Homo sapiens GRCh38.89 reference genome using STAR version 2.5.3a
The RSEM software version 1.3.0 was used to generate the count tables
Raw counts were filtered, whereby only genes with a cpm above 1 in at least 4 samples were retained
Filtered counts were normalized using edgeR standard normalization method
Genome_build: GRCh38.89 reference genome (ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/Homo_sapiens.GRCh38.89.gtf.gz)
Supplementary_files_format_and_content: Normalized counts in a tab delimited format

growth_protocol: Adenocarcinoma alveolar basal cell lines (A549) were maintained in Dulbecco’s Modified Eagle Medium (DMEM), supplemented with 10% fetal bovine serum and 5000 units.mL-1 penicillin-streptomycin at 37°C, 5% CO2 and >95% relative humidity. Confluent cell cultures (after 2-3 days) were passaged via trypsination (0.5% trypsin-EDTA) and split in a ration 1:6.

extract_protocol:
RNA was extracted using the Qiagen RNEasy kit following manufacturers instruction including DNAse digestion
250 ng of RNA was used to perform an Illumina sequencing library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR, according to Illumina's protocol 'Sequencing Library qPCR Quantification protocol guide', version February 2011. A High sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US) was used to control the library's size distribution and quality. Sequencing was performed on a high throughput Illumina NextSeq 500 flow cell generating 75 bp single reads.

treatment_protocol: Confluent cell cultures were trypsinized and transferred in 3mL fresh DMEM to Nunc 6-well multiplates at a concentration of 320,000 cells.well-1. After seeding, cells were incubated for 10 hours at 37°C, 5% CO2 and >95% relative humidity to stimulate growth and adherence to the surface. Then, cells were treated according to one of five treatments (see sample section, characteristics: treatment)

tag: exposure time

tag: cell line

tag: treatment

value: Exposure to high dose natural sea spray aerosols


title: E1_H3K27ac_FA

value: FA


title: Bulk_Sch_rep1 [296_ACCTCA]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
296_ACCTCA


title: Natural SSA High 10Da

source_name: Adenocarcinoma alveolar basal cell lines


title: E2_ER_FA


title: E1_ER_DSG


title: Natural SSA High 10Ba


title: Bulk_Fb_rep2 [309_GGAGAA]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
309_GGAGAA

source_name: Bulk_Fb [Bulk RNA-seq]

value: fibroblasts


title: E1_ER_FA


title: Bulk_Fb_rep1 [293_TGGTGA]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
293_TGGTGA


title: B4_H3K27ac_DSG


title: B219D

tag: sample well

tag: Sex

value: M

tag: age at sample collection (years)


title: A023D

tag: sentrix id


title: B091D

value: F


title: AB1889

description: Amp batch AB1889

source_name: Immune cells sorted from melanoma tumors

tag: sample source

tag: facs gate


title: Bulk_DC2_rep2 [310_AGCATG]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
310_AGCATG

source_name: Bulk_DC2 [Bulk RNA-seq]

tag: tissue

tag: cell type

value: dermal condensates (DC) 2


title: Bulk_DC2_rep1 [294_AGTGAG]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
294_AGTGAG

tag: strain


title: B4_H3K27ac_FA

tag: chip antibody


title: AB2094

description: Amp batch AB2094


title: Natural SSA Mid 9Da

value: Exposure to mid dose natural sea spray aerosols


title: B4_H3K4me3_DSG

value: H3K4me3 (Abcam; ab8580)

tag: case/control


title: Natural SSA High 10Aa


title: AB2095

description: Amp batch AB2095

tag: plate id


title: Natural SSA Mid 9Ba


title: Natural SSA Mid 9Ca


title: Bulk_DC1_rep1 [295_GCACTA]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
295_GCACTA

source_name: Bulk_DC1 [Bulk RNA-seq]

tag: developemental stage

value: dermal condensates (DC) 1


title: Natural SSA Mid 9Aa


title: Bulk_DC1_rep2 [311_GAGTCA]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
311_GAGTCA


title: B128F

tag: sentrix position


title: A053L


title: B4_FOXA1_DSG

value: FOXA1 (Santa Cruz; sc-6554)

tag: patient id


title: B107F


title: B071L


title: B4_H3K4me3_FA


title: B4_FOXA1_FA


title: B4_ER_DSG

value: ER (Santa Cruz; sc-543)

value: DSG


title: Bulk_pre-DC_rep1 [291_AACCAG]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
291_AACCAG

source_name: Bulk_pre-DC [Bulk RNA-seq]

value: backskin

value: pre-DC


title: B4_ER_FA


title: B064L

value: PBMC


title: Natural SSA Low 8Da

tag: exposure time

tag: cell line

value: Exposure to low dose natural sea spray aerosols


title: Bulk_pre-DC_rep2 [307_AAGAGG]

description:
processed data file : E15.0_bulkRNAseq_Final.xlsx
307_AAGAGG


title: A026L

tag: sample well


title: B039D

tag: Sex


title: Natural SSA Low 8Aa

tag: treatment


title: B3_H3K27ac_DSG

value: H3K27ac (Active Motif; 39133)


title: lab SSA High 7Da

value: Exposure to high dose lab sea spray aerosols


title: Natural SSA Low 8Ba


title: B177H

tag: age at sample collection (years)

tag: sentrix id


title: Natural SSA Low 8Ca


title: lab SSA High 7Ca


title: B3_H3K27ac_FA

value: FA


title: lab SSA High 7Ba


title: B3_H3K4me3_DSG


title: lab SSA High 7Aa


title: lab SSA Mid 6Da

value: Exposure to mid dose lab sea spray aerosols


title: B3_H3K4me3_FA


title: B3_FOXA1_DSG


title: B3_FOXA1_FA


title: B004D

value: M


title: B3_ER_DSG


title: B080F


title: lab SSA Mid 6Ba


title: A064D

value: F


title: B3_ER_FA


title: B179F


title: lab SSA Mid 6Ca


title: lab SSA Mid 6Aa


title: B2_H3K27ac_DSG


title: lab SSA Low 5Da

value: Exposure to low dose lab sea spray aerosols


title: B217D


title: B2_H3K27ac_FA


title: lab SSA Low 5Ca


title: C017D


title: B152D


title: lab SSA Low 5Ba


title: lab SSA Low 5Aa


title: B2_H3K4me3_DSG


title: B2_FOXA1_DSG


title: B2_H3K4me3_FA


title: hYTX High 4Da

value: Exposure to high dose homoyessotoxin


title: B2_FOXA1_FA


title: Lean-4d-Cel-biological rep1

city: Boston

first: Umut

last: Ozcan

state: MA

address: 3 Blackfan Circle, CLS 16

department: Endocrinology

institute: Boston Children's Hospital

hyb_protocol: Per manufacturer's protocol (Affymetrix GeneChip Hybridization, Stain and Wash kit)

scan_protocol: Scanned On an Affymetrix GCS3000 7G scanner

data_processing: Data were analyzed with Affymetrix software to normalize and background correct using RMA

source_name: Lean mice

label_protocol: Per manufacturer's protocol (Affymetrix Ambion WT Expression kit and GeneChip WT Terminal labeling kit)

growth_protocol: 8-week-old C57BL/6J  male mice were fed with normal chow diet for 2 weeks

extract_protocol: Trizol extraction and subsequent purification of total RNA using QIAgen RNeasy MinElute Cleanup kit were performed according to the manufacturer's instructions.

treatment_protocol: Mice were intraperitoneally injected with celastrol for 6h (250ug/kg), 1day or 4 days (100 ul in DMSO 25 ul/day)

tag: phenotype

value: lean

tag: gender

value: male

tag: age

value: brain

tag: tissue region

value: hypothalamus

value: treated with celastrol

tag: time

value: 4 day


title: B2_ER_DSG

tag: chip antibody

value: ER (Santa Cruz; sc-543)

tag: case/control

value: DSG


title: hYTX High 4Ca


title: B074F

tag: tissue

value: PBMC

tag: plate id


title: A007D

tag: sentrix position


title: B116L


title: C060F


title: Lean-4d-Cel-biological rep2

tag: strain


title: Lean-1d-Cel-biological rep3

value: 1 day


title: Lean-4d-Cel-biological rep3


title: Lean-1d-Cel-biological rep2


title: A061D


title: B033F


title: EMVB195D

value: Buccal


title: B052D


title: B2_ER_FA

tag: patient id

value: FA


title: B1_H3K27ac_DSG

value: H3K27ac (Active Motif; 39133)


title: B006L

tag: sample well

value: M


title: hYTX Mid 3Da

tag: exposure time

tag: cell line

value: Exposure to mid dose homoyessotoxin


title: hYTX High 4Aa

tag: treatment


title: A069D

tag: Sex

value: F

tag: age at sample collection (years)

tag: sentrix id


title: B1_H3K27ac_FA


title: Lean-1d-Cel-biological rep1

tag: phenotype

tag: gender

tag: age


title: hYTX Mid 3Ca


title: C084F


title: B1_H3K4me3_DSG

tag: chip antibody

value: H3K4me3 (Abcam; ab8580)


title: Lean-6h-Cel-biological rep3

value: lean

tag: tissue region

tag: time

value: 6 h


title: Lean-6h-Cel-biological rep4

value: male

tag: tissue

value: brain


title: EMVB027F

tag: plate id

tag: sentrix position


title: B1_H3K4me3_FA

tag: patient id

tag: case/control


title: hYTX Mid 3Ba

tag: exposure time


title: EMVB175D

tag: sample well


title: EMVB057D


title: B1_FOXA1_DSG

value: FOXA1 (Santa Cruz; sc-6554)


title: hYTX Mid 3Aa

tag: cell line

tag: treatment


title: hYTX Low 2Da

value: Exposure to low dose homoyessotoxin


title: hYTX Low 2Ca


title: B1_FOXA1_FA


title: EMVC058D

tag: Sex

tag: age at sample collection (years)


title: B1_ER_DSG

value: ER (Santa Cruz; sc-543)


title: EMVB033F

tag: sentrix id


title: Lean-4d-DMSO-biological rep4

treatment_protocol: Mice were intraperitoneally injected with DMSO for 6h, 1day or 4 days (25 ul/day)

tag: strain

tag: phenotype

tag: gender

value: hypothalamus

value: treated with DMSO

value: 4 day


title: Lean-6h-Cel-biological rep2

tag: age

tag: tissue region

value: treated with celastrol


title: Lean-6h-Cel-biological rep1

tag: tissue

tag: time


title: hYTX High 4Ba

value: Exposure to high dose homoyessotoxin


title: Lean-4d-DMSO-biological rep3


title: hYTX Low 2Ba


title: B1_ER_FA

tag: chip antibody

value: FA


title: EMVB187D

value: Buccal

tag: plate id

value: M

tag: sentrix position


title: EMVB091D

value: F


title: hYTX Low 2Aa

tag: exposure time


title: EMVB160F

tag: sample well


title: Lean-4d-DMSO-biological rep2


title: P4_H3K27ac_DSG

value: H3K27ac (Active Motif; 39133)

tag: patient id

tag: case/control

value: DSG


title: mTor inhibitor 11Da

tag: cell line

tag: treatment

value: Exposure to Torkinib


title: P4_H3K27ac_FA


title: Lean-4d-DMSO-biological rep1

value: lean

value: male


title: Lean-1d-DMSO-biological rep4

value: brain

value: 1 day


title: EMVB084L

tag: Sex

tag: age at sample collection (years)

tag: sentrix id


title: mTor inhibitor 11Ca


title: P4_FOXA1_DSG

value: FOXA1 (Santa Cruz; sc-6554)


title: mTor inhibitor 11Ba


title: P4_FOXA1_FA


title: Lean-1d-DMSO-biological rep3

tag: strain

tag: phenotype

tag: gender

value: hypothalamus


title: mTor inhibitor 11Aa


title: P4_AR_DSG

value: AR (Santa Cruz; sc-816)


title: negative control 1Da2

value: control


title: EMVB152D

tag: tissue


title: EMVB052D


title: Lean-1d-DMSO-biological rep2

tag: age

tag: tissue region

value: treated with DMSO

tag: time


title: P4_AR_FA

tag: chip antibody


title: EMVB125F

tag: plate id

tag: sentrix position


title: Lean-6h-DMSO-biological rep4

value: 6 h


title: Lean-1d-DMSO-biological rep1


title: P3_H3K27ac_DSG

tag: patient id


title: negative control 1Da

tag: exposure time


title: negative control 1Ca2

tag: cell line


title: negative control 1Ca

tag: treatment


title: P3_H3K27ac_FA

tag: case/control

value: FA


title: P3_FOXA1_DSG


title: negative control 1Ba2


title: Lean-6h-DMSO-biological rep3


title: EMVC017D

value: Buccal

tag: sample well

tag: Sex

tag: age at sample collection (years)


title: EMVB026D

value: M

tag: sentrix id


title: P3_FOXA1_FA


title: negative control 1Ba


title: EMVB029D


title: Lean-6h-DMSO-biological rep2

tag: strain

tag: phenotype

tag: gender


title: db/db-4d-Cel-biological rep4

source_name: db/db mice

growth_protocol: 8-week-old db/db male mice were fed with normal chow diet for 2 week

tag: disease state

value: db/db

tag: age

tag: tissue

tag: tissue region

value: treated with celastrol

value: 4 day


title: Lean-6h-DMSO-biological rep1

tag: time


title: P3_AR_DSG

tag: chip antibody

tag: patient id

value: DSG


title: negative control 1Aa2

tag: exposure time

tag: cell line


title: EMVB003L

tag: plate id

tag: sentrix position


title: EMVB006L

tag: sample well

tag: Sex


title: P2_H3K27ac_DSG

value: H3K27ac (Active Motif; 39133)

tag: case/control


title: EMVB064L-rep

value: F

tag: age at sample collection (years)

tag: sentrix id


title: db/db-4d-Cel-biological rep2

tag: gender

value: male

value: brain

tag: treatment


title: SUVH1-GFP rep3 (ChIP-seq)

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.3.4 with parameters -k 1 -N 1 -p 40 --local -q
peaks were called using macs2 version 2.1.1.20160309 with the following setting: macs2 callpeak -f BAM -p 1e-3 -g 1.2e8 --bdg --nolambda --nomodel
The macs2 bdgdiff was used to determine differentially expressed peaks between wild-type and mutant plant with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: bg files were generated using bedtools genomecov and were further converted to bigWig using bedGraphToBigWig

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 22ºC

extract_protocol:
Lysates were clarified from sonicated nuclei and SUVH1-DNA complexes were isolated with anti-GFP antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: seedlings

tag: genotype

value: SUVH1-GFP in wild type

value: anti-GFP antibody


title: negative control 1Aa

value: control


title: P2_H3K27ac_FA

source_name: primary prostate cancer


title: db/db-4d-Cel-biological rep1

tag: disease state

tag: age

tag: tissue

value: hypothalamus


title: db/db-1d-Cel-biological rep4

tag: tissue region

tag: time

value: 1 day


title: P2_FOXA1_DSG

tag: chip antibody

value: FOXA1 (Santa Cruz; sc-6554)

tag: patient id


title: WT rep2 (ChIP-seq)

value: wild type


title: EMVB219D-rep

value: Buccal

tag: plate id

value: M


title: CD11b SP mouse NK Rep2 K27ac

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

description: Ultra-low Input (100 k cells)

data_processing:
ChIP-seq reads were aligned ot the hg19 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad
Bigwigs for visulazation were created using bedGraphToBigWig
RNA seq counts were determined using STAR
Genome_build: hg19

source_name: CD27-CD11b+ NK cells

extract_protocol:
Lysates were clarified from MNase treated nuclei and histone-DNA complexes were isolated with antibody. ATAC-seq were processed as per manufacturers instructions (Illumina FC-121-1030). RNA was purified using Rneasy Plus Microkit, and prepared using SMARTer Universal Low Input RNA kit (Clontech)
Nextera DNA Library Preparation Kit, Illuminia

tag: cell type

value: CD11b SP NK

tag: sample type

tag: antibody

value: H3K27ac (abcam 4729)


title: db/db-4d-Cel-biological rep3

value: db/db

value: treated with celastrol

value: 4 day


title: db/db-1d-Cel-biological rep2

value: male


title: P2_FOXA1_FA

tag: case/control

value: FA


title: EMVB030D

tag: sample well

tag: Sex

value: F

tag: age at sample collection (years)

tag: sentrix position


title: P3_AR_FA

value: AR (Santa Cruz; sc-816)


title: EMVB007L

tag: sentrix id


title: db/db-1d-Cel-biological rep3

tag: disease state

tag: gender

value: brain

tag: treatment


title: EMVC059H

tag: tissue


title: DP mouse NK Rep2 K27ac

description: Ultra-low Input (100 k cells)

source_name: CD27+CD11b+ NK cells

value: DP NK


title: P2_AR_DSG

value: DSG


title: P2_AR_FA


title: EMVB219D


title: DP mouse NK Rep1 K27ac

description: Ultra-low Input (100 k cells)


title: CD27 SP mouse NK Rep2 K27ac

description: Ultra-low Input (100 k cells)

source_name: CD27+CD11b- NK cells

value: CD27 SP NK


title: EMVB116L


title: CD11b SP mouse NK Rep1 K27ac

description: Ultra-low Input (100 k cells)


title: EMVB004D


title: db/db-6h-Cel-biological rep2

tag: age

tag: tissue region

value: hypothalamus

tag: time

value: 6 h


title: db/db-6h-Cel-biological rep3


title: P1_H3K27ac_FA

tag: chip antibody

value: H3K27ac (Active Motif; 39133)

tag: patient id


title: db/db-6h-Cel-biological rep1


title: EMVB177H

value: Buccal

tag: plate id

value: M


title: P1_FOXA1_DSG

value: FOXA1 (Santa Cruz; sc-6554)


title: EMVB121D


title: CD27 SP mouse NK Rep1 K27ac

description: Ultra-low Input (100 k cells)

tag: cell type

tag: sample type

tag: antibody

value: H3K27ac (abcam 4729)


title: EMVC083F

tag: sample well

tag: Sex


title: P1_AR_DSG

tag: case/control


title: EMVB064L

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: db/db-4d-DMSO-biological rep3

growth_protocol: 8-week-old db/db male mice were fed with normal chow diet for 2 weeks

treatment_protocol: Mice were intraperitoneally injected with DMSO for 6h, 1day or 4 days and then daily (25 ul/day)

tag: disease state

value: db/db

tag: gender

tag: treatment

value: treated with DMSO


title: P1_AR_FA


title: db/db-4d-DMSO-biological rep4

value: male

tag: age

tag: tissue

tag: tissue region

value: 4 day


title: e14.5control_replicate

city: New Haven

first: Jonathan

last: Levinsohn

state: CT

address: 333 Cedar

institute: Yale University

description:
R2 read is biological, R1 and I reads are technical.
Reads were generated from 10x Genomic library constructed. Library constructs begin and end with a P5 and P7. Constructs contain a Read1 sequence primer followed by a 16 bp barcode, followed by a 10 bp randomer, followed by cDNA sequence.  Read2 primer sequence is directly 3’ of the cDNA sequence.
processed data file: genes.tsv

data_processing:
Raw 10X sequencing data was processed into a matrix employing the standard 10X Cell Ranger pipeline. Briefly, base call files were fastq format which were aligned to the mm10 reference genome followed by nUMI and barcode counting, constructing the nUMI count matrices.
nUMI matrices were filtered, centered and normalized using Seurat (Butler et al., 2018; Macosko et al., 2015). Briefly, for each original run condition (i.e. E13.5 wildtype), cells were filtered to have > 1,000 genes, and nUMI > 2,500, but < 50,000. Data was then log scaled, centered and normalized to nUMI.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_matrix.mtx: Text files containing nUMI counts for each barcoded cell across each gene.
Supplementary_files_format_and_content: *_barcodes.tsv: Text files with names of each barcode as listed from matrix.mtx files.
Supplementary_files_format_and_content: genes.tsv: Text file with names of each gene as listed from matrix.mtx files.

source_name: Whole Skin

extract_protocol:
Embryonic dorsolateral/flank skin was micro-dissected and pooled (3-4 embryos per sample) and dissociated into a single-cell suspension using 0.25% trypsin (Gibco, Life Technologies) for 30 minutes at 37° C. Single-cell suspensions were then stained with DAPI (Fisher Scientific, NBP2-31156) just prior to fluorescence-activated cell sorting.
Chromium Single cell 3’ Library and Gel Bead Kit v2 Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V2 User Guide. After cDNA libraries were created, they were subjected to HiSeq 2500 (Illumina) sequencing.

treatment_protocol: PDGFRαCreER(Lo);β-catfl/fl;mTmG mice were given a single dose of Tamoxifen dissolved in corn oil (20mg/ml, Sigma) at E11.5 by oral gavage at 30 µg/gm and 15 µg/gm body weight respectively.

tag: strain/background

tag: genotype/variation

value: WT

value: Skin

tag: developmental stage

value: embryonic day 14.5


title: e13LOF

description:
PDGFRαCreER(Lo);β-catfl/fl;mTmG
R2 read is biological, R1 and I reads are technical.
Reads were generated from 10x Genomic library constructed. Library constructs begin and end with a P5 and P7. Constructs contain a Read1 sequence primer followed by a 16 bp barcode, followed by a 10 bp randomer, followed by cDNA sequence.  Read2 primer sequence is directly 3’ of the cDNA sequence.
processed data file: genes.tsv

value: PDGFRalphaCreER(Lo);beta-catfl/fl;mTmG

tag: cell type

value: embryonic day 13.5


title: P1_FOXA1_FA

tag: chip antibody

tag: patient id

value: FA


title: EMVB130F

tag: sample well

tag: plate id

tag: Sex

value: F


title: db/db-4d-DMSO-biological rep2

value: brain

value: hypothalamus

tag: time


title: e14LOF


title: MCF7_H3K27ac_DSG

source_name: MCF7 cell line

value: H3K27ac (Active Motif; 39133)

tag: case/control

value: DSG


title: e13.5control_replicate


title: db/db-1d-DMSO-biological rep4

tag: disease state

value: 1 day


title: MCF7_H3K27ac_FA


title: db/db-4d-DMSO-biological rep1

tag: gender


title: EMVB204D

value: Buccal

value: M

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: EMVB180F-rep

tag: tissue


title: EMVB218D


title: db/db-1d-DMSO-biological rep3

value: db/db

tag: age

tag: tissue region

tag: treatment

value: treated with DMSO


title: EMVB071L


title: e14.5control

tag: strain/background

tag: genotype/variation

tag: cell type

tag: developmental stage


title: MCF7_H3K4me3_DSG

tag: chip antibody

value: H3K4me3 (Abcam; ab8580)

tag: patient id


title: e13.5control

value: WT


title: P1_H3K27ac_DSG


title: db/db-1d-DMSO-biological rep2

value: male

tag: time


title: MCF7_H3K4me3_FA

tag: case/control


title: ET03_WT+LPS

city: CHICAGO

first: Shuang

last: Zhang

state: IL

address: 300 E. Superior St.

institute: Northwestern University

data_processing:
Adapters were trimmed using cutadapt version 1.14 and default parameters and a GTF file for mm10
Trimmed reads were aligned to mm10 using TopHat version 2.1.0 and default parameters
Transcript abundance was measured with Cufflinks version 2.2.1 and default parameters and a GTF file for mm10
Differential expression was performed using cuffdiff and default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: peritoneal macrophage

growth_protocol: DMEM

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: apoptotic cells were added to macrophages in a 5:1 ratio for 5 hrs before macrophages were harvested for RNA extraction; LPS was used at 100ng/ml for 5 hr treatment

value: primary peritoneal macrophages

tag: coculture

value: LPS for 5hrs


title: EMVB107F

first: Sarah

tag: sample well

tag: plate id

tag: Sex


title: ET02_WT+AC

value: apoptotic cells for 5 hrs


title: MCF7_FOXA1_DSG

value: FOXA1 (Santa Cruz; sc-6554)


title: MCF7_FOXA1_FA

value: FA


title: MCF7_ER_DSG

value: ER (Santa Cruz; sc-543)


title: MCF7_ER_FA


title: ET01_WT


title: db/db-6h-DMSO-biological rep4

tag: disease state

tag: gender

value: brain

value: hypothalamus

value: 6 h


title: db/db-6h-DMSO-biological rep3

tag: age

tag: tissue


title: EMVB144F

value: F

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: EMVB062L

value: Buccal


title: db/db-1d-DMSO-biological rep1

tag: tissue region

tag: treatment

value: 1 day


title: db/db-6h-DMSO-biological rep2

value: db/db


title: db/db-6h-DMSO-biological rep1

value: treated with DMSO


title: db/db-1d-Cel-biological rep1

value: treated with celastrol


title: Mock: Cells_PBS_rep1

city: Nanjing

first: Yanbo

last: Wang

address: 163 Xianlin Road

institute: Nanjing University

description: Transcription profiling in macrophages treated without miR-122

hyb_protocol: Agilent SureHyb

scan_protocol: Agilent DNA Microarray Scanner

data_processing: Aglient Feature Extraction

source_name: RAW246.1 cells, treated, PBS

label_protocol: Agilent Quick Am Labeling

growth_protocol: DMEM medium

extract_protocol: RIPA buffer, 30min

treatment_protocol: treated with 5μg/mL synthetic miR-122

value: macrophage

tag: cell type


title: LNCAP_H3K27ac_FA

source_name: LNCAP cell line

tag: chip antibody

value: H3K27ac (Active Motif; 39133)

tag: patient id


title: miR-122: Cells_without miR-122_rep1

description: Transcription profiling in macrophages treated with miR-122

source_name: RAW246.1 cells, treated, miR-122


title: EMVC084F

value: M


title: EMVB217D


title: DIO-4d-Cel-biological rep3

source_name: diet-induced obese mice

growth_protocol: 4-week-old C57BL/6J male mice were fed with 45% high fat diet for 16 weeks

tag: strain

value: DIO

value: male

tag: time

value: 4 day


title: LNCAP_H3K4me3_DSG

value: H3K4me3 (Abcam; ab8580)

tag: case/control

value: DSG


title: LNCAP_H3K4me3_FA

value: FA


title: EMVB128F

tag: sample well

tag: plate id


title: KO3: Zscan5b knoclout Embryonic Stem Cell Replicate3

city: Tokyo

first: Seiji

last: Ogawa

country: Japan

institute: Keio University

description: Gene expression Zscan5b knockout

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.3.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Embyronic Stem Cell

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of mouse embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. L)

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

value: Embyronic Stem Cell

tag: genotype

value: Zscan5b knockout


title: KO2: Zscan5b knoclout Embryonic Stem Cell Replicate2

description: Gene expression Zscan5b knockout


title: DIO-4d-Cel-biological rep1

tag: disease state

tag: gender

value: brain

value: hypothalamus


title: EMVB109F

tag: tissue

value: Buccal

tag: Sex

value: F


title: DIO-4d-Cel-biological rep2

tag: age


title: LNCAP_FOXA1_DSG

value: FOXA1 (Santa Cruz; sc-6554)


title: WT2: Control Embyronic Stem Cell Replicate 2

description: Gene expression wild type

value: wild type


title: DIO-1d-Cel-biological rep4

value: treated with celastrol

value: 1 day


title: WT3: Control Embyronic Stem Cell Replicate 3

description: Gene expression wild type


title: DIO-1d-Cel-biological rep3


title: LNCAP_FOXA1_FA


title: EMVB210F

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: KO1: Zscan5b knoclout Embryonic Stem Cell Replicate1

description: Gene expression Zscan5b knockout


title: EMVC024H

value: M


title: 3D-Lef rep2

first: HASAN

middle: ERBIL

last: ABACI

address: Russ Berrie Medical Science Pavilion  1150 St. Nicholas Avenue

department: DERMATOLOGY

institute: COLUMBIA UNIVERSITY

data_processing:
RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
Reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR(2.5.2b) and featureCounts(v1.5.0-p3)
Genome_build: mm8
Supplementary_files_format_and_content: raw counts

source_name: Dermal Papilla Cells

extract_protocol:
Dermal papilla cells were isolated from freshly discarded scalp tissue from hair restoration surgery using microdissection. Total RNA was isolated from cells maintained at indicated conditions by using the RNeasy Mini Kit (Qiagen) in accordance with the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Scalp skin

tag: condition

value: cells overexpressing Lef1 cultured as 3D spheres in hanging drops at passage 3


title: WT1: Control Embyronic Stem Cell Replicate 1

description: Gene expression wild type


title: EMVB102F


title: 3D-Lef rep1


title: LNCAP_AR_FA

tag: chip antibody

value: AR (Santa Cruz; sc-816)


title: EMVB180F


title: 3D rep3


title: DIO-1d-Cel-biological rep1

value: DIO

value: male

tag: tissue region

tag: treatment


title: DIO-1d-Cel-biological rep2

tag: strain

tag: time


title: 3D rep2

value: cells cultured as 3D spheres in hanging drops at passage 3


title: DIO-6h-Cel-biological rep4

value: 6 h


title: EMVB074F

tag: sample well


title: Input CD56dim

data_processing:
ChIP-seq reads were aligned ot the hg19 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad
Bigwigs for visulazation were created using bedGraphToBigWig
Genome_build: hg19

source_name: CD56Bright natural killer cells

extract_protocol: Lysates were clarified from MNase treated nuclei and histone-DNA complexes were isolated with antibody. ATAC-seq were processed as per manufacturers instructions (Illumina FC-121-1030)

tag: cell type

value: CD56Bright natural killer cells

tag: individual

value: Donor 3

tag: antibody


title: 3D rep1


title: CARE093P

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

value: PBMC

tag: plate id


title: CARE088P

tag: tissue


title: CARE071P

tag: Sex


title: DIO-6h-Cel-biological rep2

tag: disease state

tag: gender

tag: age

value: brain

value: hypothalamus


title: CD56Dim Donor 4 ATAC

source_name: CD56Dim natural killer cells

value: CD56Dim natural killer cells

value: Donor 4

value: DNA - accessability. Illumina FC-121-1030


title: 2D-Lef rep3


title: DIO-6h-Cel-biological rep3

value: treated with celastrol


title: Input CD56bright


title: CARE071P_rep

value: F

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: CARE068P

value: M


title: CD56Dim Donor 3 ATAC


title: 2D-Lef rep1

value: Scalp skin

tag: condition

value: cells overexpressing Lef1 cultured on 2D at passage 3


title: CD56Dim Donor 2 ATAC

value: Donor 2


title: 2D-Lef rep2


title: EMVC006D

value: Buccal


title: CARE038P


title: DIO-4d-DMSO-biological rep2

value: DIO

value: male

tag: tissue region

tag: treatment

value: treated with DMSO

value: 4 day


title: DIO-4d-DMSO-biological rep3

tag: strain

tag: time


title: CD56Dim Donor 1 ATAC

tag: cell type

value: Donor 1


title: DIO-6h-Cel-biological rep1

value: brain

value: 6 h


title: DIO-4d-DMSO-biological rep1

value: hypothalamus


title: 2D rep3


title: DIO-1d-DMSO-biological rep3

value: 1 day


title: CD56Bright Donor 4 ATAC

value: CD56Bright natural killer cells

tag: individual

value: Donor 4

value: DNA - accessability. Illumina FC-121-1030


title: CARE088B_rep

tag: sample well

value: F


title: CD56Bright Donor 3 ATAC

value: Donor 3

tag: antibody


title: 2D rep2

tag: tissue

value: Scalp skin

value: 2D at passage 3


title: LNCAP_AR_DSG

tag: chip antibody

value: AR (Santa Cruz; sc-816)

tag: patient id

tag: case/control

value: DSG


title: CARE093B_rep

value: Buccal

tag: plate id

tag: Sex

value: M


title: CD56Bright Donor 2 ATAC

value: Donor 2


title: 2D rep1


title: CD56Bright Donor 1 ATAC

value: Donor 1


title: CD56Dim Donor 4 H3K27ac

description: Ultra-low Input (100 k cells)

value: CD56Dim natural killer cells

value: H3K27ac (abcam 4729)


title: Intact