title: 72431

first: Margareta

middle: D

last: Pisarska

address: 8700 Beverly Blvd

department: OB/GYN, Div REI

institute: Cedars Sinai Medical Center

data_processing:
Cell Ranger 2.0.0 (10X Genomics) was used to demultiplex reads and convert raw base call files into fastq format. Reads alignment was performed by using STAR (version 2.5.1) with hg38 transcriptome reference from Gencode 25 annotation, containing all protein-coding and long non-coding RNA genes. Expression counts for each gene in all samples were collapsed to unique molecular identifier (UMI) counts using Cell Ranger 2.0.0 (10X Genomics).
Genome_build: hg38
Supplementary_files_format_and_content: csv with raw expression matrix for all of six samples

source_name: chorionic villi

extract_protocol:
Fresh placental tissues of 5~10mg were placed in collection medium and transferred to lab and kept at 4°C overnight before cell preparation. The collection medium was αMEM with sodium heparin (100,000 units/100ml H2O, Sigma), gentamycin (0.5%, Invitrogen) and antibiotic-antimycotic (2%, Invitrogen). The tissue was washed in cold PBS to remove maternal contamination and minced with a sterile scalpel, then mixed with 0.25% trypsin, 300U/ml collagenase and 200μg/ml DNAse I and incubated in a 37°C, 5% CO2 incubator for 90 minutes with occasional agitation. After centrifugation at 1200 rpm for 10min, cell pellets were carefully resuspended in Chang medium (Irvine Scientific). To avoid overpopulation of erythrocytes in the captured cell population, 1xRBC lysis buffer was applied to the cell suspension for 15min at room temperature, after which, cells were carefully washed and resuspended in 100μl Chang medium and strained using a 70μm flowmi cell strainer (Bel-Art) immediately before library construction.
Single-cell RNA-seq libraries were prepared per Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Single cell suspensions were loaded on a Chromium Controller instrument (10X Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA), following which, GEMs were harvested and the cDNAs were amplified and cleaned up with SPRIselect Reagent Kit. Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA).

value: primary placental tissue

tag: developmental stages

value: first trimester

tag: fetal sex

value: male


title: WI38_A_rep1

status: Public on Aug 20 2020

type: SRA

city: Urbana

first: Prasanth Kumar

middle: Vijayan

last: Kannanganattu

state: Illinois

address: 601S, Goodwin Avenue

department: Cell and Developmental Biology

country: USA

institute: University of Illinois at Urbana-Champaign

library_source: transcriptomic

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina)
RNA-seq reads were aligned to human reference genome GRCh38 assembly using HISAT2
raw gene counts were first analyzed by HTSEQ-Count
Genome_build: GRCh38
Supplementary_files_format_and_content: Individual files include gene count information are presented in txt format

molecule: total RNA

organism: Homo sapiens

source_name: WI-38 cells

growth_protocol: WI-38 cells are cultured in 10% FBS+MEM with essential amino acid and sodium pyruvate.

extract_protocol:
Total RNA was extracted using RNeasy minikit from Qiagen
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina), polyadenylated mRNAs were captured with oligodT beads.

treatment_protocol: To induce cellular quiescence, WI-38 cells are cultured in 0.1% serum for 72 hours. Then, serum re-activation is performed by adding back the regular 10% serum growth medium.

tag: treatment

value: Asynchronous WI-38 cells


title: 6_Thor_Hyper_induced_-FBS_+Rapa_replicate1

city: Beijing

first: Hua

last: Jin

state: Choose a State or Province

address: Rm 225-1, Bldg Qiushilou, Beijing Institute of Technology,

country: China

institute: Beijing Institute of Technology

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

data_processing:
Library strategy: TRIBE
Trimmomatic-0.30/trimmomatic-0.30.jar SE -phred33 CROP:70 HEADCROP:6 LEADING:25 TRAILING:25 AVGQUAL:$avgquality MINLEN:19
Genome_build: Drosophila dm3 (BDGP Release 5); Human hg38 (GRCh38)
Supplementary_files_format_and_content: *.threshold.txt: Edited sites
Supplementary_files_format_and_content: *bw: bigWig files

organism: Drosophila melanogaster

source_name: late stage embryo-derived S2 cells

growth_protocol: S2 cells were grown in Hyclone SFX-insect media with 10% of FBS. PC3 cells were grown in F-12K Medium (ATCC) with 10% of FBS.

extract_protocol:
GFP-positive cells were sorted and collected with a BD FACSAria II machine. Total RNA was extracted with TRIzol LS reagent.
TRIBE: Standard Illumina TruSeq RNA Library Kit.

tag: cell line

tag: transfected plasmids

value: pAC5.1-eGFP and pMTA-thor-hyperADARcd

tag: expression of gene in pmta

value: Induced the expression overnight

value: Serum depletion and 50nM of Rapamycin for 5 hrs


title: Arabidopsis Col-0 with SA treatment rep3

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

data_processing:
Reads were mapped to the genome using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml) software with two mismatches allowed. Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/) was used for differential expression analysis. Differentially expressed genes were identified based on a fold change > 2 and q-value < 0.05 when comparing the test group sample to the control group sample. Data were summarized in file SA-NPR1-EIN3_GEO submission_processed data.xls
Genome_build: TAIR10
Supplementary_files_format_and_content: SA-NPR1-EIN3_GEO submission_processed data.xls (FPKMs)

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 with SA treatment

growth_protocol: Etiolated seedlings were grown in the dark for 3.5 days after stratification at 4 degrees for 3 days.

extract_protocol:
RNeasy Plant Mini Kit
stander Illumina mRNA-seq protocol

treatment_protocol: Etiolated seedlings were treated with MS liquid supplemented with or without 500 μM SA for 4 hrs.

tag: age

tag: genotype

value: wild type (Col-0)

tag: tissue

value: etiolated seedlings

value: SA


title: 5_Thor_Hyper_induced_replicate2

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

value: DMSO for 5 hrs


title: 100pg 600nM rep1

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
10pg.150nM_mate1.fastq.gz
10pg.150nM_mate2.fastq.gz

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie version1.1.1 with the default parameters
reads per million normalized bigWig files were generated using the GenomicRanges R/Bioconductor package and UCSC tool bedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: reads per million normalized bigWig

molecule: genomic DNA

source_name: Raji cells

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717).  Briefly, 10^7 cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp.  30 mg chromatin was immunoprecipitated with 3 μg anti-H3K4me3 antibody over night at 4 degrees.  Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.  ChIP DNA was quantitated by Qubit assay and diluted to the indicated starting amounts.
ChIP-seq libraries were generated using the indicated amount of input DNA with the KAPA Hyper Prep Kit according to the manufacturers instructions.

tag: chip antibody

tag: library construction

value: Raji


title: Arabidopsis Col-0 with SA treatment rep2


title: 72425

city: Los Angeles

state: CA


title: 10_Thor_Hyper_induced_+Torin 1_replicate1

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

value: 50nM of Torin-1 for 5 hrs


title: Arabidopsis Col-0 with SA treatment rep1


title: 1ng 1.5uM rep3

description:
1ng.1.5uM.rep.1cycle_mate1.fastq.gz
1ng.1.5uM.rep.1cycle_mate2.fastq.gz

value: KAPA Hyper Prep Kit according to the manufacturers instructions


title: 3_Hyper_only_replicate2

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

value: pAC5.1-eGFP and pMTA-hyperADARcd


title: Arabidopsis Col-0 with MS treatment rep3

source_name: Arabidopsis Col-0 with MS treatment

value: MS


title: 4_Thor_Hyper_induced_replicate1

description:
TRIBE, RNA-seq
Poly(A) tailed RNA


title: 2_Hyper_only_replicate1

description:
TRIBE, RNA-seq
Poly(A) tailed RNA


title: 72426

data_processing:
Cell Ranger 2.0.0 (10X Genomics) was used to demultiplex reads and convert raw base call files into fastq format. Reads alignment was performed by using STAR (version 2.5.1) with hg38 transcriptome reference from Gencode 25 annotation, containing all protein-coding and long non-coding RNA genes. Expression counts for each gene in all samples were collapsed to unique molecular identifier (UMI) counts using Cell Ranger 2.0.0 (10X Genomics).
Genome_build: hg38
Supplementary_files_format_and_content: csv with raw expression matrix for all of six samples.

value: female


title: 72424

value: primary placental tissue


title: 1ng 1.5uM rep2

description:
1ng.1.5uM.rep_mate1.fastq.gz
1ng.1.5uM.rep_mate2.fastq.gz


title: 1ng 1.5uM rep1

description:
1ng.1.5uM_mate1.fastq.gz
1ng.1.5uM_mate2.fastq.gz


title: Arabidopsis Col-0 with MS treatment rep2


title: 1_GFP_only

description:
TRIBE, RNA-seq
Poly(A) tailed RNA

value: Uninduced


title: 72406

value: first trimester


title: Arabidopsis Col-0 with MS treatment rep1


title: si-MILIP [MAFG_AS1]

status: Public on Aug 19 2020

city: Callaghan

first: Yuchen

last: Feng

state: NSW

address: Life science building, University Drive

country: Australia

institute: The university of Newcastle

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads. TopHat v2.0.12 was used to map the clean reads to whole genome.
FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, was used to estimate gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments(Trapnell, Cole, et al., 2010). HTSeq software v0.6.1 was used to analyze the gene expression levels in this experiment, using the union mode.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, log2foldchange, pvalue, qvalue

source_name: A549_MILIP Knockdown

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin

extract_protocol:
RNA was extracted using ISOLATE II RNA Mini Kit (Cat. BIO52073) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were seeded in 6-well plate (1.68X10^5/well). Transfections were performed after 24h by using Lipofectamine™ 3000 Transfection Reagent (Thermo Fisher, L3000008) according to the manufacturer’s instructions.

tag: cell type

value: lung cancer cell line

tag: genotype/variation

value: MILIP siRNA


title: si-ctrl [A549ctrl]

value: control siRNA


title: 100pg 600nM rep2

description:
10pg.150nM.rep_mate1.fastq.gz
10pg.150nM.rep_mate2.fastq.gz


title: G22T

city: chengdu

first: qian

last: bu

address: gaopeng street

institute: sichuan university

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4)
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: excel format with FPKM and counts

source_name: glioma

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: glioma

tag: patient diagnosis

tag: subject id


title: G28T


title: G27T


title: 72423

value: male


title: G3T


title: G28N

source_name: adjacent tissues of glioma

value: adjacent tissues of glioma


title: G27N


title: G22N


title: G9N


title: G3N


title: MDSC_GM-CSFonly_1

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from MDSC differentiated without IL-6.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

organism: Mus musculus

source_name: bone marrow differentiated 4 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Bone marrow cells were isolated and 2.5x10^6 cells were cultured for four days in 10 ml RPMI-1640 medium supplemented with 10 % heat-inactivated FBS, 1 % penicillin/streptomycin, 10 mM HEPES, 1 mM sodium pyruvate, 50 μM β-mercaptoethanol, 1 mM MEM non-essential amino acids (all Thermo Fisher).

extract_protocol: Total RNA was isolated by RNeasy Mini Kit (Qiagen). DNA digest was performed with on-column RNase-free DNase Set (Qiagen) according to manufacturer’s instructions. RNA concentration was determined by the microplate reader Tecan Infinite M200 using a Nanoquant plate.

treatment_protocol: Cells were supplemented for the four days with 40 ng/ml GM CSF and 40 ng/ml IL-6 or 40 ng/ml GM CSF only.

value: differentiated bone marrow

value: MDSC (myeloid-derived suppressor cells)

value: GM-CSF

tag: replicate


title: MDSC_IL-6,GM-CSF_3

description: Gene expression data from MDSC differentiated with IL-6.


title: Fabp26KO-F-1_B: Fabp2&6DKO_female_430B_replicate1

city: Ste-Anne-de-Bellevue

first: Luis

middle: B

last: Agellon

state: QC

address: 21111 Lakeshore Road

department: School of Human Nutrition

country: Canada

institute: McGill University

description: gene expression of the small intestine

hyb_protocol: cDNA was hybridized to Affymetrix 430A and 430B chips following the procedures specified by the manufacturer.

scan_protocol: Signals were acquired using the Affymetrix GeneChip Scanner Model 3000.

data_processing: The data were processed and analyzed using the R statistical environment and Bioconductor software (www.bioconductor.org) and to log2 scale using the RMA algorithm with background correction

source_name: small intestine from Fabp2 and Fabp6-simultaneously deleted C57BL/6J  mouse

label_protocol: Fluorescently labeled cDNA probes for each RNA pool was prepared following the procedures specified by the manufacturer.

growth_protocol: Mice were housed in a sterile and temperature controlled environment and fed a standard lab diet (Purina 5001).

extract_protocol: The small intestine, starting from the base of the stomach and ending just before the cecum, was excised and then flushed with ice-cold saline prior to tissue homogenization.  RNA was extracted from homogenates using Trizol (Invitrogen) and assessed for integrity (RIN>7) prior to use in microarray analysis.

treatment_protocol: No treatment

value: small intestine

value: 10-week old


title: Fabp26KO-M-2_B: Fabp2&6DKO_male_430B_replicate2

description: gene expression of the small intestine


title: G9T


title: MDSC_IL-6,GM-CSF_1


title: Fabp26KO-F-2_B: Fabp2&6DKO_female_430B_replicate2

description: gene expression of the small intestine


title: Fabp6KO-F-2_B: Fabp6KO_female_430B_replicate2

description: gene expression of the small intestine

source_name: small intestine from Fabp6-deleted C57BL/6J mouse

value: Fabp6-/- C57BL/6J


title: MDSC_GM-CSFonly_3


title: RNA_3.34Null-cXENp1

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
Reads were aligned to the genome using STAR software (v2.5.3) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.

growth_protocol: Feeder-free mouse embryonic stem cells (ESCs) were cultured on 0.1% gelatin-coated plates under standard conditions: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 1% penicillin-streptomycin. Feeder-free mouse extraembryonic endoderm stem cells (XENs) were cultured on 0.1% gelatin-coated plates with MEF-conditioned standard XEN medium: advanced RPMI 1640 supplemented with 15% FBS, 0.1 mM β-mercaptoethanol and 1% penicillin-streptomycin.

extract_protocol:
Total RNAs were extracted using the RNeasy kit (#74136, Qiagen) according to the manufacturer’s instructions.
About 0.1~1 µg total RNA from each sample was used to prepare PolyA RNA-seq libraries, and massively parallel sequencing was performed with the HiSeq4000 platform. Paired-end 150 bp-length reads were produced.

treatment_protocol: ESCs were differentiated to XENs following a published protocol (Niakan et al., 2013). Briefly, ESCs (Passage 0) were trypsinized and cultured on gelatin-coated plates with XEN medium. 24 Twenty-four hrs later, cells were treated with all-trans retinoic acid (0.01 µM) and activin A (10 ng/mL) for 48 hrs (Passage 1), then trypsinized and transfertransferred onto iMEF feeders and XEN medium for another 3~5 days until cells are were confluent (Passage 2). Cells were trypsinized again and cultured on gelatin-coated plates with XEN medium (Passage 3). XEN colonies form at passage 2 when cells were recovered on iMEF feeders. These colonies can could be picked and maintained in XEN culture condition.

tag: strain background

value: Chemical-induced XENs from ESCs (cXENs)


title: RNA_3.34Null-cXENp3


title: RNA_3.34Null-Rescue-cXENp1

value: Zfp281KO+Zfp281 Rescue


title: RNA_3.34Null-Rescue-cXENp3


title: Fabp6KO-M-1_B: Fabp6KO_male_430B_replicate1

description: gene expression of the small intestine


title: MDSC_GM-CSFonly_2


title: Fabp2KO-F-1_B: Fabp2KO_female_430B_replicate1

description: gene expression of the small intestine

source_name: small intestine from Fabp2-deleted C57BL/6J mouse

value: Fabp2-/- C57BL/6J


title: Fabp6KO-F-1_B: Fabp6KO_female_430B_replicate1

description: gene expression of the small intestine


title: MDSC_IL-6,GM-CSF_2


title: Fabp2KO-F-2_B: Fabp2KO_female_430B_replicate2

description: gene expression of the small intestine


title: RNA_2.6Null-cXENp3


title: Fabp2KO-M-2_B: Fabp2KO_male_430B_replicate2

description: gene expression of the small intestine


title: Fabp26KO-M-1_B: Fabp2&6DKO_male_430B_replicate1

description: gene expression of the small intestine


title: RNA_2.6Null-cXENp1


title: RNA_2.6Null-ESC

value: Embryonic stem cells (ESCs)


title: WT-F-2_B: WT_female_430B_replicate2

description: gene expression of the small intestine

source_name: small intestine from C57BL/6J mouse


title: Fabp2KO-M-1_B: Fabp2KO_male_430B_replicate1

description: gene expression of the small intestine


title: Fabp6KO-M-2_B: Fabp6KO_male_430B_replicate2

description: gene expression of the small intestine


title: RNA_3WT-cXENp3

value: WT


title: WT-M-2_B: WT_male_430B_replicate2

description: gene expression of the small intestine


title: RNA_3WT-cXENp1


title: XEN_Input

description: ChIP Input in XENs

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the mouse genome mm9 using the bowtie2 (v2.3.4) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
ChIP-seq peaks were determined by the MACS program (v.2.0.10), using input as the control data, and all other parameters followed the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of MACS called peaks.

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006).
ChIP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina HiSeq 4000 Sequencer. Data with 150 bp paired-end reads were obtained.

tag: strain

value: extraembryonic endoderm cells (XENs)

value: none (input)


title: XEN_H3K27me3_ChIP

source_name: H3K27me3 ChIP in XENs

value: XEN

value: Extraembryonic endoderm stem cells

value: Millipore, #07-449


title: RNA_3.34Null-ESC


title: XEN_Suz12_ChIP

description: Suz12 ChIP in XENs

value: Active Motif, #39357


title: RNA_3WT-ESC


title: XEN_Zfp281_ChIP

description: Zfp281 ChIP in XENs

value: Abcam, ab101318


title: RNA_3.34Null-Rescue-ESC


title: ESC_Zfp281_ChIP

description: Zfp281 ChIP in ESCs

value: embryonic stem cells (ESCs)


title: WT-F-1_B: WT_female_430B_replicate1

description: gene expression of the small intestine


title: ESC_Suz12_ChIP

description: Suz12 ChIP in ESCs


title: Fabp26KO-F-1: Fabp2&6DKO_female_430A_replicate1

description: gene expression of the small intestine


title: Fabp26KO-M-2: Fabp2&6DKO_male_430A_replicate2

description: gene expression of the small intestine


title: Fabp2KO-F-2: Fabp2KO_female_430A_replicate2

description: gene expression of the small intestine


title: Fabp2KO-F-1: Fabp2KO_female_430A_replicate1

description: gene expression of the small intestine


title: Fabp6KO-F-2: Fabp6KO_female_430A_replicate2

description: gene expression of the small intestine


title: Fabp26KO-M-1: Fabp2&6DKO_male_430A_replicate1

description: gene expression of the small intestine


title: ESC_Input

description: ChIP Input in ESCs


title: Fabp6KO-M-2: Fabp6KO_male_430A_replicate2

description: gene expression of the small intestine


title: Fabp6KO-M-1: Fabp6KO_male_430A_replicate1

description: gene expression of the small intestine


title: 3345_CD8m

city: San Diego

first: Rekha

last: Dhanwani

address: 9420 Athena Circle

institute: La Jolla Institure for Immunology

description: processed data file: all_counts.tsv

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the human GRCh38 reference using STAR (v 2.6.1c).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5) and features with 0 counts across all samples were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: all_counts.tsv: Tab-separated count matrix with rows as genes and columns as samples.

source_name: PBMC HC

growth_protocol: Frozen PBMCs were thawed, stained for T cell surface and memory markers, and sorted in Trizol.

extract_protocol:
100,000 PBMCs, CD4 and CD8 memory T cells were sorted and collected in Trizol in a 1.5 ml tube. Tubes were vortexed, spun and stored at -80C until processed. RNA was extracted using RNA microRNA kit (Qiagen) on a Qiacube.
Purified total RNA was amplified following the Smart-Seq2 protocol. cDNA was purified using AMPure XP beads, and barcoded Illumina sequencing libraries were generated, loaded and sequenced on the Illumina sequencing platform HiSeq 2500.

tag: disease state

value: Healthy control

value: CD8 memory T cells

tag: gender

value: Male


title: 3277_CD8m

description: processed data file: all_counts.tsv

value: Female


title: 3204_CD8m

description: processed data file: all_counts.tsv


title: WT-M-1_B: WT_male_430B_replicate1

description: gene expression of the small intestine

value: small intestine

value: 10-week old


title: 3195_CD8m

description: processed data file: all_counts.tsv


title: Fabp6KO-F-1: Fabp6KO_female_430A_replicate1

description: gene expression of the small intestine

value: Fabp6-/- C57BL/6J


title: 3190_CD8m

description: processed data file: all_counts.tsv


title: 3207_CD8m

description: processed data file: all_counts.tsv


title: 3278_CD8m

description: processed data file: all_counts.tsv


title: Fabp2KO-M-2: Fabp2KO_male_430A_replicate2

description: gene expression of the small intestine

value: Fabp2-/- C57BL/6J


title: Fabp26KO-F-2: Fabp2&6DKO_female_430A_replicate2

description: gene expression of the small intestine


title: WT-M-2: WT_male_430A_replicate2

description: gene expression of the small intestine


title: WT-M-1: WT_male_430A_replicate1

description: gene expression of the small intestine


title: WT-F-1: WT_female_430A_replicate1

description: gene expression of the small intestine


title: TNFAIP8 knockdown 3

city: Jinan

first: Yihua

last: Pang

address: Wenhuaxi road

institute: Qilu hospital

data_processing:
Raw data was filtered with SOAPnuke (version 1.5.2) by removing reads containing sequencing adapter, low-quality base(less than or equal to 5), unknown base ('N' base).
Clean data were aligned to the hg38 genome assembly performed using HISAT2 (version 2.1.0).
The expression level of gene was calculated by StringTie (version1.2.3).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normailized counts

extract_protocol:
Total RNA was extracted using TRIzol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: TNFAIP8-shRNA lentivirus


title: 3181_CD8m

description: processed data file: all_counts.tsv


title: WT-F-2: WT_female_430A_replicate2

description: gene expression of the small intestine


title: 3476_CD8m

description: processed data file: all_counts.tsv

source_name: PBMC AD

value: Alzheimer's disease


title: Control 3

value: scrambled shRNA lentivirus


title: Fabp2KO-M-1: Fabp2KO_male_430A_replicate1

description: gene expression of the small intestine


title: Heart_sham_8weeks

city: Cincinnati

first: Yasuhide

last: Kuwabara

state: Ohio

address: 240 Albert Sabin Way, Building S

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression at 8 weeks after sham operated hearts

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Heart, sham, 8W

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: total RNA was extracted with TRIZOL reagent

value: Heart

value: male

value: sham

tag: time

value: 16 weeks


title: Heart_sham_2weeks

description: Gene expression at 2 weeks after sham operated hearts

source_name: Heart, sham, 2W

value: 10 weeks


title: Heart_TAC_8weeks

description: Gene expression at 8 weeks after TAC operated hearts

source_name: Heart, TAC, 8W

value: TAC


title: Heart_TAC_2weeks

description: Gene expression at 2 weeks after TAC operated hearts

source_name: Heart, TAC,2W


title: TNFAIP8 knockdown 2


title: 3353_CD8m

description: processed data file: all_counts.tsv


title: TNFAIP8 knockdown 1


title: 3342_CD8m

description: processed data file: all_counts.tsv


title: Control 2


title: Control 1


title: SCC23 cells, siBmi1

first: Cunyu

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

description: extracting RNA after shBMI1 transfected

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm9
Supplementary_files_format_and_content: xls files including RPKM values for each RNA-seq samples.

extract_protocol:
Total RNA was extracted using the RNeasy® Mini Kit
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

tag: cell line

value: head and neck SCC cells

tag: passage

value: shBMI1 transfection


title: 3330_CD8m

description: processed data file: all_counts.tsv

value: CD8 memory T cells

value: Male


title: 3199_CD8m

description: processed data file: all_counts.tsv

value: Female


title: SCC23 cells, siCtrl

description: extracting RNA after shCtrl transfected

value: control transfection


title: SCC23 cells, PTC209

description: extracting RNA after PTC209 treatment


title: PC9-si13L-2-input

first: Nasha

last: Zhang

state: Shandong

address: No. 440 Jiyan Road

department: Cancer Research Center

institute: Shandong Cancer Hospital and Institute

data_processing:
SOAPnuke version 1.4.0 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using SOAPaligner/SOAP2 with the following setting -p 4 -v 2 -s 35.
peaks were called using MACS14 with the following setting: -s 50 -g hs -p 1e-5 -w --space 50 -m 10,30.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MACS2.

source_name: PC9 transient transfected

growth_protocol: Human PC9 cells were cultured in RPMI-1640 media supplied with 10% fetal bovine serum (Hyclone) at 37°C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with the antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: PC9 cells were transfected with miR-4497 mimics, si13L-1, si13L-2 or control siRNA.

value: lung adenocacinoma

tag: transfected with


title: PC9-Mimics-input

value: miR-4497 mimic


title: PC9-Mimics-H3K27ac

value: anti-H3K27ac(Abcam, ab4729)


title: 3165_CD8m

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: PC9-si13L-1-input


title: PC9-si13L-2-H3K27ac


title: 3180_CD8m

description: processed data file: all_counts.tsv

value: Healthy control


title: 3437_CD8m

description: processed data file: all_counts.tsv


title: PC9-si13L-1-H3K27ac


title: 3197_CD8m

description: processed data file: all_counts.tsv


title: SCC23 cells, DMSO

description: extracting RNA after DMSO treatment

value: DMSO


title: 3152_CD8m

description: processed data file: all_counts.tsv


title: PC9_NC_input

value: control siRNA


title: 3118_CD8m

description: processed data file: all_counts.tsv


title: PC9_NC-H3K27ac


title: 960-WT-Abx-Rg-IleumRNA

city: Nutley

first: Kevin

last: Tong

state: NJ

address: 111 Ideation Way

department: CDI

institute: Hackensack Meridian Health

data_processing:
Read alignment and mapping done with Kallisto, v0.45.0
Normalized abundance measurements generated by DESeq2, Build 3.9
Genome_build: mm9

source_name: Ileum

growth_protocol: 9-10-week old female germ-free C57BL/6J mice maintained in flexible isolators at the University of Arizona gnotobiotic facility were used according to an approved IACUC protocol 07-126 (to P.R.K.). Study was limited to female mice to reduce aggression upon cage transfer and experimental grouping.

extract_protocol:
RNA extraction was performed using Qiagen RNeasy Mini kit.
MGIEasy Library Prep

treatment_protocol: Fecal microbiota transplantation (FMT) was performed by administering fecal slurry prepared from pooled stools from either WT (N=9), Lyz1KO (N=9) or Villin-Lyz1TG (N=10) mice by oral gavage with 100mL of suspension and by painting the abdominal pelt with the same amount (Day 0). Upon colonization, mice were randomly assigned to control or DSS group (N=5) and transferred to Tecniplast iso-positive ventilated cages (one FMT group/treatment/cage). Mice were allowed to acclimate to the new environment for 7 days (Day 7), after which control mice were continued on autoclaved water, while DSS group received 3% DSS in drinking water for another 7 days (till day 14). Body weight was monitored daily. Mice were euthanized on day 14 and were harvested for RNA isolation..

tag: stain

value: Wildtype

value: R. gnavus

value: Antibiotic treated


title: 3831_CD8

description: processed data file: all_counts.tsv


title: 961-Lyz1KO-Abx-Rg-IleumRNA


title: 827-WT-Abx-Rg-IleumRNA


title: 649-WT-Abx-Rg-IleumRNA


title: 725-WT-IleumRNA


title: 3322_CD8

description: processed data file: all_counts.tsv


title: 630-WT-IleumRNA


title: 391-Lyz1KO-Abx-IleumRNA


title: 3183_CD8

description: processed data file: all_counts.tsv


title: 3157_CD8

description: processed data file: all_counts.tsv


title: 241-Lyz1KO-IleumRNA


title: 2983_CD8

description: processed data file: all_counts.tsv


title: 239-Lyz1KO-IleumRNA


title: 228-WT-IleumRNA


title: 2978_CD8

description: processed data file: all_counts.tsv


title: 226-WT-IleumRNA


title: 156-Lyz1KO-Abx-Rg-IleumRNA


title: 2948_CD8

description: processed data file: all_counts.tsv


title: Memory WT-4

city: Heidelberg

first: Ahmed

last: Sadik

address: Im Neunheimer Feld 280

department: Metabolic Crosstalk in Cancer

institute: DKFZ

description: Memory WTreplicate4

hyb_protocol: 3,8 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 2.0 ST Array.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

source_name: Mouse spleen CD8 T-cells

label_protocol: The Affymetrix GeneChip WT Pico Reagent Kit is used to generate labeled ss-cDNA from input amounts of 1ng total RNA.

growth_protocol: WT or Il4i1 KO BM chimeric mice were transplanted with murine CLL cells from Eµ-TCL1 mice. Effector and Knockout CD8+ T cells were sorted from spleen.

extract_protocol: RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol

value: female


title: 154-Lyz1KO-Abx-IleumRNA


title: 155-Lyz1KO-Abx-IleumRNA


title: Memory WT-2

description: Memory WTreplicate2


title: 144-Lyz1KO-IleumRNA


title: 148-Lyz1KO-Abx-Rg-IleumRNA


title: Memory WT-3

description: Memory WTreplicate3


title: Memory WT-1

description: Memory WTreplicate1


title: Memory KO-4

description: Memory KOreplicate4


title: 2930_CD8

description: processed data file: all_counts.tsv


title: Lyz1KO_ileal LPL and stromal cells

city: Newark

last: Gao

address: 195 University Avenue

department: Biological Sciences

institute: Rutgers, the State University of New Jersey

data_processing:
Cell Ranger v3.0.1 used for data processing. cDNA libraries were sequenced with a configuration of 26/8/0/98 cycles (Read1-10XBarcode+UMI/i7index/i5index, Read2-mRNA reads). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command. Subsequence UMI and cell barcode de-convolution was performed using 10X Genomics’ cellranger count command to generate the final digital gene expression matrices, t-SNE plot, and cloupe files.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files

extract_protocol: The distal ileum of adult WT and KO mice (separately housed) were dissected and briefly rinsed in ice-cold PBS (Fisher Scientific, SH30256LS). The tissue was opened longitudinally, rinsed in ice-cold PBS, and further sliced to 1-2 mm pieces. The pieces were rinsed in 30mL of ice-cold PBS by inverting the falcon tube 10-15 times. The pieces were then transferred into fresh 30ml of ice-cold PBS. This step was repeated until the solution remained clear after inverting. Each piece was then transferred to 30 mL crypt isolation buffer, containing 5 mM EDTA (Invitrogen, Catalog No.AM9260G), 2% BSA (Sigma, Catalog No.A3294), and HBSS Ca/Mg-free (Sigma, Catalog No.H9394), and allowed to shake at 37˚C for 15 minutes. The tubes were subsequently vigorously shaken to release the epithelial layer from the pieces after which the solution was discarded. This was repeated in another 30ml of crypt isolation buffer. The pieces were then incubated in DMEM/F12 medium (ThermoFisher, 12634-010) for 10 minutes on a petri dish, at room temperature. The solution was discarded, and the pieces were thoroughly minced. 10ml of Hank’s balanced salt solution with calcium and magnesium (Sigma, Catalog No.55037C) containing 100 U/mL Collagenase II (ThermoFisher, Catalog No.17101015), 500 U/mL DNase I (Sigma,  Catalog No.DN25), was added to the minced tissue and allowed to shake at 37˚C for 30 minutes. When tissues completely digested, the solution was passed through a 70µM cell strainer into a 50mL falcon tube. The tubes were centrifuged at 200g for 10 minutes. The pellets were resuspended in 1mL of FACS solution (2% BSA in PBS). The single-cell suspensions were stained with DAPI and immediately subjected to sorting by BD Biosciences Aria II Flow Cytometer (BD FACSAria II). Single viable lamina propria lymphocytes and mesenchymal cells were gated by forward scatter, side scatter and by negative staining for DAPI.  Cell number and viability were determined by a Propidium Iodide based fluorescence assay using Moxi GO II System, Orflo Prod#MXG102 (ORFLO Technologies, LLC). Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3′ Reagent v3 Kit (10X Genomics, Pleasanton, CA) on the 10X Chromium Controller as per the manufacturer’s protocol. Live cells in single cell suspension with 95% viability were mixed with Gel beads, RT reagents and Partitioning Oil into a Single-Cell 3′ Chip and loaded onto 10X Chromium Controller for GEM generation. Briefly, the protocol includes RT, cleanup, cDNA amplification, fragmentation, end repair & A-tail prep, adapter ligation and incorporation of sample indices into finished libraries, which are compatible with Illumina next-generation sequencing platforms. Sample quantification and quality control were determined using Qubit Fluorometer (Invitrogen, Life Technologies) and TapeStation (Agilent Technologies, Santa Clara CA) respectively. cDNA libraries were sequenced on Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA) with a configuration of 28/8/0/91-bp for cell barcode, sample barcode and mRNA reads respectively as recommendation by 10X Genomics.

tag: tissue

value: Ileum

value: Lamina propria lymphocytes and stromal cells

tag: genotype

tag: age

value: 6 weeks


title: Memory KO-3

description: Memory KOreplicate3


title: 3677_CD8

description: processed data file: all_counts.tsv

tag: cell type

value: CD8 memory T cells

value: Male


title: 388-WT-Abx-IleumRNA

tag: genotype/variation


title: 143-Lyz1KO-IleumRNA


title: WT_ ileal LPL and stromal cells

value: Wild type


title: 3635_CD8

description: processed data file: all_counts.tsv


title: 3420_CD8

description: processed data file: all_counts.tsv

value: Female


title: Memory KO-2

description: Memory KOreplicate2


title: 3454_CD8

description: processed data file: all_counts.tsv


title: 3417_CD8

description: processed data file: all_counts.tsv


title: Memory KO-1

description: Memory KOreplicate1


title: 3434_CD8

description: processed data file: all_counts.tsv


title: CAS1_NTC01_06

description: Biological replicate 6

hyb_protocol: According to Affymetrix WT PLUS Reagent Kit user manual,  5.5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45 °C on Affymetrix Human Gene 2.0 ST Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731)

data_processing: The Affymetrix microarray chips “human gene 2.0 ST” were analyzed using the oligo package and annotated using NetAffx4 OtCEL files were imported from disk followed by RMA normalization and summary.

label: Biotin

label_protocol: The Affymetrix WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100 ng total RNA

growth_protocol: Ctrl and IL4I1-KO CAS-1 cells (CAS-1 cells obtained from ICLC were transduced with transEDIT CRISPR All-in-one lentiviral expression vectors non-targeting control -NTC- and targeting IL4I1, transOMIC Technologies, CAHS1001-259307-GVO-TRI) were cultured in phenol-red free high glucose DMEM medium (Gibco, 31053028) supplemented with 10 % FBS (Gibco, 10270106), 2 mM L-glutamine (Gibco, 25030-024), 1 mM sodium pyruvate (Gibco, 11360-039), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco, 15140-122).

extract_protocol: Total RNA was harvested from cultured cells using the RNeasy Mini Kit (Qiagen, 80204)

treatment_protocol: CAS-1 cells with stable downregulation of IL4I1 were generated using transEDIT CRISPR All-in-one lentiviral expression vectors targeting IL4I1 (transOMIC Technologies, CAHS1001-259307-GVO-TRI). Cells were exposed to viral supernatants containing either sgControl (sgCtrl) or sgIL4I1 for 24 h, in presence of 8 μg/mL polybrene (Merck Millipore, TR-1003-G). Transduced cells were selected by sorting ZsGreen positive cells using a BD FACSAria Fusion (BD Biosciences), yielding mixed populations of non-targeting control (NTC, sgCtrl) and IL4I1 knockout (KO, sgIL4I1-2) cell lines. For the generation of clonal cell lines, single ZsGreen positive cells, derived from sgCtrl and sgIL4I1-2 cell lines, were sorted into single wells of 96-well plates. Presence of a single cell per well and single cell-derived colonies was identified during the first week after sorting. Single cell-derived clones were expanded and validation of IL4I1 KO was confirmed by qRT-PCR and IL4I1 enzymatic activity. The mixed population-based sgCtrl and the clonal cell lines sgCtrl.01 (NTC.01) and sgIL4I1-2.4 were used for experiments. For gene expression experiments involving Ctrl and IL4I1-KO CAS-1 cells, 4 x 105 cells per well were seeded in 2 mL of complete DMEM medium in six well plates and incubated for 24 h. Complete DMEM was replaced with 1.5 mL of FBS-free DMEM medium and cells were incubated for 72 h.

tag: experiment

tag: condition


title: Effector WT-3

description: Effector WTreplicate3


title: 3407_CD8

description: processed data file: all_counts.tsv


title: CAS1_NTC01_05

description: Biological replicate 5


title: Effector WT-2

description: Effector WTreplicate2


title: Effector WT-4

description: Effector WTreplicate4


title: 3344_CD8

description: processed data file: all_counts.tsv


title: RNA_XEN5

tag: strain background

value: WT

value: Extraembryonic endoderm stem cells (XENs)


title: CAS1_NTC01_04

description: Biological replicate 4


title: CAS1_NTC01_02

description: Biological replicate 2


title: CAS1_NTC01_01

description: Biological replicate 1


title: CAS1_NTC_05

description: Biological replicate 5

value: NTC


title: Effector KO-4

description: Effector KOreplicate4

tag: strain


title: Effector KO-3

description: Effector KOreplicate3


title: RNA_XENB1


title: Effector WT-1

description: Effector WTreplicate1


title: 3292_CD8

description: processed data file: all_counts.tsv

tag: disease state

value: Healthy control


title: CAS1_NTC_04

description: Biological replicate 4


title: CAS1_NTC_03

description: Biological replicate 3


title: Effector KO-1

description: Effector KOreplicate1

tag: gender


title: CAS1_NTC_06

description: Biological replicate 6


title: Effector KO-2

description: Effector KOreplicate2


title: CAS1_NTC_02

description: Biological replicate 2


title: CAS1_IL4I1_KO_05

description: Biological replicate 5


title: CAS1_NTC01_03

description: Biological replicate 3


title: BB_androgenetic_blasto_DNAme_rep2

city: Vancouver

first: Matthew

last: Lorincz

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

institute: University of British Columbia

description: Post-Bisulfite Adaptor Tagging (PBAT)

data_processing:
Reads were trimmed using Trimmomatic v0.32
Trimmed reads were aligned to the mm10 reference genome and a diploid pseudogenome using MEA and default parameters (Richard Albert et al. 2018)
RNA-seq: PCR duplicates and multi-aligned reads (q<255) were filtered out using Picard tools v1.92 and samtools v1.1
WGBS: PCR duplicates were filtered out using Picard tools v1.92 and samtools v1.1
Aligned read maps were converted to Wiggle format using bedtools v2.22.1 and bedGraphToBigWig (UCSC).
RNA-seq: total and allele-specific tracks were normalized by the number of uniquely aligned total reads
Genome_build: mm10
Supplementary_files_format_and_content: 3x bigWigs (total, maternal, paternal)

extract_protocol:
5 blastocyst pools were collected in triplicate.
Lysates of androgenetic blastocysts were spiked with 0.1 ng lambda phage DNA and subjected to WGBS library construction according to the PBAT protocol for single-read sequencing (Miura et al. 2012, Kobayashi et al. 2013).

tag: developmental stage

value: androgenetic blastocyst

value: 2X paternal (C57BL/6NJcl) genomes

tag: molecule subtype

value: bisulphite converted genomic DNA


title: BB_androgenetic_blasto_DNAme_rep1

description: Post-Bisulfite Adaptor Tagging (PBAT)


title: 3279_CD8

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: H1299-radiation treatment

hyb_protocol: The pre-hybridization of HmiOA v7.1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on HmiOAv7.1 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 520-550 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
Among the probe triplicates, the median value were selected into signal normalization processed by R program (2.12.1). We ﬁltered out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling normalization method.
Based on the normalized intensities, we calculate average ratios and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: H1299-radiation treatment

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy5, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

growth_protocol: Human A549 and H1299 cells were cultured in RPMI-1640 media supplied with 10% fetal bovine serum (Hyclone) at 37°C with 5% CO2.

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: A549 and H1299 cells treated with X-ray radiation (4.906Gy or 1.529Gy).

tag: cell line

value: NSCLC


title: 3182_CD8

description: processed data file: all_counts.tsv


title: BD_2C_Dnmt3aMatKO_DNAme_rep1

description: Post-Bisulfite Adaptor Tagging (PBAT)

extract_protocol:
Cumulus cells were removed using hyaluronidase after insemination and embryos were cultured in KSOM at 37oC and 5% CO2. Zona pellucida and polar bodies of 2C embryos were removed.
DNA from 20-30 pooled 2C embryos per replicate was purified and spiked with 1% unmethylated lambda phage DNA, and WGBS libraries were generated by PBAT with 4 cycles of library amplification (Au Yeung et al. 2019, Miura et al. 2012).

value: C57BL/6J x DBA/2J F1 hybrid

value: early-mid 2 cell embryo

value: Dnmt3a2lox;Zp3-cre x WT


title: CAS1_NTC_01

description: Biological replicate 1


title: H1299-control


title: A549-radiation treatment

source_name: A549-radiation treatment


title: CAS1_IL4I1_KO_03

description: Biological replicate 3


title: CAS1_IL4I1_KO_04

description: Biological replicate 4


title: 3175_CD8

description: processed data file: all_counts.tsv


title: 3170_CD8

description: processed data file: all_counts.tsv


title: A549-control


title: Adult MG RNA-seq

city: Seattle

first: Thomas

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structure

institute: University of Washington

description: Adult MG RNA-seq

data_processing:
ATAC filtration:  Adapter and barcode sequence were removed from the reads and low-quality sequences (Phred score <33) were removed using Trim Galore (Krueger 2015)
ATAC mappting: Remaining reads were mapped using Bowtie2 (Langmead and Salzberg 2012), marking duplicate reads with Picard (http://broadinstitute.github.io/picard/), and removing reads using Samtools (Li et al. 2009).
ATAC-seq peak calling: Peaks were called using HOMER (Heinz et al. 2010) findPeaks dnase style with a minimum distance of 415 and size of 150.
ATAC peak overlaps: Bedops -e 1 function was used to compare peak files for overlaps between samples(Neph et al. 2012)
RNA-seq mapping: Reads that passed Illumina’s base call quality filter were mapped to mm10 using TopHat v2.0.12
RNA-seq counts: To generate counts for each gene using htSeq-count v0.6.1p1, in “intersection-strict” overlap mode, genes with zero counts across all samples were removed, and data normalized using edgeR v3.12.0.
RNA-seq thin counts:  Further analysis was done using Bioconductor and R (version 3.2.3).  Prior to testing, samples with higher reads were thinned to the level of other samples using thinCounts.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files in bed or xlsx file format

source_name: Retinal Müller glia

extract_protocol:
Retinas were isolated via dissection away from surrounding tissues and then washed in PBS. Fluorescence was confirmed via live imaging under an inverted fluorescent microscope (Zeiss). Retinas were then incubated on a nutator in Papain and DNase I for 10 min at 37 °C. Retinas were then triturated to generate a single-cell suspension and transferred to a tube containing an equal volume of Ovomucoid. The suspension was then spun down at 300g for 10 min at 4 °C. Cells were resuspended in a solution of 100:1:1 Neurobasal:DNase:Ovomucoid, and passed through a 35 μm filter before sorting using a BD FACSAria III Cell Sorter (BD Biosciences). Gating was performed to isolate intact cells from debris and to isolate positive fluorescent glial or progenitor cells. Progenitor cells were isolated from Sox2+ Amacrine cells by removing the higher fluorescent neuronal population. Positive fractions containing fluorescently labelled MG were then spun down at 300g and resuspended for the appropriate assay.
For RNA-Seq, FAC-sorted cells were resuspended into Qiazol and RNA was extracted using the Qiagen RNeasy MinElute kit. Samples were tested for QC using nanodrop, and sent for sequencing. 500 ng per sample (50 ng μl−1) was sequenced on an Illumina HiSeq.
ATAC libraries were prepared through subsequent PCR using Illumina Nextera kit (Cat. No. FC-121-1030) using a test qPCR output to estimate the number of cycles necessary to properly amplify the library. Amplified libraries were purified with the Qiagen PCR cleanup minelute kit and eluted into 20 μl. Library QC was performed using gel electrophoresis, and quantitated on a Qubit 3.0 Fluorometer with the dsDNA HS Assay kit and A260/280 and A260/230 checked by nanodrop before sending for Illumina NextGen sequencing on a Next Seq 500 in rapid mode employing a paired-end 50 base read length sequencing strategy (Seattle Genomics). RNA-seq libraries were prepared for sequencing using standard Illumina protocols

value: Adult

value: rlbp-creER;flox-stop-tdtomato


title: CAS1_IL4I1_KO_01

description: Biological replicate 1


title: 3155_CD8

description: processed data file: all_counts.tsv

value: CD8 memory T cells


title: CAS1_IL4I1_KO_02

description: Biological replicate 2


title: P8 MG RNA-seq

description: P8 MG RNA-seq


title: P2 Progenitor RNA-seq

description: P2 Progenitor RNA-seq

source_name: Retinal Progenitor cells


title: 3189_CD8

description: processed data file: all_counts.tsv


title: 3153_CD8

description: processed data file: all_counts.tsv

value: Male


title: BD_2C_Dnmt3aMatWT_DNAme_rep1

description: Post-Bisulfite Adaptor Tagging (PBAT)

value: Dnmt3a2lox x WT


title: U-87MG_SMI 03 - 04

description: Biological replicate 4

hyb_protocol: According to Affymetrix WT PLUS Reagent Kit user manual,  5.5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Affymetrix Human Gene 2.0 ST Arrays.

data_processing:
The Affymetrix microarray chips “human gene 2.0 ST” were analyzed using the oligo package and annotated using NetAffx4 OtCEL files were imported from disk or ded by RMA normalization and summary.
Probes were filtered out during the normalization steps, resulting in ~16K IDs.

label_protocol: The Affymetrix WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100ng total RNA

growth_protocol: Human GBM cell line U-87MG was obtained from ATCC. Cells were cultivated in complete DMEM medium. At 80-90% confluency cells were harvested and seeded for experiments.

treatment_protocol: Cells were treated with a concentration of 25µM I3P or 1µM SR1 either alone or in combination treatments. Control cells were treated with the carrier control i.e. 0.1% DMSO.

value: I3P + SR1


title: 3139_CD8

description: processed data file: all_counts.tsv


title: U-87MG_SMI 03 - 03

description: Biological replicate 4


title: 3125_CD8

description: processed data file: all_counts.tsv


title: P12 MG RNA-seq

description: P12 MG RNA-seq


title: Input-Mel-CtrlshRNA

city: Boston

first: Jialiang

last: Huang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: Input-Mel-CtrlshRNA.bw

data_processing:
RNA-seq reads were aligned to the reference mouse genome mm10 using STAR (Dobin et al., 2013) with default parameters. Aligned reads were counted in the genomic transcripts annotations from GenomicFeatures (Lawrence et al., 2013) using Rsamtools (Morgan M, 2016).
ATAC-seq data were trimmed for adapter sequences and low alignment quality using Cutadapt (Ref. XXX), with parameters -q 30 --minimum-length 36. Paired-end reads were aligned to mm10 using Bowtie2 (Langmead et al., 2009) using the parameter -X 2000 allowing fragments of up to 2 kb to align (Buenrostro et al., 2015). ATAC-seq peaks were called using MACS2 (Zhang et al., 2008) with following parameters (--nomodel --nolambda --keep-dup all --call-summits) (Buenrostro et al., 2015).
ChIP-seq data were aligned to mm10 using Bowtie2 (Langmead et al., 2009) with default parameters. Duplicates were removed and library size was estimated using PICARD tools (http://picard.sourceforge.net). ChIP-seq peaks were called using MACS2 (Zhang et al., 2008) with following parameters (--nomodel --keep-dup 1 --extsize=146 -q 0.01).
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig  generated using macs2 pileup, following by bedGraphToBigWig; Peak  were called using MACS2 ;tab-delimited text files include log2(cpm+1) values for RNA-seq Samples

source_name: Mel cell, control shRNA

growth_protocol: EryP was collected from peripheral blood of E10.5 mouse embryos in HBSS supplemented with 10% FBS and 0.25% EDTA. EryD was collected by mechanically dissociation of E13.5 whole fetal liver. All mouse embryos were obtained from C57BL/6 mouse. MEL cells were cultured in DMEM supplemented with 10% fetal bovine serum, 2mM L-glutamine and Penicillin and Streptomycin. 2% DMSO in culture medium was used to induce MEL cells differentiation. Medium was changed on differentiation day 3.

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher) and was cleaned with RNeasy Plus Mini Kit (QIAGEN) following manufacturer’s instructions. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (Thermo Fisher).
ChIP-seq libraries were constructed using Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. RNA-seq library was prepared using Next Ultra Directional RNA Library Prep Kit Illumina (New England Biolabs). ATAC-seq libraries were generated using Ad1_noMX and Ad2.1-2.4 barcoded primers and were amplified for 6-9 total cycles.

treatment_protocol: 1,000,000 MEL cells were mixed with lenti virus of Phf19 shRNAs (Sigma), human PHF19 shRNAs (Sigma), Dox-inducible Myb shRNAs (Sigma), and control shRNA (Sigma), supplemented with 10ug/ml polybrene (Sigma-Aldrich). Lentiviral vectors bearing the coding sequence of the Puromycin-resistance gene permitted a positive selection of 2mg/ml Puromycin (Sigma-Aldrich) treatment.

value: Mel cell

tag: chip antibody


title: CAS1_IL4I1_KO_06

description: Biological replicate 6


title: 3169_CD8

description: processed data file: all_counts.tsv


title: Peripheral blood, Subject 4

first: Mandakh

last: Bekhbat

address: 1365 Clifton Rd NE, Room 5204

department: Psychiatry and Behavioral Sciences

institute: Emory University

description:
replicate 1
4.AVG_Signal

hyb_protocol: Hybridization to Illumina Human HT-12 Expression BeadChips (Illumina) was performed using the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina) and standard Illumina hybridization protocol.

scan_protocol: BeadChips were scanned on the Illumina HiScan (Illumina) using standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in GenomeStudio version 1.9.0.

source_name: Human peripheral blood

label_protocol: Each sample was linearly amplified by TotalPrep-96 RNA Amplification Kit for Array Analysis (Illumina, San Diego CA, USA).

extract_protocol: RNA was extracted using Ambion Tempus RNA Spin kit (Thermo Fisher, Asheville, NC, USA) according to manufacturer instructions. Quality control was performed using Tecan iControl (Life Sciences, Switzerland) and with the Agilent Bioanalyzer 2100 RNA Nano assay (Agilent, Santa Clara, CA, USA).

tag: individual

value: Subject 4

tag: Sex

tag: bmi

tag: race

value: Black

tag: hamd score excluding item 8

tag: college (yes/no)

tag: psychomotor composite score

value: peripheral blood


title: Peripheral blood, Subject 22

description:
replicate 1
22.AVG_Signal

value: Subject 22

tag: age

value: Female

value: White

tag: tissue


title: Input-Mel-MybshRNA

description: Input-Mel-MybshRNA.bw

source_name: Mel cell, Myb shRNA

tag: cell type


title: H3K27ac-Mel-MybshRNA

description:
H3K27ac-Mel-MybshRNA.bw
H3K27ac-Mel-MybshRNA.bed

value: H3K27ac (Active Motif, 39133)


title: Peripheral blood, Subject 5

description:
replicate 1
5.AVG_Signal

value: Subject 5


title: 3115_CD8

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: Peripheral blood, Subject 3

description:
replicate 1
3.AVG_Signal

value: Subject 3


title: H3K27ac-Mel-CtrlshRNA

description:
H3K27ac-Mel-CtrlshRNA.bw
H3K27ac-Mel-CtrlshRNA.bed


title: 3022_CD8

description: processed data file: all_counts.tsv


title: Gata1-Mel-MybshRNA

description:
Gata1-Mel-MybshRNA.bw
Gata1-Mel-MybshRNA.bed

value: Gata1 (Abcam, ab11852)


title: U-87MG_SMI 02 - 04

description: Biological replicate 3

tag: experiment

tag: condition


title: U-87MG_SMI 02 - 03

description: Biological replicate 3


title: U-87MG_SMI 03 - 02

description: Biological replicate 4


title: 3019_CD8

description: processed data file: all_counts.tsv

tag: disease state

value: Healthy control

tag: gender


title: U-87MG_SMI 03 - 01

description: Biological replicate 4

value: DMSO


title: Gata1-Mel-CtrlshRNA

description:
Gata1-Mel-CtrlshRNA.bw
Gata1-Mel-CtrlshRNA.bed


title: 2972_CD8

description: processed data file: all_counts.tsv

value: CD8 memory T cells


title: U-87MG_SMI 02 - 02

description: Biological replicate 3


title: Peripheral blood, Subject 34

description:
replicate 1
34.AVG_Signal

value: Subject 34


title: Input-FL-Fbbio

description: Input-FL-Fbbio.bw

source_name: Fetal liver, P300-FB-biotin

value: Fetal liver

tag: developmental stage


title: U-87MG_SMI 02 - 01

description: Biological replicate 3

tag: cell line


title: Peripheral blood, Subject 35

description:
replicate 1
35.AVG_Signal

value: Subject 35


title: Peripheral blood, Subject 56

description:
replicate 1
56.AVG_Signal

value: Subject 56

value: Male


title: U-87MG_SLI_A57_04

description: Biological replicate 2


title: P300-FL-Fbbio-Rep3

description:
P300-FL-Fbbio.bw
P300-FL-Fbbio.bed

tag: chip antibody


title: 3015_CD8

description: processed data file: all_counts.tsv

source_name: PBMC HC


title: Peripheral blood, Subject 9

description:
replicate 1
9.AVG_Signal

tag: individual

value: Subject 9

value: peripheral blood


title: 2999_CD8

description: processed data file: all_counts.tsv

value: Female


title: 2964_CD8

description: processed data file: all_counts.tsv


title: U-87MG_SLI_A57_03

description: Biological replicate 2

value: I3P + SR1


title: P300-FL-Fbbio-Rep1

description:
P300-FL-Fbbio.bw
P300-FL-Fbbio.bed


title: P300-FL-Fbbio-Rep2

description:
P300-FL-Fbbio.bw
P300-FL-Fbbio.bed


title: Input-FL

description: Input-FL.bw

source_name: Fetal liver


title: U-87MG_SLI_A57_01

description: Biological replicate 2


title: U-87MG_SLI_A56_03

description: Biological replicate 1


title: U-87MG_SLI_A56_04

description: Biological replicate 1


title: Peripheral blood, Subject 42

description:
replicate 1
42.AVG_Signal

value: Subject 42

tag: Sex

value: White


title: Peripheral blood, Subject 87

description:
replicate 1
87.AVG_Signal

value: Subject 87

tag: bmi


title: Myb-FL-Rep2

description:
Myb-FL.bw
Myb-FL.bed

value: Myb (Abcam, ab45150)


title: Peripheral blood, Subject 52

description:
replicate 1
52.AVG_Signal

value: Subject 52

tag: race

value: Black


title: Peripheral blood, Subject 67

description:
replicate 1
67.AVG_Signal

value: Subject 67

tag: hamd score excluding item 8


title: 2951_CD8

description: processed data file: all_counts.tsv

value: Healthy control

value: CD8 memory T cells


title: 2950_CD8

description: processed data file: all_counts.tsv


title: U-87MG_SLI_A57_02

description: Biological replicate 2


title: 2965_CD8

description: processed data file: all_counts.tsv


title: Myb-FL-Rep1

description:
Myb-FL.bw
Myb-FL.bed

value: Fetal liver


title: Peripheral blood, Subject 94

description:
replicate 1
94.AVG_Signal

value: Subject 94

tag: college (yes/no)


title: Peripheral blood, Subject 97

description:
replicate 1
97.AVG_Signal

value: Subject 97

tag: psychomotor composite score


title: Peripheral blood, Subject 106

description:
replicate 1
106.AVG_Signal

value: Subject 106

tag: age


title: 3345_CD4m

description: processed data file: all_counts.tsv

value: CD4 memory T cells

value: Male


title: Tal1-EryD

description:
Tal1-EryD.bw
Tal1-EryD.bed

source_name: Definitive erythroblast

value: erythroblast

value: Tal1 (Santa Cruz, sc-12984X)


title: Tal1-EryP

description:
Tal1-EryP.bw
Tal1-EryP.bed

source_name: Primitive erythroblast


title: 3278_CD4m

description: processed data file: all_counts.tsv


title: 3277_CD4m

description: processed data file: all_counts.tsv

value: Female


title: U-87MG_SLI_A56_01

description: Biological replicate 1

value: DMSO


title: 3207_CD4m

description: processed data file: all_counts.tsv


title: Gata1-EryD

description:
Gata1-EryD.bw
Gata1-EryD.bed

value: Gata1 (Abcam, ab11852)


title: Gata1-EryP

description:
Gata1-EryP.bw
Gata1-EryP.bed


title: 3195_CD4m

description: processed data file: all_counts.tsv


title: U-87MG_SLI_A56_02

description: Biological replicate 1


title: Input-EryD-Rep2

description: Input-EryD.bw


title: Peripheral blood, Subject 49

description:
replicate 1
49.AVG_Signal

value: Subject 49

value: White

tag: tissue

value: peripheral blood


title: Input-EryD-Rep1

description: Input-EryD.bw

tag: cell type


title: 3190_CD4m

description: processed data file: all_counts.tsv


title: Peripheral blood, Subject 17

description:
replicate 1
17.AVG_Signal

value: Subject 17


title: IL4I1_shAHR_U87_IL4I1_shC_02

description: Biological replicate 2

data_processing: The Affymetrix microarray chips “human gene 2.0 ST” were analyzed using the oligo package and annotated using NetAffx4 OtCEL files were imported from disk or ded by RMA normalization and summary.

growth_protocol: U-87MG, shCtrl and shAHR U-87MG cells expressing IL4I1 were cultured in phenol-red free high glucose DMEM medium (Gibco, 31053028) supplemented with 10 % FBS (Gibco, 10270106), 2 mM L-glutamine (Gibco, 25030-024), 1 mM sodium pyruvate (Gibco, 11360-039), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco, 15140-122).

treatment_protocol: For treatment of U-87MG or shCtrl U-87MG cells with established and presumed AHR ligands (FICZ, KynA, I3CA, I3P, HPP, PP), 4 x 105 cells per well were seeded in six well plates and incubated for 24 h prior to treatment. Cells were treated metabolites for 24 h. DMSO was used as a solvent with a maximal final concentration of 0.2 % in culture medium. IL4I1_shAHR_U87: Human IL4I1 cDNA clone flanked by Gateway compatible recombination sites was purchased from MyBiosource (MBS1270935). The cDNA clone was recombined into the lentivirus compatible Gateway expression vector pLX301 (a gift from D. Root, Addgene plasmid 25895). Production of lentiviruses was achieved by transfecting HEK293T with pMD2.G (a gift from D. Trono, Addgene plasmid 12259), psPAX2 (a gift from D. Trono, Addgene plasmid 12260), and lentiviral plasmid, using FuGENE HD (Promega, E2311) according to the manufacturer's protocol. Viral supernatants were harvested at 48 h and 72 h, pooled and filtered through a 0.45 μm pore filter. Stable IL4I1-expressing (pLX301-IL4I1) and control (pLX301) cell lines were generated by infecting U-87MG cells for 24 hours with respective viral supernatants in presence of 8 μg/mL polybrene (Merck Millipore, TR-1003-G), followed by selection with medium containing 1 μg/mL puromycin (AppliChem, A2856). Stable expression of IL4I1 was confirmed by qRT-PCR, western blot and IL4I1 enzymatic activity. Stable knockdown of AHR in U-87MG cells was achieved using shERWOOD UltramiR lentiviral shRNA targeting AHR (transOMIC Technologies, TLHSU1400-196-GVO-TRI). Glioma cells were infected with viral supernatants containing either shAHR#1 (ULTRA-3234821), shAHR#2 (ULTRA-3234823) or shControl (shCtrl, ULTRA-NT#4) sequences to generate stable cell lines. For gene expression experiments involving shCtrl and shAHR U-87MG cells expressing IL4I1, 4 x 105 cells per well were seeded in 2 mL in six well plates and incubated for 120 h.

tag: experiment


title: Input-EryP-Rep2

description: Input-EryP.bw


title: IL4I1_shAHR_U87_IL4I1_shC_03

description: Biological replicate 3

tag: condition


title: IL4I1_shAHR_U87_IL4I1_shAHR2_03

description: Biological replicate 3


title: Peripheral blood, Subject 39

description:
replicate 1
39.AVG_Signal

value: Subject 39

value: Black


title: IL4I1_shAHR_U87_IL4I1_shC_01

description: Biological replicate 1


title: Peripheral blood, Subject 100

description:
replicate 1
100.AVG_Signal

value: Subject 100


title: 3204_CD4m

description: processed data file: all_counts.tsv

tag: disease state

value: Healthy control


title: IL4I1_shAHR_U87_IL4I1_shAHR2_02

description: Biological replicate 2


title: 3180_CD4m

description: processed data file: all_counts.tsv

tag: gender


title: 3476_CD4m

description: processed data file: all_counts.tsv

source_name: PBMC AD

value: Alzheimer's disease


title: Peripheral blood, Subject 84

description:
replicate 1
84.AVG_Signal

value: Subject 84


title: Peripheral blood, Subject 63

description:
replicate 1
63.AVG_Signal

value: Subject 63


title: IL4I1_shAHR_U87_IL4I1_shAHR2_01

description: Biological replicate 1


title: H3K27ac-EryD-Rep2

description:
H3K27ac-EryD.bw
H3K27ac-EryD.bed

tag: developmental stage

value: H3K27ac (Active Motif, 39133)


title: IL4I1_shAHR_U87_IL4I1_shAHR1_03

description: Biological replicate 3

tag: cell line


title: 3181_CD4m

description: processed data file: all_counts.tsv

value: CD4 memory T cells


title: Peripheral blood, Subject 90

description:
replicate 1
90.AVG_Signal

value: Subject 90


title: H3K27ac-EryD-Rep1

description:
H3K27ac-EryD.bw
H3K27ac-EryD.bed

value: erythroblast

tag: chip antibody


title: IL4I1_shAHR_U87_IL4I1_shAHR1_02

description: Biological replicate 2


title: IL4I1_shAHR_U87_IL4I1_shAHR1_01

description: Biological replicate 1


title: Peripheral blood, Subject 10

description:
replicate 1
10.AVG_Signal

tag: individual

value: Subject 10

value: Female


title: H3K27ac-EryP-Rep2

description:
H3K27ac-EryP.bw
H3K27ac-EryP.bed


title: 3353_CD4m

description: processed data file: all_counts.tsv

value: Male


title: 3342_CD4m

description: processed data file: all_counts.tsv


title: Input-EryP-Rep1

description: Input-EryP.bw


title: Peripheral blood, Subject 6

description:
replicate 1
6.AVG_Signal

value: Subject 6

tag: Sex

value: White


title: IL4I1_shAHR_U87_C_shC_03

description: Biological replicate 3

value: shC


title: H3K27ac-EryP-Rep1

description:
H3K27ac-EryP.bw
H3K27ac-EryP.bed


title: IL4I1_shAHR_U87_C_shAHR2_03

description: Biological replicate 3


title: Peripheral blood, Subject 14

description:
replicate 1
14.AVG_Signal

value: Subject 14

tag: bmi

value: peripheral blood


title: IL4I1_shAHR_U87_C_shC_01

description: Biological replicate 1


title: IL4I1_shAHR_U87_C_shC_02

description: Biological replicate 2


title: ATACseq-EryD

description:
ATACseq-EryD.bw
ATACseq-EryD.bed


title: Peripheral blood, Subject 96

description:
replicate 1
96.AVG_Signal

value: Subject 96

tag: race

value: Black


title: Peripheral blood, Subject 55

description:
replicate 1
55.AVG_Signal

value: Subject 55

tag: hamd score excluding item 8


title: 3199_CD4m

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: 3330_CD4m

description: processed data file: all_counts.tsv


title: 3437_CD4m

description: processed data file: all_counts.tsv


title: ATACseq-EryP

description:
ATACseq-EryP.bw
ATACseq-EryP.bed


title: RNAseq-EryD-Rep3


title: IL4I1_shAHR_U87_C_shAHR2_02

description: Biological replicate 2


title: 3165_CD4m

description: processed data file: all_counts.tsv


title: 3152_CD4m

description: processed data file: all_counts.tsv


title: RNAseq-EryD-Rep2


title: Peripheral blood, Subject 99

description:
replicate 1
99.AVG_Signal

value: Subject 99

tag: college (yes/no)


title: RNAseq-EryD-Rep1


title: 3118_CD4m

description: processed data file: all_counts.tsv


title: IL4I1_shAHR_U87_C_shAHR1_03

description: Biological replicate 3


title: Peripheral blood, Subject 72

description:
replicate 1
72.AVG_Signal

value: Subject 72

tag: psychomotor composite score


title: 3831_CD4

description: processed data file: all_counts.tsv

value: Healthy control

value: CD4 memory T cells


title: Peripheral blood, Subject 82

description:
replicate 1
82.AVG_Signal

value: Subject 82

tag: age


title: RNAseq-EryP-Rep3

value: erythroblast


title: Peripheral blood, Subject 45

description:
replicate 1
45.AVG_Signal

value: Subject 45

value: Female

tag: tissue


title: Peripheral blood, Subject 40

description:
replicate 1
40.AVG_Signal

value: Subject 40

value: Male


title: 3322_CD4

description: processed data file: all_counts.tsv

tag: cell type


title: IL4I1_shAHR_U87_C_shAHR2_01

description: Biological replicate 1

tag: experiment


title: RNAseq-EryP-Rep1


title: 3183_CD4

description: processed data file: all_counts.tsv


title: 3157_CD4

description: processed data file: all_counts.tsv


title: Peripheral blood, Subject 51

description:
replicate 1
51.AVG_Signal

value: Subject 51

value: White


title: IL4I1_shAHR_U87_C_shAHR1_01

description: Biological replicate 1

tag: condition


title: I3P_HPP_PP_U87_PP40uM_05

description: Biological replicate 5

tag: agent

value: PP 40uM


title: I3P_HPP_PP_U87_PP40uM_04

description: Biological replicate 4


title: 2983_CD4

description: processed data file: all_counts.tsv

tag: disease state

tag: gender


title: RNAseq-EryP-Rep2

tag: developmental stage


title: I3P_HPP_PP_U87_PP40uM_03

description: Biological replicate 3

tag: cell line


title: IL4I1_shAHR_U87_C_shAHR1_02

description: Biological replicate 2


title: I3P_HPP_PP_U87_PP40uM_02

description: Biological replicate 2


title: RRBS_Jurkat_rep4

city: Charlottesville

first: Zhenjia

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
ChIP-seq sequence reads were aligned to the hg38 genome using bwa, MACS2 was used to call peaks.
RNA-seq datasets were processed using Salmon followed with Deseq2.
Hi-C data were processed using HiC-Pro.
Methylation calls were performed with Bismark.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: bigwig

source_name: Jurkat

extract_protocol:
Bisulfite conversion was performed with the Zymo Research Pico Methyl-Seq Library Prep Kit
Libraries were prepped with the Zymo Research Pico Methyl-Seq Library Prep Kit
Bisulfite conversion was performed with the Zymo Research Pico Methyl-Seq Library Prep Kit
Libraries were prepped with the Zymo Research Pico Methyl-Seq Library Prep Kit

value: Jurkat


title: RRBS_Jurkat_rep5


title: 2978_CD4

description: processed data file: all_counts.tsv

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the human GRCh38 reference using STAR (v 2.6.1c).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5) and features with 0 counts across all samples were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: all_counts.tsv: Tab-separated count matrix with rows as genes and columns as samples.


title: Peripheral blood, Subject 2

city: Atlanta

description:
replicate 1
2.AVG_Signal

tag: individual

value: Subject 2

value: peripheral blood


title: RRBS_Jurkat_rep3


title: ChIP-seq_CUTLL1_SMC3_input

data_processing:
ChIP-seq sequence reads were aligned to the hg38 genome using bwa, MACS2 was used to call peaks.
ATAC-seq sequence reads were aligned to the hg38 genome using bowtie.
RNA-seq datasets were processed using Salmon.
Hi-C data were processed using HiC-Pro.
Methylation calls were performed with Bismark.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: peak

growth_protocol: RPMI supplemented with 10% FBS, 1x glutamine and 1x penicillin/streptamycin

extract_protocol:
1% formaldehyde crosslinking for 10 minutes and nuclei isolated and sonicated with Qsonica Q500 micro tip
Illumina TruSeq DNA sample library prep kit

treatment_protocol: Normal growth conditions

tag: antibody


title: Peripheral blood, Subject 29

description:
replicate 1
29.AVG_Signal

value: Subject 29

tag: Sex

tag: bmi


title: 2948_CD4

description: processed data file: all_counts.tsv

extract_protocol:
100,000 PBMCs, CD4 and CD8 memory T cells were sorted and collected in Trizol in a 1.5 ml tube. Tubes were vortexed, spun and stored at -80C until processed. RNA was extracted using RNA microRNA kit (Qiagen) on a Qiacube.
Purified total RNA was amplified following the Smart-Seq2 protocol. cDNA was purified using AMPure XP beads, and barcoded Illumina sequencing libraries were generated, loaded and sequenced on the Illumina sequencing platform HiSeq 2500.


title: Peripheral blood, Subject 59

description:
replicate 1
59.AVG_Signal

value: Subject 59

tag: race

tag: hamd score excluding item 8


title: Peripheral blood, Subject 93

description:
replicate 1
93.AVG_Signal

value: Subject 93

value: Black

tag: college (yes/no)

tag: psychomotor composite score


title: I3P_HPP_PP_U87_I3P40uM_05

description: Biological replicate 5

value: I3P 40uM


title: ChIP-seq_CUTLL1_SMC3_rep2


title: I3P_HPP_PP_U87_PP40uM_01

description: Biological replicate 1


title: Peripheral blood, Subject 112

description:
replicate 1
112.AVG_Signal

value: Subject 112

tag: age

tag: tissue


title: 2930_CD4

description: processed data file: all_counts.tsv

value: Healthy control

tag: cell type

value: CD4 memory T cells


title: ChIP-seq_CUTLL1_SMC3_rep1


title: Peripheral blood, Subject 107

description:
replicate 1
107.AVG_Signal

value: Subject 107


title: 3677_CD4

description: processed data file: all_counts.tsv


title: Peripheral blood, Subject 101

description:
replicate 1
101.AVG_Signal

value: Subject 101


title: 3635_CD4

description: processed data file: all_counts.tsv

value: Male


title: ATAC-seq_Jurkat_GSI_washout

extract_protocol:
Zymo DNA Clean & Concentrator Kit
Transposed libraries were prepped with NEBNext master mix and ATAC-seq dual index adapters

treatment_protocol: Inhibitor replenished every 24 hours and washed out 16 hours before collection

tag: treatment

value: Gamma secretase inhibitor, 72 hours with 16 hour washout


title: Peripheral blood, Subject 7

description:
replicate 1
7.AVG_Signal

value: Subject 7

value: Female


title: I3P_HPP_PP_U87_I3P40uM_03

description: Biological replicate 3

tag: experiment

tag: agent


title: 3420_CD4

description: processed data file: all_counts.tsv

tag: disease state

tag: gender


title: Peripheral blood, Subject 115

description:
replicate 1
115.AVG_Signal

value: Subject 115

value: White


title: ATAC-seq_Jurkat_DMSO

treatment_protocol: DMSO added in same volume as inhibitor every 24 hours and 4 hours before collection

value: Jurkat

value: DMSO 72 hours


title: 3454_CD4

description: processed data file: all_counts.tsv


title: RRBS_Patient2

data_processing:
ChIP-seq sequence reads were aligned to the hg38 genome using bwa, MACS2 was used to call peaks.
ATAC-seq sequence reads were aligned to the hg38 genome using bowtie.
RNA-seq datasets were processed using Salmon.
Hi-C data were processed using HiC-Pro.
Methylation calls were performed with Bismark.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: ChIP-seq: peak file in BED, RNA-seq: transcript level quantification from salmon, Hi-C: raw matrix, DNA methylation: bigwig or bismark.cov

source_name: Patient xenograft

extract_protocol:
Bisulfite conversion was performed with the Zymo Research Pico Methyl-Seq Library Prep Kit
Libraries were prepped with the Zymo Research Pico Methyl-Seq Library Prep Kit

value: T-ALL from patient xenograft


title: ATAC-seq_Jurkat_GSI_3d

treatment_protocol: Inhibitor replenished every 24 hours and 4 hours before collection

value: Gamma secretase inhibitor, 72 hours


title: 3417_CD4

description: processed data file: all_counts.tsv


title: I3P_HPP_PP_U87_I3P40uM_02

description: Biological replicate 2

tag: cell line


title: 3434_CD4

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: RRBS_Patient1


title: RRBS_Jurkat_rep2


title: 3407_CD4

description: processed data file: all_counts.tsv


title: I3P_HPP_PP_U87_I3P40uM_04

description: Biological replicate 4

value: I3P 40uM


title: I3P_HPP_PP_U87_HPP40uM_02

description: Biological replicate 2

value: HPP 40uM


title: RRBS_Jurkat_rep1


title: I3P_HPP_PP_U87_HPP40uM_05

description: Biological replicate 5


title: I3P_HPP_PP_U87_I3P40uM_01

description: Biological replicate 1


title: Peripheral blood, Subject 26

description:
replicate 1
26.AVG_Signal

tag: individual

value: Subject 26

value: Black

value: peripheral blood


title: I3P_HPP_PP_U87_HPP40uM_04

description: Biological replicate 4


title: 3344_CD4

description: processed data file: all_counts.tsv

value: Healthy control

value: CD4 memory T cells


title: I3P_HPP_PP_U87_HPP40uM_01

description: Biological replicate 1


title: Peripheral blood, Subject 27

description:
replicate 1
27.AVG_Signal

value: Subject 27


title: Peripheral blood, Subject 98

description:
replicate 1
98.AVG_Signal

value: Subject 98


title: 3292_CD4

description: processed data file: all_counts.tsv

value: Female


title: Peripheral blood, Subject 88

description:
replicate 1
88.AVG_Signal

value: Subject 88


title: Peripheral blood, Subject 64

description:
replicate 1
64.AVG_Signal

value: Subject 64

value: White


title: RRBS_Tcell_rep5

source_name: T-cell

value: T-cell


title: Peripheral blood, Subject 102

description:
replicate 1
102.AVG_Signal

value: Subject 102


title: I3P_HPP_PP_U87_HPP40uM_03

description: Biological replicate 3


title: Peripheral blood, Subject 83

description:
replicate 1
83.AVG_Signal

value: Subject 83

value: Male


title: 3279_CD4

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: RRBS_Tcell_rep3


title: I3P_HPP_PP_U87_DMSO_04

description: Biological replicate 4

value: DMSO


title: 3189_CD4

description: processed data file: all_counts.tsv


title: RRBS_Tcell_rep2


title: I3P_HPP_PP_U87_DMSO_03

description: Biological replicate 3


title: I3P_HPP_PP_U87_DMSO_05

description: Biological replicate 5


title: I3P_HPP_PP_U87_DMSO_02

description: Biological replicate 2


title: Peripheral blood, Subject 92

description:
replicate 1
92.AVG_Signal

value: Subject 92


title: Peripheral blood, Subject 43

description:
replicate 1
43.AVG_Signal

value: Subject 43


title: Peripheral blood, Subject 76

description:
replicate 1
76.AVG_Signal

value: Subject 76

value: Black

value: peripheral blood


title: 3175_CD4

description: processed data file: all_counts.tsv

value: CD4 memory T cells


title: ChIPseq_Patient2_histone_modification_input

extract_protocol:
Phenol/chloroform DNA extraction
Libraries were prepped with a KAPA high throughput library prep kit using a Sciclone® G3 NGS and NGSx Workstation

value: T-ALL from patient xenograft

tag: chip antibody


title: RRBS_Tcell_rep4


title: 3170_CD4

description: processed data file: all_counts.tsv

value: Female


title: ChIPseq_Patient2_H3K4me1


title: I3P_HPP_PP_U87_DMSO_01

description: Biological replicate 1


title: U87_I3CA50uM_04

description: Biological replicate 4

value: I3CA 50uM


title: 3169_CD4

description: processed data file: all_counts.tsv

value: Healthy control


title: ChIPseq_Patient2_H3K27me3


title: Peripheral blood, Subject 70

description:
replicate 1
70.AVG_Signal

value: Subject 70

tag: Sex


title: Peripheral blood, Subject 89

description:
replicate 1
89.AVG_Signal

value: Subject 89

tag: bmi


title: U87_I3CA50uM_02

description: Biological replicate 2


title: Peripheral blood, Subject 79

description:
replicate 1
79.AVG_Signal

value: Subject 79

tag: race

value: White


title: ChIPseq_Patient2_H3K27ac


title: 3182_CD4

description: processed data file: all_counts.tsv

value: Male


title: 3155_CD4

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: RRBS_Tcell_rep1

value: T-cell


title: U87_I3CA50uM_03

description: Biological replicate 3


title: 3153_CD4

description: processed data file: all_counts.tsv


title: ChIPseq_Patient1_histone_modification_input


title: U87_I3CA50uM_01

description: Biological replicate 1


title: Peripheral blood, Subject 28

description:
replicate 1
28.AVG_Signal

value: Subject 28

tag: hamd score excluding item 8


title: 3139_CD4

description: processed data file: all_counts.tsv


title: Peripheral blood, Subject 25

description:
replicate 1
25.AVG_Signal

value: Subject 25

tag: college (yes/no)


title: Peripheral blood, Subject 111

description:
replicate 1
111.AVG_Signal

value: Subject 111

tag: psychomotor composite score


title: 3125_CD4

description: processed data file: all_counts.tsv


title: ChIPseq_Patient1_H3K4me1


title: U87_DMSO_04

description: Biological replicate 4

value: DMSO


title: ChIPseq_Patient1_H3K27me3


title: ChIPseq_Patient1_H3K27ac


title: 3115_CD4

description: processed data file: all_counts.tsv


title: 3114_CD4

description: processed data file: all_counts.tsv


title: Peripheral blood, Subject 110

description:
replicate 1
110.AVG_Signal

value: Subject 110

tag: age

value: peripheral blood


title: ChIPseq_Tcell_histone_modification_input


title: U87_DMSO_01

description: Biological replicate 1


title: 3022_CD4

description: processed data file: all_counts.tsv

value: CD4 memory T cells


title: 2972_CD4

description: processed data file: all_counts.tsv

value: Female


title: ChIPseq_Tcell_H3K27me3


title: Peripheral blood, Subject 114

description:
replicate 1
114.AVG_Signal

value: Subject 114

value: Black

tag: tissue


title: ChIPseq_Tcell_H3K27ac

tag: cell type


title: 3015_CD4

description: processed data file: all_counts.tsv

value: Healthy control


title: ChIPseq_Jurkat_CTCF_GSI3d_w4hr_rep2_input

value: Jurkat

tag: treatment

value: Compound E (CAS 209986-17-4), was applied at a 1 uM concentration every 24 hours for 72 hours


title: U87_shC_KynA50uM_04

description: Biological replicate 4

tag: experiment

value: KynA 50uM

tag: shRNA

value: shCtrl


title: U87_DMSO_02

description: Biological replicate 2

tag: agent


title: U87_DMSO_03

description: Biological replicate 3


title: ChIPseq_Jurkat_CTCF_GSI3d_w4hr_rep1_input


title: Peripheral blood, Subject 104

description:
replicate 1
104.AVG_Signal

value: Subject 104


title: U87_shC_KynA50uM_03

description: Biological replicate 3


title: 2964_CD4

description: processed data file: all_counts.tsv

tag: disease state

tag: gender


title: 2999_CD4

description: processed data file: all_counts.tsv


title: U87_shC_KynA50uM_02

description: Biological replicate 2

tag: cell line


title: Peripheral blood, Subject 19

description:
replicate 1
19.AVG_Signal

tag: individual

value: Subject 19

value: Male


title: 2965_CD4

description: processed data file: all_counts.tsv


title: ChIPseq_Jurkat_CTCF_GSI3d_w4hr_rep1

tag: chip antibody

value: CTCF


title: Peripheral blood, Subject 113

description:
replicate 1
113.AVG_Signal

value: Subject 113

tag: Sex

tag: bmi


title: Peripheral blood, Subject 37

description:
replicate 1
37.AVG_Signal

value: Subject 37

tag: race

tag: hamd score excluding item 8


title: Peripheral blood, Subject 61

description:
replicate 1
61.AVG_Signal

value: Subject 61

tag: college (yes/no)

tag: psychomotor composite score


title: U87_shC_FICZ100nM_04

description: Biological replicate 4

value: FICZ 100nm


title: Peripheral blood, Subject 48

description:
replicate 1
48.AVG_Signal

value: Subject 48

tag: age

tag: tissue

value: peripheral blood


title: Peripheral blood, Subject 31

description:
replicate 1
31.AVG_Signal

value: Subject 31

value: Female


title: U87_shC_FICZ100nM_03

description: Biological replicate 3


title: U87_shC_KynA50uM_01

description: Biological replicate 1


title: U87_shC_FICZ100nM_02

description: Biological replicate 2


title: Peripheral blood, Subject 105

description:
replicate 1
105.AVG_Signal

value: Subject 105

value: White


title: 2951_CD4

description: processed data file: all_counts.tsv

value: Healthy control

tag: cell type

value: CD4 memory T cells


title: Peripheral blood, Subject 30

description:
replicate 1
30.AVG_Signal

value: Subject 30

value: Black


title: Peripheral blood, Subject 24

description:
replicate 1
24.AVG_Signal

value: Subject 24


title: 2950_CD4

description: processed data file: all_counts.tsv

value: Male


title: ChIPseq_Jurkat_CTCF_GSI3d_rep1_input

value: Jurkat

tag: treatment

value: Compound E (CAS 209986-17-4), was applied at a 1 uM concentration every 24 hours for 72 hours


title: 3345_PBMC

description: processed data file: all_counts.tsv

value: PBMC


title: ChIPseq_Jurkat_CTCF_GSI3d_rep2_input


title: 3278_PBMC

description: processed data file: all_counts.tsv


title: ChIPseq_Jurkat_CTCF_DMSO_rep2_input


title: ChIPseq_Jurkat_CTCF_GSI3d_rep1

value: CTCF


title: 3207_PBMC

description: processed data file: all_counts.tsv


title: 3204_PBMC

description: processed data file: all_counts.tsv


title: ChIPseq_Jurkat_CTCF_GSI3d_rep2


title: ChIPseq_Jurkat_CTCF_DMSO_rep1_input


title: ChIPseq_Jurkat_CTCF_DMSO_rep1


title: U87_shC_DMSO_02

description: Biological replicate 2

tag: experiment

value: DMSO

tag: shRNA

value: shCtrl


title: ChIPseq_Jurkat_CTCF_DMSO_rep2


title: Peripheral blood, Subject 46

description:
replicate 1
46.AVG_Signal

value: Subject 46

value: peripheral blood


title: 3195_PBMC

description: processed data file: all_counts.tsv

tag: disease state


title: U87_shC_DMSO_01

description: Biological replicate 1

tag: agent


title: U87_shC_DMSO_04

description: Biological replicate 4

tag: cell line


title: U87_shC_FICZ100nM_01

description: Biological replicate 1

value: FICZ 100nm


title: Peripheral blood, Subject 13

description:
replicate 1
13.AVG_Signal

tag: individual

value: Subject 13


title: U87_shC_DMSO_03

description: Biological replicate 3


title: Peripheral blood, Subject 15

description:
replicate 1
15.AVG_Signal

value: Subject 15

value: Female


title: Peripheral blood, Subject 103

description:
replicate 1
103.AVG_Signal

value: Subject 103


title: 3190_PBMC

description: processed data file: all_counts.tsv

value: Healthy control

tag: gender


title: Peripheral blood, Subject 20

description:
replicate 1
20.AVG_Signal

value: Subject 20

tag: Sex

value: White


title: peripheral blood mononuclear cells at healthy subject, biological rep6

city: Beijing

first: sheng

middle: zhu

last: yang

address: No. 1 Dongjiaomin Lane, Dong Cheng District

institute: Beijing Tongren Hospital

description:
Gene expression data from peripheral blood mononuclear cells in healthy subjects. No lesion; TPHA (-); TRUST (-); HIV (-); Hepatitis B (-); Hepatitis C (-)
whole blood

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on Affymetrix® GeneChip® miRNA Array. Washing, staining, and scanning, refer to the Genechip® Expression  Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G.The instructions for using the scanner and scanning arrays can be found in the Affymetrix® Command  Console® User Manual (P/N 702569).

data_processing:
The data were analyzed with Partek Genomics Suite 6.6. Use Expression Console software for data summarization, normalization, and quality control (v. 1.2 and  higher). Please refer to the website for Expression Console for instructions on miRNA Array analysis.  Affymetrix recommends using RMA + DABG for analysis.
Affymetrix GeneChip Command Console (AGCC) software

source_name: Peripheral blood mononuclear cells from healthy subject

label_protocol: FlashTag Biotin HSR RNA Labeling Procedure

growth_protocol: Blood samples (8–10 ml in EDTA) were obtained by venipuncture from secondary syphilis patients and healthy subjects.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The miRNAs expression profiles in peripheral blood mononuclear cells(PBMCs) of 6 untreated syphilis patients and 6 healthy controls were detected by miRNAs expression microarray (Gene Tech (Shanghai) Company Limited ).

treatment_protocol: PBMCs were extracted immediately after the collection of whole blood using a standard procedure of Ficoll gradient centrifugation, performed in accordance with the manufacturer’s instructions.

value: peripheral blood mononuclear cells


title: peripheral blood mononuclear cells at healthy subject, biological rep5


title: 3277_PBMC

description: processed data file: all_counts.tsv


title: ChIPseq_Patient2_CTCF_input

value: T-ALL from patient xenograft

tag: chip antibody


title: 3181_PBMC

description: processed data file: all_counts.tsv


title: peripheral blood mononuclear cells at healthy subject, biological rep4


title: Peripheral blood, Subject 54

description:
replicate 1
54.AVG_Signal

value: Subject 54

tag: bmi

tag: race


title: Peripheral blood, Subject 85

description:
replicate 1
85.AVG_Signal

value: Subject 85

tag: hamd score excluding item 8

tag: college (yes/no)


title: peripheral blood mononuclear cells at healthy subject, biological rep3


title: ChIPseq_Patient2_CTCF_rep2

value: CTCF


title: Peripheral blood, Subject 66

description:
replicate 1
66.AVG_Signal

value: Subject 66

tag: age

value: Male

tag: psychomotor composite score


title: 3180_PBMC

description: processed data file: all_counts.tsv

tag: cell type

value: PBMC


title: ChIPseq_Patient1_CTCF_rep2


title: ChIPseq_Patient1_CTCF_input


title: ChIPseq_Patient2_CTCF_rep1


title: 3476_PBMC

description: processed data file: all_counts.tsv

value: Alzheimer's disease


title: Peripheral blood, Subject 86

description:
replicate 1
86.AVG_Signal

value: Subject 86

value: Black

tag: tissue

value: peripheral blood


title: 3353_PBMC

description: processed data file: all_counts.tsv


title: 3342_PBMC

description: processed data file: all_counts.tsv


title: peripheral blood mononuclear cells at healthy subject, biological rep2


title: ChIPseq_Patient1_CTCF_rep1


title: ChIPseq_CUTLL1_CTCF_GSI_input


title: peripheral blood mononuclear cells at healthy subject, biological rep1


title: peripheral blood mononuclear cells at secondary syphilis patient, biological rep5

description:
Gene expression data from peripheral blood mononuclear cells in untreated secondary syphilis patients. Lesion; TPHA (+); TRUST (+),1:32; HIV (-); Hepatitis B (-); Hepatitis C (-)
whole blood

source_name: Peripheral blood mononuclear cells from secondary syphilis patient


title: peripheral blood mononuclear cells at secondary syphilis patient, biological rep4


title: Peripheral blood, Subject 108

description:
replicate 1
108.AVG_Signal

value: Subject 108

value: Female


title: Peripheral blood, Subject 91

description:
replicate 1
91.AVG_Signal

value: Subject 91


title: peripheral blood mononuclear cells at secondary syphilis patient, biological rep6

description:
Gene expression data from peripheral blood mononuclear cells in untreated secondary syphilis patients. Lesion; TPHA (+); TRUST (+),1:128; HIV (-); Hepatitis B (-); Hepatitis C (-)
whole blood


title: Peripheral blood, Subject 41

description:
replicate 1
41.AVG_Signal

value: Subject 41


title: 3330_PBMC

description: processed data file: all_counts.tsv


title: ChIPseq_CUTLL1_CTCF_GSI


title: 3437_PBMC

description: processed data file: all_counts.tsv


title: 3199_PBMC

description: processed data file: all_counts.tsv


title: Peripheral blood, Subject 109

description:
replicate 1
109.AVG_Signal

value: Subject 109