title: RNA_PBMC_IFN_TRAM_2

source_name: PBMC

growth_protocol: human PBMCs (100 million cells/vial) were purchased from iXCells Biotechnologies (10HU-003CR100M). PBMCs cells were cultured in cell culture medium (Xvivo10 [Lonza, 04-380Q, with gentamicin and phenol red], 1.8% human serum [AB plasma, Sigma, H4522], 100 ngml human M-CSF [Invitrogen, 14-8789-80]).

extract_protocol:
~0.5X10^6 cells were harvested for mRNA using mRNeasy Mini Kit (Qiagen, No. 217004).
We used 0.4 μg total RNA for RNA-seq library preparation by TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126).

treatment_protocol: PBMC cells were pre-treated with panobinostat (0.0034 μM), trametinib (0.011 μM), or DMSO (control) for one hour and then treated with either BSA (control), IL-4 (20 ng/ml, M2 polarization) or IFNγ (20 ng/ml) and LPS (10 ng/ml, M1 polarization) for 24 hours.

tag: cell type

value: peripheral blood monocyte


title: HT29_ORF_SMURF1_216

status: Public on Oct 16 2021

type: RNA

city: Montréal

first: John

middle: D

last: Rioux

state: QC

address: 5000 Bélanger St.

department: Research Center

country: Canada

institute: Montreal Heart Institute

hyb_protocol: Samples were blocked with Agilent blocking reagent and incubated for 17h at 65C in the Agilent Microarray Hybridization oven

scan_protocol: Agilent SureScan Microarray scanner

data_processing:
We used Limma v3.26.9 and sva v3.18.0 packages (Bioconductor v3.1-3.2) to load the fluorescence intensity files and handle the data into R V3.2.0. Arrays failing Agilent quality control according to the Agilent Feature Extraction software were flagged.  Manual quality control of each array was also performed.
Quality control was performed within each batch of arrays. Fluorescence signal was processed to remove local background (bakgroundCorrect, method “normexp”) and then normalized using cyclic loess algorithm.
Batch effects were then corrected using ComBat for known batches and sva for unknown systematic artefacts (both from sva library v3.18.0). Given the experiment was performed in three parts (E1-E4 & P7, E5-E11, E14-E15), the batches from each part were combined first and then combined together.
To reduce impact of residual background, noise and batch effects on very low expression values, the fluorescence intensity values were truncated at 8, and translated down by the same amount.
Duplicated probes were combined, and repeated samples removed. The truncating threshold was determined based on the distribution of negative control probes and detected vs non-detected signals. Data provided includes only samples included in the final dataset.

molecule: total RNA

organism: Homo sapiens

source_name: HT-29 SMURF1 transduction, UniqueID 216

label_protocol: Agilent One-Color Microarray-Based Exon Analysis Low Input Quick Amp WT Labeling kit using Cyanine 3-CTP label.

growth_protocol: The colorectal adenocarcinoma cell line HT-29 (ATCC HTB-38) was maintained at confluence between 20% and 80% at all times in McCoy’s 5A (Wisent, 317-010CL) 10% FBS. All experiments described herein were performed in cell at passages below 25.

extract_protocol:
The RNeasy Plus Mini kit (#74036, Qiagen Inc Canada) according to manufacturer’s protocol.
The RNA samples were quantified, and quality controlled using an Agilent RNA 6000 Nano kit (Agilent, Cat No./ID 5067-1511) on 2100 Bioanalyzer system.
Number (RIN) below 8 were discarded; RIN values were routinely in the range of 9.2-10

treatment_protocol:
ORFs for IBD gene candidates were cloned into a GATEWAY® compatible polycistronic lentiviral expression vector, pLVX-EF1a-IRES-PURO/eGFP expressing an enhanced green fluorescent protein (eGFP) and puromycin N-acetyl-transferase fusion protein.
Proliferative HT-29 cells at 50% confluency in 12 well plate (Corning) were transduced in triplicate with the different ORFs (multiplicity of infection) MOI of 40-100 with 8µg/ml of polybrene (Sigma, Cat: H-9268).
Twenty-four hours post-transduction, media was changed and 3ug/ml puromycin (Millipore Sigma) was added.
The appearance and confluence of the cultures were recorded daily, and cells were grown for an average of 8 days (with a range of 5-27 days) to select successfully transduced cells and reach confluence before RNA extraction.
Transduction of the whole set of IBD gene candidate ORFs was performed in batches of about 15 ORFs, each done in triplicate, and including an empty vector control.

tag: orf

tag: uniqueid

tag: arraybatch

tag: transductiondate


title: RNA_PBMC_IFN_TRAM_1

type: SRA

city: Charlestown

first: Alexander

middle: G

last: Marneros

state: MA

address: 13th Street

department: Department of Dermatology, Cutaneous Biology Research Center

country: USA

institute: Massachusetts General Hospital, Harvard Medical School

library_source: transcriptomic

data_processing:
We followed the nf-core/rnaseq workflow version 1.3 (https://github.com/nf-core/rnaseq) for all rna-seq data, with default parameters. The detail includes as following:
low-quality reads were eliminated using FastQC and trim_galory software, remaining only high quality reads.
The remaining clean reads were aligned against the iGenome Ensembl human referenece genome GRCh37 using by STAR. STAR is a read aligner designed for RNA sequencing.
Next, we generated counts relative to genes by featureCounts and StringTie with default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

tag: treatment

value: TRAM

tag: polarization

value: IFNLPS


title: KO rep1

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

country: China

institute: Zhejiang University School of Medicine

data_processing:
The software STAR (55) (version 2.4.0e) was used to generate genome indices for mouse reference genome (GRCm38/mm10, December 2011), with two particular specifications including gene annotations, i.e., GENCODE (56) (vM23, September 2019), and exon-exon junctions, i.e., 35 nucleotides used in constructing the splice junctions database.
Next, the high quality paired-end RNA-seq reads were aligned to mouse reference genome, and the consequence of alignment served as the input  for featureCounts (57) to quantify raw read counts for 55,385 annotated genes, including 21,856 protein-coding genes.
Moreover, the normalized unit of reads per kilobase per million mapped reads (RPKM) was generated for every gene annotated in GENCODE, in order to fit the primary request of principle component analysis (PCA). The R function prcomp was used to perform PCA by using the genes having RPKM ≥ 1 in at least two samples, and the returned two vectors were used as coordinates to make a scatter plot in a 2-dimensional plane.
We used R package DESeq2 (58) (version 1.14.1) to identify differentially expressed (DEX) genes between WT and KO. The raw read count per gene served as the input for DESeq2. The GC content correction from CQN package was incorporated to DESeq2 (59). Since four samples were collected in either condition, they were treated as biological replicates to improve the reliability of DEX genes identification. Statistical tests for differential expression were based on a model using the negative binomial distribution. The reported statistical significances were corrected for multiple testing using the Benjamini-Hochberg procedure with a false discovery rate less than 0.01. In addition, to be called DEX genes we required the fold change > 1.5. The up- and down- regulated genes in KO condition were separately queried to Gene Ontology Consortium for gene ontology enrichment assessment, including biological process (BP), molecular function (MF), and cellular component (CC).
Moreover, we utilized the software GSEA (60) to survey the statistically significant concordant differences between KO and WT by using the normalized gene RPKM values, and consequently compared the KO up-regulated gene sets to “C7: immunologic signatures” to explore any overrepresented functional term.
Genome_build: GRCm38/mm10, December 2011
Supplementary_files_format_and_content: Count table for each sample

organism: Mus musculus

source_name: CD8+ TILs

extract_protocol:
CD8+ TILs were isolated from MC38 tumor-bearing Cd4-Cre+Lsd1f/f and Lsd1f/f mice on day 18 as described above. CD8+ TILs from two individual tumor-carrying Lsd1f/f mice were combined as a biological replicate, and CD8+ TILs from each individual tumor-carrying Cd4-Cre+Lsd1f/f mouse was used as a biological replicate. CD8+ TILs were stained with antibodies against CD45.2 (clone 104), TCR (clone H57-587), CD8 (clone YTS156.7.7), CD44 (clone IM7) and PD-1 (clone 29F.1A12), and 7-AAD Viability Staining Solution was used to exclude dead cells. The CD45.2+TCR+CD8+CD44+PD-1+ cells were then sorted on a BD Aria. Approximately 10,000~20,000 sorted cells for each biological replicate were directly lysed in 1 ml TRIzol Reagent (Life Technologies, cat#15596018). After incubation for 5 mins, 0.2 ml chloroform was added and mixed by inverting the tubes several times. Samples were incubated for 2~3 mins and later centrifuged for 15 minutes at 12,000g at 4 °C. The upper aqueous phase containing the RNA was collected and mixed with equal volume of 70% ethanol, which was then loaded into a spin column from a RNeasy Micro Kit (Qiagen, cat#74004) and subjected to RNA isolation according to the instruction manual. The on-column DNase digestion was conducted to eliminate DNA contamination.
Purified total RNA was quantified by Qubit (Invitrogen) and used to generate rRNA-depleted RNA with a NEBNext® rRNA Depletion Kit (New England Biolabs, cat#E6310S) according to the manufacturer’s instructions. The rRNA-depleted RNA was purified with a RNA Clean & Concentrator-5 kit (Zymo Research, cat#R1016) and then used to generate a directional RNA library with a NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, cat#E7760L) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, cat#E7335L) according to the manufacturer’s instructions. Library concentrations and quality were assessed on a Bioanalyzer and by qPCR. The library was sequenced at Nextseq 500 (Illumina) to generate reads from paired-ends (43 bp + 42 bp).

tag: strain

value: C57BL/6 mice

tag: tissue

value: Implanted MC38 tumor

tag: genotype


title: HT29_ORF_ZFP36L1_252

source_name: HT-29 ZFP36L1 transduction, UniqueID 252


title: RNA_THP1_DMSO_IFNLPS_1

growth_protocol: THP-1 cells were obtained from ATCC (ATCC Cat# TIB-202, RRID:CVCL_0006) and cultured in RPMI1640+10% FBS+1% Anti-Anti (Life technologies, 15240).

extract_protocol:
0.5X10^6 cells were harvested for mRNA using mRNeasy Mini Kit (Qiagen, No. 217004).
We used 0.4 μg total RNA for RNA-seq library preparation by TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126).

treatment_protocol: Primed THP-1 cells with PMA 100 nM were pre-treated with panobinostat (0.0034 μM), Treametinib (0.011 μM ), or DMSO (control) for one hour and then treated with either BSA (control), IL-4 (20 ng/ml, M2 polarization) or IFNγ (20 ng/ml) and LPS (10 ng/ml, M1 polarization) for 24 hours.

tag: cell line

value: DMSO


title: HT29_ORF_TRIB1_234

source_name: HT-29 TRIB1 transduction, UniqueID 234


title: RNA_PBMC_CTRL_TRAM_2

value: control


title: HT29_ORF_TM9SF4_222

source_name: HT-29 TM9SF4 transduction, UniqueID 222


title: HT29_ORF_AUH_261

source_name: HT-29 AUH transduction, UniqueID 261

value: AUH


title: RNA_THP1_DMSO_CTRL_1

value: Control


title: HT29_ORF_TMED10_266

source_name: HT-29 TMED10 transduction, UniqueID 266


title: HT29_ORF_SSR2_263

source_name: HT-29 SSR2 transduction, UniqueID 263


title: RNA_PBMC_IL4_TRAM_1


title: RNA_PBMC_IL4_PANO_1

value: PANO


title: RNA_PBMC_CTRL_PANO_2


title: HT29_ORF_C1orf106_20

source_name: HT-29 C1orf106 transduction, UniqueID 20


title: HT29_ORF_TRIB1_233

source_name: HT-29 TRIB1 transduction, UniqueID 233


title: HT29_ORF_ZFP36L1_251

source_name: HT-29 ZFP36L1 transduction, UniqueID 251


title: RNA_THP1_DMSO_CTRL_2


title: RNA_PBMC_IL4_TRAM_2


title: RNA_PBMC_IFN_PANO_1


title: RNA_PBMC_IFN_PANO_2


title: HT29_ORF_RORC_185

source_name: HT-29 RORC transduction, UniqueID 185

value: RORC


title: HT29_ORF_FOXO1_69

source_name: HT-29 FOXO1 transduction, UniqueID 69


title: HT29_ORF_TMED10_267

source_name: HT-29 TMED10 transduction, UniqueID 267


title: OCI-AML3 + 1uM AZA Day 8_rep 2 [OCIday8rep2]

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the hg19 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: OCI-AML3 + 1uM AZA Day 8

growth_protocol: Cells were grown in RPMI 10% FCS + 1%P/S supplemented with L-glut.

extract_protocol:
Cells were harvested and cell pellets were snap frozen on dry ice. Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (CAT#FC-122-1001) was used with 1ug total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell were exposed to 1uM Azacitidine for 8 days. Azacitidine was renewed every 2 days when the cell media was replenished/replaced.

value: Acute myeloid leukemia

tag: origin

value: Peripheral Blood of 57yo man with AML (FAB M4) with NPM1 and DNMT3A R882C mutations

tag: cell treatment

value: 1uM Azacitidine Treatment for 8days


title: OCI-AML3 + 1uM AZA Day 8_rep3 [OCIday8rep3]


title: RNA_PBMC_IL4_PANO_2


title: RNA_PBMC_IFN_DMSO_1


title: HT29_ORF_SMURF1_215

source_name: HT-29 SMURF1 transduction, UniqueID 215


title: OCI-AML3 + 1uM AZA Day 4_rep 2 [OCIday4rep2]

source_name: OCI-AML3 + 1uM AZA Day 4

value: 1uM Azacitidine Treatment for 4 days


title: HT29_ORF_AUH_260

source_name: HT-29 AUH transduction, UniqueID 260


title: HT29_ORF_TMEM17_227

source_name: HT-29 TMEM17 transduction, UniqueID 227


title: HT29_ORF_IFIH1_95

source_name: HT-29 IFIH1 transduction, UniqueID 95


title: HT29_ORF_GNB2_80

source_name: HT-29 GNB2 transduction, UniqueID 80


title: OCI-AML3 + 1uM AZA Day 4_rep 3 [OCIday4rep3]


title: RNA_PBMC_CTRL_TRAM_1

source_name: PBMC


title: HT29_ORF_TM9SF4_221

source_name: HT-29 TM9SF4 transduction, UniqueID 221


title: OCI-AML3 + 1uM AZA Day 3_rep 3 [OCIday1rep3]

source_name: OCI-AML3 + 1uM AZA Day 3

value: 1uM Azacitidine Treatment for 24h


title: RNA_PBMC_IL4_DMSO_2


title: OCI-AML3 + 1uM AZA Day 2_rep 2 [OCIday1rep2]

source_name: OCI-AML3 + 1uM AZA Day 2


title: RNA_PBMC_IFN_DMSO_2


title: HT29_ORF_RIPK2_176

source_name: HT-29 RIPK2 transduction, UniqueID 176


title: RNA_PBMC_CTRL_PANO_1


title: HT29_ORF_RIT1_179

source_name: HT-29 RIT1 transduction, UniqueID 179


title: OCI-AML3 + 1uM AZA Day 1 [OCIday1rep1]

source_name: OCI-AML3 + 1uM AZA Day 1


title: HT29_ORF_HNF4A_89

source_name: HT-29 HNF4A transduction, UniqueID 89


title: HT29_ORF_DUSP16_50

source_name: HT-29 DUSP16 transduction, UniqueID 50


title: HT29_ORF_CPEB4_32

source_name: HT-29 CPEB4 transduction, UniqueID 32


title: O2

city: chengdu

first: li

last: tongtong

state: sichuan

address: sichuan

institute: xinong

data_processing:
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
The clustering of the index-coded samples was performed on a cBot Cluster Generation   System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s   instructions. After cluster generation, the library preparations were sequenced on an   Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.   In this step, clean data (clean reads) were obtained by removing reads containing adapter,   reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30   and GC content the clean data were calculated. All the downstream analyses were based on   the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome   website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired_x0002_end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected   Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based   on the gene model annotation file and thus a better mapping result than other non-splice   mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM   of each gene was calculated based on the length of the gene and reads count mapped to this   gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per   Millions base pairs sequenced, considers the effect of sequencing depth and gene length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Gene Ontology (GO) enrichment analysis of differentially expressed genes was   implemented by the GOseq R package, in which gene length bias wascorrected. GO terms   with corrected Pvalue less than 0.05 were considered significantly enriched by differential   expressed genes.
Supplementary_files_format_and_content: raw counts

organism: Rattus norvegicus

source_name: MCROGLIA

growth_protocol: Rats were grow up to 3 mouths

extract_protocol:
then small RNA library was constructed and
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.)

treatment_protocol: Rats' mother was treatmented with control vehicle adenovirus or CYP11A1 gene containing adenovirus

value: Primary cell

value: treated with CYP11A1 gene containing adenovirus

value: Sprague Dawley


title: O3


title: HT29_ORF_GNA12_77

source_name: HT-29 GNA12 transduction, UniqueID 77


title: RNA_PBMC_CTRL_DMSO_1

value: peripheral blood monocyte


title: OCI-AML3 + 1uM AZA Day 4 [OCIday4rep1]

source_name: OCI-AML3 + 1uM AZA Day 4


title: HT29_ORF_NR5A2_131

source_name: HT-29 NR5A2 transduction, UniqueID 131


title: HT29_ORF_KIF3B_107

source_name: HT-29 KIF3B transduction, UniqueID 107


title: HT29_ORF_FOSL1_62

source_name: HT-29 FOSL1 transduction, UniqueID 62


title: RNA_PBMC_CTRL_DMSO_2


title: C3

value: treated with control vehicle adenovirus


title: RNA_PBMC_IL4_DMSO_1


title: HT29_ORF_NUPR1_140

source_name: HT-29 NUPR1 transduction, UniqueID 140


title: THP1_Tram_CTRL_input

library_source: genomic

data_processing:
We followed the nf-core/chipseq workflow version 1.3 (https://github.com/nf-core/rnaseq) for all chip-seq data, with default parameters. The detail includes as following:
low-quality reads were eliminated using FastQC and trim_galory software, remaining only high quality reads.
The remaining high-quality reads were aligned against the iGenome Ensembl human reference genome GRCh37 by BWA and SAMtools.
Next, the normalized bigWig files were scaled to one million mapped reads through BEdtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010)
To identify detailed sequences captured by ChIP-Seq, we then use a peak calling method to explore areas of a genome that have been enriched with aligned reads, indicating the potential regulatory elements, such as the enhancers, super enhancers, and transcription factor binding sites.
MACS2 (Zhang et al., 2008) is a model-based method dedicated to identification of read rich areas (peak calling) from ChIP-Seq data.
HOMER (Heinz et al., 2010) was employed to link the selected peaks to genes and IGV (Robinson et al., 2017) or DNANexus software was applied to visualize the distribution of peaks with their intensity values throughout the whole genome.
Genome_build: GRCh37
Supplementary_files_format_and_content: ChIP-Seq data include normalized bigWig files and bedGraph tab-delimited text files for each Sample

molecule: genomic DNA

extract_protocol: We used 4x106 cells per sample from 6 well dishes for H3K27ac ChIP-Seq (n=2/group). During cell harvesting, cell culture medium was removed and cells were treated with PBS+1% PFA (Amresco, M134) at RT for 15 minutes and then quenched with 0.125 M glycine at RT for 5 minutes. After washing 6 times with cold PBS, the nuclei were extracted by incubating cells in RLB buffer (50 mM HEPES pH7.9, 140 mM NaCl, 2 mM EDTA, 2 mM EGTA, 1% Triton X-100, and cOmplete ULTRA Protease Inhibitor Cocktail, Sigma 582988001) on ice for 1 hour. After washing with MNase buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1% Triton X-100, 1 mM CaCl2, 1 mM DTT), chromatins were digested with 66 units MNase (New England Biolabs, M0247S) at 37 oC for 10 minutes and the reactions were stopped using EGTA (5   M) on ice for 5 minutes. Chromatins were sonicated with a Branson Microtip Sonifier 450 (4x15 second at output 4.5 and duty cycle 60%). The sizes of the chromatins after these treatments were ~150-500 bp in length. For ChIP, we incubated the chromatins with 20   l Dynabead protein G (Thermo Fisher Scientific, 10004D) and 1.5   g anti-H3K27ac antibodies (Abcam Cat# ab4729, RRID:AB_2118291) in IP dilution buffer (20 mM Tris HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 2 mM EGTA) at 4 oC overnight. IPed chromatins were sequentially washed with IP dilution buffer+0.1% Triton, ChIP wash I (20 mM Tris HCl pH8.0, 150 mM NaCl, 0.5% Triton, 2 mM EDTA, 2 mM EGTA), ChIP wash II (20 mM Tris HCl pH8.0,  500 mM NaCl, 1% Triton, 2 mM EDTA, 2 mM EGTA), ChIP wash III (20 mM Tris HCl pH8.0, 250 mM LiCl, 1% Triton, 2 mM EDTA, 2 mM EGTA) and TE buffer. Chromatins were eluted using elution buffer (20 mM Tris HCl pH8.0, 5 mM EDTA, 5 mM EGTA, 1% SDS) at 65oC for 2 x 15 minutes. Chromatins were digested using RNase ONE Ribonuclease (Promega, PAM4261, 1:10 dilution) at 37oC for 1 hour and Pronase (Roche, 10165921001, 1.5   g/  l) at 42oC for 2 hours and 65oC for 6 hours. Digested chromatins were purified using Qiagen PCR purification kits. ChIP-Seq libraries were prepared using a standard protocol, including End-Repair, dA-Tailing, Single-Index Adapter Ligation and final PCR Amplification (17 cycles) using Phusion DNA polymerase. ChIP-Seq libraries were purified from 2% agarose gels. Concentrations of ChIP-Seq libraries were determined using a Bioanalyzer. ChIP-Seq libraries were sequenced using a NextSeq 500/550 High Output V2.5 75 cycles kit from Illumina on a Nextseq 550 platform and all data were deposited to GEO. For normalization controls, 1% of the chromatin that was used for ChIP was used to make input libraries.

value: TRAM

tag: chip antibody

value: none (input)


title: C1


title: OCI-AML3 + 1uM AZA Day 8 [OCIday8rep1]

source_name: OCI-AML3 + 1uM AZA Day 8


title: O1


title: HT29_ORF_PUSL1_172

source_name: HT-29 PUSL1 transduction, UniqueID 172


title: THP1_Tram_IL4_input


title: OCI-AML3- No AZA_rep 3 [OCIday0rep3]

source_name: OCI-AML3- No AZA

value: No Treatment


title: HT29_ORF_ARHGEF2_17

source_name: HT-29 ARHGEF2 transduction, UniqueID 17


title: HL60 + 1uM AZA Day 8 [HL60day8Rep1]

source_name: HL60 + 1uM AZA Day 8

value: Peripheral Blood of 35yo woman with AML (FAB M2 Classification)


title: HT29_ORF_FOS_59

source_name: HT-29 FOS transduction, UniqueID 59

value: FOS


title: HT29_ORF_ARFRP1_14

source_name: HT-29 ARFRP1 transduction, UniqueID 14


title: OCI-AML3- No AZA_rep 2 [OCIday0rep2]


title: THP1_DMSO_IL4_input

value: DMSO


title: HT29_ORF_Empty_5

source_name: HT-29 Empty transduction, UniqueID 5

value: Empty


title: HT29_ORF_CEBPB_23

source_name: HT-29 CEBPB transduction, UniqueID 23

value: CEBPB


title: OCI-AML3- No AZA  [OCIday0rep1]

value: Acute myeloid leukemia

value: Peripheral Blood of 57yo man with AML (FAB M4) with NPM1 and DNMT3A R882C mutations


title: HL60 + 1uM AZA Day 8_rep 3 [HL60day8Rep3]

value: 1uM Azacitidine Treatment for 8days


title: THP1_Pano_IFNLPS_input

value: PANO

value: IFNLPS


title: HT29_ORF_FOXO1_68

source_name: HT-29 FOXO1 transduction, UniqueID 68


title: HT29_ORF_CTH_38

source_name: HT-29 CTH transduction, UniqueID 38

value: CTH


title: ChIP_mouse_WT_UNSTIM_3_H3K27ac_IP

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

description: pkLstAssign_oneFeatGene_H3K27ac_WTcytos.bed

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated from BAM files by using either bedtools (v.2.26.0)  and UCSC’s bedGraphToBigWig (v4), or by using the bamCoverage function from deepTools (v3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled pileups of reads aligned to the genome. BED files are genomic ranges that represent the reference peak atlas used for analysis, with names representing unique peak IDs for each atlas.

source_name: splenic NK cells

extract_protocol:
DNA and proteins from sorted NK cells were cross-linked for 8 minutes at room temperature using 1% formaldehyde. Cross-linked cells incubated in cell lysis buffer (25 mM HEPES, 1.5 mM MgCl2, 10mM KCl, 0.1% NP-40, 1mM DTT, 1x proteinase inhibitor) and nuclei were isolated by centrifugation at 5400 rpm for 5.5 minutes. ChIP was performed using 1.5 μg of rabbit polyclonal anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473) or 8 µg anti-Stat5 (#AF2168, R&D Systems) and Dynabeads Protein G (Invitrogen).
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Whenever possible, fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter catalog # A63882) and Illumina libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with up to 10ng input DNA and 8-11 cycles of PCR. Barcoded libraries were run on a HiSeq 2500 in Rapid or High Output mode or a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq Rapid SBS Kit v2, HiSeq SBS Kit v4, or HiSeq 3000/4000 SBS Kit, respectively (Illumina). An average of 46 million paired reads were generated per sample.

value: WT

tag: condition

value: UNSTIM

tag: replicate

tag: antibody

tag: experimentid


title: HL60 + 1uM AZA Day 8_rep 2 [HL60day8Rep2]

tag: cell type


title: THP1_Tram_IFNLPS_input


title: THP1_Pano_CTRL_input

value: control


title: HL60 + 1uM AZA Day 4_rep 2 [HL60day4Rep2]

source_name: HL60 + 1uM AZA Day 4

value: 1uM Azacitidine Treatment for 4 days


title: THP1_DMSO_IFNLPS_input

value: none (input)


title: Fgfr3creER_p53cKO_P4M_RNA [Sample_2963-YM-11]

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

data_processing:
Reads files were downloaded and concatenated into a single .fastq file for each sample.
The quality of the raw reads data for each sample was checked using FastQC to identify quality problems.
Tuxedo Suite software package was subsequently used for alignment (using TopHat and Bowtie2), differential expression analysis, and post-analysis diagnostics.
FastQC was used for a second round of quality control (post-alignment).
HTSeq/DESeq2 was used for differential expression analysis using UCSC mm10 as the reference genome sequence. Only non-ambiguously mapped reads were counted.
Meta-analysis of RNA-seq data was performed using iPathwayGuide software (Advaita).
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: DESeq2: depth_normalized_counts, raw_counts, rlog_normalized_counts, Tuxedo: Fpkm, RawCounts, ScaledCounts

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were cultured for 8 passages.
SMART-Seq v4 Ultra Low Input RNA Kit

value: Femurs

tag: cells

value: Cultured tdTomato+ skeletal cells in bone marrow

tag: age

tag: cell type/passage

value: Cultured single clone, passage 6-8


title: Fgfr3creER_p53cKO_P4M_RNA [Sample_2963-YM-12]


title: ChIP_mouse_WT_UNSTIM_3_H3K27ac_input


title: HL60 + 1uM AZA Day 4_rep 3 [HL60day4Rep3]

value: Peripheral Blood of 35yo woman with AML (FAB M2 Classification)


title: ChIP_mouse_WT_UNSTIM_2_H3K27ac_input


title: ChIP_mouse_WT_IL2IL15_2_H3K27ac_IP


title: Fgfr3creER_p53cKO_P4M_RNA [Sample_2963-YM-10]


title: HL60 + 1uM AZA Day 2_rep 2 [HL60day1Rep2]

source_name: HL60 + 1uM AZA Day 2

value: 1uM Azacitidine Treatment for 24h


title: THP1_Pano_IL4_input

tag: treatment


title: ChIP_Tram_IL4_1

value: TRAM

tag: polarization

value: anti-H3K27ac (Abcam Cat# ab4729, RRID:AB_2118291)


title: ChIP_Tram_IFNLPS_2


title: ChIP_mouse_WT_IFNA_3_H3K27ac_IP

value: IFNA


title: ChIP_mouse_WT_IFNA_3_H3K27ac_input


title: Fgfr3creER_p53cKO_P28_RNA [Sample_2963-YM-5]

value: Postnatal day 28

value: Cultured single clone, passage 8


title: ChIP_mouse_WT_UNSTIM_1_H3K27ac_IP


title: Fgfr3creER_p53cKO_P28_RNA [Sample_2963-YM-8]


title: ChIP_Tram_IFNLPS_1

value: IFNLPS


title: Fgfr3creER_p53cKO_P28_RNA [Sample_2963-YM-4]


title: HL60 + 1uM AZA Day 4 [HL60day4Rep1]

value: Acute myeloid leukemia


title: ChIP_Tram_CTRL_2


title: THP1_DMSO_CTRL_input

value: DMSO


title: HL60- No AZA_rep 2 [HL60day0Rep2]

source_name: HL60- No AZA

value: No Treatment


title: HT29_ORF_C1orf106_21

source_name: HT-29 C1orf106 transduction, UniqueID 21

tag: orf

tag: uniqueid

tag: arraybatch

tag: transductiondate


title: ChIP_mouse_WT_UNSTIM_2_H3K27ac_IP

tag: genotype

value: WT

value: UNSTIM


title: Fgfr3creER_p53cKO_P4M_RNA [Sample_2963-YM-9]

tag: tissue


title: ChIP_Tram_IL4_2

tag: cell line

tag: chip antibody


title: ChIP_Pano_IL4_1

value: PANO


title: Fgfr3creER_WT_P23_RNA [Sample_1303-YM-7]

value: Fgfr3-creER; R26R(tdTomato/+)

value: Femurs

value: Postnatal day 23


title: DI3

first: shanshan

last: huang

address: No.1229 Gudun Road

institute: Zhejiang Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: BMDM Cells_DI

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Bone Marrow

tag: group

value: DI+LPS+ATP(DI)


title: ChIP_mouse_WT_IL2IL15_2_H3K27ac_input

tag: condition

tag: replicate

tag: antibody

tag: experimentid


title: ChIP_Pano_IFNLPS_2


title: DI2

tag: age


title: Fgfr3creER_p53cKO_P28_RNA [Sample_2963-YM-6]

tag: cells

value: Cultured tdTomato+ skeletal cells in bone marrow

tag: cell type/passage


title: Fgfr3creER_p53cKO_P28_RNA [Sample_2963-YM-7]


title: HL60- No AZA_rep 3 [HL60day0Rep3]

tag: cell type

tag: origin

value: Peripheral Blood of 35yo woman with AML (FAB M2 Classification)

tag: cell treatment


title: HL60 + 1uM AZA Day 3_rep 3 [HL60day1Rep3]

source_name: HL60 + 1uM AZA Day 3

value: 1uM Azacitidine Treatment for 24h


title: Fgfr3creER_WT_P23_RNA [Sample_1303-YM-6]


title: ChIP_mouse_WT_IL12IL18_1_H3K27ac_input


title: ChIP_Tram_CTRL_1

tag: treatment

value: TRAM

tag: polarization

value: control

value: anti-H3K27ac (Abcam Cat# ab4729, RRID:AB_2118291)


title: Fgfr3CE;R26RtdT [1531-YM-1]

description: FACS-sorted at 23

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the LIGER R package.
We filtered out cells with less than 1000 genes per cell and with more than 30% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: cellular barcodes, gene identifiers, UMI counts

source_name: Femurs

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v3
10X Genomics Chromium Single Cell 3' v3 Libraries

tag: genotype

value: tdTomato+ stromal cells in bone marrow

value: Postnatal day 23 (tamoxifen at P21)


title: ChIP_mouse_WT_UNSTIM_1_H3K27ac_input


title: HL60 + 1uM AZA Day 1 [HL60day1Rep1]

source_name: HL60 + 1uM AZA Day 1

tag: cell line

value: Acute myeloid leukemia


title: Fgfr3creER_WT_P23_RNA [Sample_1303-YM-10]

tag: tissue

value: Cultured single clone, passage 8


title: Fgfr3creER_WT_P23_RNA [Sample_1303-YM-9]


title: DI1

tag: strain


title: control1

source_name: BMDM Cells_control

tag: group

value: LPS+ATP(control)


title: ChIP_mouse_WT_IL12IL18_1_H3K27ac_IP

value: WT

tag: condition


title: shAdamtsl2_C2C12_rep3

city: New York

first: Dirk

last: Hubmacher

state: New York(NY)

address: 1468 Madison Av, Annenberg Building 20-80B

department: Orthopaedics

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Using DESeq2, a comparison of gene expression between the two groups of samples was performed
The Wald test was used to generate p-values and log2 fold changes.
Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison
Genome_build: Mus musculus GRCm38 reference genome (ENSEMBL)
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

extract_protocol:
1 ml TRIzol according to manufacturer'2 protocol
polyA selection for mRNA
RNAseq, 20-30 Mio reads (HiSeq 2 × 150 PE HO HiSeq 2 × 150bp configuration, Illumina HiSeq 4000)

treatment_protocol: Upon reaching confluence, C2C12 cells were switched to DMEM + 2% horse serum (day 0) and cultured for 3 days (day 3), when total mRNA was extracted

value: Adamtsl2 knockdown

tag: time

value: differentiation day 3


title: Gas1CE;R26RtdT [1961-YM]

description: FACS-sorted at 23

value: Gas1-creER; R26R(tdTomato/+)


title: ChIP_Pano_CTRL_1

value: PANO

tag: chip antibody


title: HL60- No AZA  [HL60day0Rep1]

value: No Treatment


title: ChIP_DMSO_IL4_1

value: DMSO


title: control2

value: Bone Marrow


title: ChIP_DMSO_IL4_2


title: Prrx1cre_P21_multiome [1871-YM-1_scATAC-seq]

description: FACS-sorted at P21

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the LIGER R package.
We filtered out cells with less than 1000 genes per cell and with more than 30% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (UMAP), unsupervised clustering, the discovery of differentially expressed cell-type specific markers, accessbility peak calling, and transcription factor binding site analysis.
Genome_build: mm10_trans_nono
Supplementary_files_format_and_content: cellular barcodes, gene identifiers, UMI counts; called peaks

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~15,000 single nuclei were loaded onto 10X Genomics Single Cell ATAC + Gene Expression
10X Genomics Single Cell Multiome ATAC + Gene Expression

value: Prrx1-cre; R26R(tdTomato/+)

value: Postnatal day 21


title: Fgfr3creER_WT_P23_RNA [Sample_1303-YM-8]

value: Fgfr3-creER; R26R(tdTomato/+)

value: Femurs

value: Cultured tdTomato+ skeletal cells in bone marrow

value: Postnatal day 23


title: ChIP_Pano_CTRL_2

value: control

value: anti-H3K27ac (Abcam Cat# ab4729, RRID:AB_2118291)


title: Prrx1cre_P21_ATAC [Sample_138264]

description: FACS-sorted at P21

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the LIGER R package.
We filtered out cells with less than 1000 genes per cell and with more than 30% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (UMAP), unsupervised clustering, accessbility peak calling, and transcription factor binding site analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cellular barcodes, called peaks,peak/cell matrix

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. tdTomato+ cells were FACS-isolated. ~18,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v3
10X Genomics Single Cell ATAC

value: tdTomato+ stromal cells in bone marrow


title: ChIP_Pano_IL4_2


title: ChIP_Pano_IFNLPS_1

value: IFNLPS


title: shAdamtsl2_C2C12_rep2

value: Adamtsl2 knockdown


title: control3

value: LPS+ATP(control)


title: Fgfr3CE_p53-cKO [1850-YM-1]

description: FACS-sorted at 4M

value: p53-deficient tdTomato+ stromal cells in bone marrow

value: 4 months


title: Prrx1cre_P21_multiome [1871-YM-1_scRNA-seq]

description: FACS-sorted at P21


title: ChIP_DMSO_IFNLPS_2


title: Fgfr3CE_p53-cHet [1829-YM-1]

description: FACS-sorted at 4M


title: 135_Con

city: Aurora

first: Amy

last: Kelly

state: Colorado

address: 12700 East 19th Avenue, Mail Stop 8613, P.O. Box 6511

institute: University of Colorado

description: Illumina_ Jansson_10_135_Con_placental cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were cleaned using Illumina's GenomeStudio and filtered using a quality score
The data were normalised using median normalization

label: biotin

source_name: primary trophoblasts

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyzer and concentration determined on Nanodrop

value: primary human trophoblast (PHT) cells


title: shAdamtsl2_C2C12_rep1

value: differentiation day 3


title: Control_C2C12_rep3

description: Ctrl-III

value: scramble


title: 135_Ric

description: Illumina_ Jansson_12_135_Ric_placental cells

value: rictorkd


title: 124_Rap

description: Illumina_ Jansson_8_124_Rap_placental cells

value: raptorkd


title: 117_Ric

description: Illumina_ Jansson_6_117_Ric_placental cells


title: 135_Rap

description: Illumina_ Jansson_11_135_Rap_placental cells


title: 124_Con

description: Illumina_ Jansson_7_124_Con_placental cells


title: 124_Ric

description: Illumina_ Jansson_9_124_Ric_placental cells


title: ChIP_DMSO_CTRL_2

value: DMSO


title: Prrx1cre_18M_RNA [2229-YM]

description: FACS-sorted at 18M

value: Prrx1-cre; R26R(tdTomato/+)

value: 18 months


title: Control_C2C12_rep1

description: Ctrl-I


title: Prrx1cre_P21_RNA [Sample_138263]

description: FACS-sorted at P21

value: Postnatal day 21


title: ChIP_DMSO_CTRL_1

value: control


title: PBMC_IL4_PANO_input

source_name: PBMC

value: peripheral blood monocyte

value: PANO

value: none (input)


title: MZ B CKO rep3

city: Smithville

first: Bin

last: Liu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
mapping with Tophat
HT-seq count to count raw reads
DESeq2 for DE analysis
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: text file for read counts

source_name: spleen

extract_protocol:
FO B cells and MZ B cells from mouse spleen were sorted by Miltenyi MZ and FO B Cell Isolation Kit (Cat#130-100-366), and total RNA was harvested using Qiagen RNeasy Mini Kit (Cat#74004).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: marginal zone (MZ) B cells

value: 8-12 weeks old


title: yedH mutant strain in hypoxia 3

city: Wuhan

first: Jiaxun

last: Zhang

address: Shizishan Road Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus (house mouse) whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium bovis BCG
Supplementary_files_format_and_content: gene_expression.xls file includes FPKM and count values for each Sample

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: yedH mutant strain in hypoxia

growth_protocol: Log phase shaking bacterials were inoculated into fresh medium at a starting OD600 of 0.01 and were treated using Wayne model for 24h

extract_protocol:
RNA was harvested using Trizol reagent. RNeasy Mini Kit （250） Qiagen#74106 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hypoxic condition following the Wayne model

value: hypoxia


title: symE 90min rep3 [RNA-seq]

city: Cambirdge

first: Mary

middle: Katherine

last: Thompson

address: 31 Ames St Room 68-570

department: Biology

institute: Massachusetts Institute of Technology

description: processed data file: T90Results.csv

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment, at all aligned positions a count was added.
cleavage ratio was calculated (+ SymE - empty vector) for assessing SymE cleavage in transcripts.
Differential expression was quantified using the DEseq2 pipeline
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: In all files other than T30Reuslts.csv and T90Results.csv the first column corresponds to the forward strand and the second two the reverse strand. Each row corresponds to the counts at a genomic position from 1 to len(genome). For each proper pair, 1 count was added to every position aligning to and between the two reads. Integer counts are raw and not normalized to library depth. T30Results.csv and T90Results.csv are csv file outputs of DE-seq looking at differential expression of symE vs an empty vector after 30 and 90 minutes of induction, respectively.

organism: Escherichia coli

source_name: Bacterial liquid culture

growth_protocol: E. coli MG1655 PCP18-araE cells harboring either pBAD24 or pBAD24::symE were grown overnight in M9 media containing carbenicillin and then back diluted into fresh M9 carb to OD600 0.02. Cultures were then grown to OD600 0.5 and 0-minute time point samples were collected. Cells were then induced with arabinose at 0.02%. Further samples were taken after 30- and 90- minutes of induction.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
Paired-end RNA-Seq libraries were prepared by random priming and strand information was maintained using the dUTP method. See publication for full details

value: MG1655 PCP18-araE

tag: plasmid

value: pBAD24 symE

tag: induction

value: 90 minutes

tag: molecule subtype

value: RNA with rRNA subtracted


title: symE 90min rep2 [RNA-seq]

description: processed data file: T90Results.csv


title: PBMC_IL4_DMSO_input


title: MZ B CKO rep2

tag: age


title: Control_C2C12_rep2

description: Ctrl-II

value: scramble

value: differentiation day 3


title: PBMC_IFN_PANO_input

tag: cell type

value: IFNLPS


title: emptyvec 90min rep3 [RNA-seq]

description: processed data file: T90Results.csv

value: pBAD24 empty


title: MZ B CKO rep1


title: yedH strain in hypoxia 3

source_name: yedH strain in hypoxia


title: MZ B Control rep3

value: WT


title: symE 90min rep1 [RNA-seq]

description: processed data file: T90Results.csv


title: emptyvec 90min rep2 [RNA-seq]

description: processed data file: T90Results.csv


title: PBMC_IFN_DMSO_input

value: DMSO


title: PBMC_CTRL_PANO_input

value: peripheral blood monocyte

value: control


title: 114_Con

description: Illumina_ Jansson_1_114_Con_placental cells

value: primary human trophoblast (PHT) cells


title: 117_Con

description: Illumina_ Jansson_4_117_Con_placental cells


title: 114_Ric

description: Illumina_ Jansson_3_114_Ric_placental cells

value: rictorkd


title: 114_Rap

description: Illumina_ Jansson_2_114_Rap_placental cells

value: raptorkd


title: yedH mutant strain in hypoxia 2


title: emptyvec 90min rep1 [RNA-seq]

description: processed data file: T90Results.csv


title: yedH strain in hypoxia 1


title: symE 30min rep3 [RNA-seq]

description: processed data file: T30Results.csv

value: 30 minutes


title: PBMC_IL4_PANO_2

value: PANO

value: anti-H3K27ac (Abcam Cat# ab4729, RRID:AB_2118291)


title: yedH mutant strain in hypoxia 1

value: hypoxia


title: FO B CKO rep3

value: spleen

value: Follicular (FO) B cells

value: 8-12 weeks old


title: symE 30min rep2 [RNA-seq]

description: processed data file: T30Results.csv

value: MG1655 PCP18-araE

value: pBAD24 symE

value: RNA with rRNA subtracted


title: PBMC_IL4_PANO_1


title: FO B CKO rep2


title: PBMC_CTRL_DMSO_input

value: none (input)


title: PBMC_IL4_DMSO_1

value: DMSO


title: yedH strain in hypoxia 2


title: BM-MSCs/3D-3

city: Busan

first: Sihyung

last: Wang

address: 63-2 Pusandaehak-ro, Kumjeong-gu

department: Integrated Biological Science

country: South Korea

institute: Pusan National University

description: Gene expression data from organoid spheroids

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip  Human Clariom S Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools(APT). We exported the result with gene level RMA analysis and perfomed the differentially expressed gene (DEG) analysis.
All data analysis and visualization of differentially expressed genes was conducted using R 3.0.2

source_name: Organoid of huamn bone marrow mesenchymal stem cells-3

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Human primary hepatic stellate cells and human bone marrow stem cells were cultured in organoid expansion medium.

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

treatment_protocol: rhTSG-6 treated in organoid spheroid by hepatic stellate cells

value: Bone marrow stem cells


title: BM-MSCs/3D-1

source_name: Organoid of huamn bone marrow mesenchymal stem cells-1


title: FO B CKO rep1


title: 117_Rap

description: Illumina_ Jansson_5_117_Rap_placental cells


title: PBMC_IL4_DMSO_2

value: peripheral blood monocyte


title: BM-MSCs/3D-2

source_name: Organoid of huamn bone marrow mesenchymal stem cells-2


title: MZ B Control rep1

value: marginal zone (MZ) B cells

value: WT


title: PBMC_IFN_PANO_2

value: IFNLPS


title: FO B Control rep2


title: FO B Control rep3


title: symE 0min rep3 [RNA-seq]

value: 0 minutes


title: emptyvec 30min rep2 [RNA-seq]

description: processed data file: T30Results.csv

value: pBAD24 empty

value: 30 minutes


title: adjacent tissue, 6B

city: zhongshan

first: yongyan

last: pei

address: Long life water, wuguishan street, zhongshan city

department: School of Pharmaceutical and Chemical Engineering

institute: Guangdong Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: adjacent tissue

extract_protocol:
These tissues were stored at 80 ℃ immediately after surgical resection.RNEasy Mini kit (Qiagen, Germany) was used to isolate total RNA. Then the concentration and purity of RNA were detected by Nanodrop 2000. The standard of library construction was OD: A260/A280 (< 2.0 and > 1.8) and A260/A230 (> 1.6). 1% agarose gel electrophoresis (Bio-Rad, USA) to analyze RNA to ensure no degradation.
The RNA library was constructed using TruSeq RNA sample preparation kit and TruSeq Small RNA (Illumina, USA). After purification, the library was quantified with Qubit 8000 (Life Technologies, USA) and verified with Agilent 2100 (Agilent Technologies, USA) to confirm the fragment size

value: adjacent tissue


title: TSG-6/3D-2

source_name: Organoid of TSG-6 given human primary hepatic stellate cells-2

value: primary hepatic stellate cells

value: Liver


title: PBMC_IFN_PANO_1

value: PANO

value: anti-H3K27ac (Abcam Cat# ab4729, RRID:AB_2118291)


title: PBMC_IFN_DMSO_2


title: TSG-6/3D-3

source_name: Organoid of TSG-6 given human primary hepatic stellate cells-3


title: emptyvec 30min rep3 [RNA-seq]

description: processed data file: T30Results.csv

value: MG1655 PCP18-araE


title: TSG-6/3D-4

source_name: Organoid of TSG-6 given human primary hepatic stellate cells-4


title: MZ B Control rep2

value: spleen

value: 8-12 weeks old


title: symE 30min rep1 [RNA-seq]

description: processed data file: T30Results.csv

value: pBAD24 symE

value: RNA with rRNA subtracted


title: FO B Control rep1

value: Follicular (FO) B cells


title: emptyvec 0min rep3 [RNA-seq]


title: hepatocellular carcinoma, 5A

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: CON/3D-2

source_name: Organoid of human primary hepatic stellate cells-2


title: PBMC_CTRL_DMSO_2

value: peripheral blood monocyte

value: DMSO

value: control


title: TSG-6/3D-1

source_name: Organoid of TSG-6 given human primary hepatic stellate cells-1


title: PBMC_IFN_DMSO_1

value: IFNLPS


title: adjacent tissue, 1B


title: symE 0min rep2 [RNA-seq]

value: 0 minutes


title: hepatocellular carcinoma, 1A


title: CON/3D-3

source_name: Organoid of human primary hepatic stellate cells-3


title: CON/3D-1

source_name: Organoid of human primary hepatic stellate cells-1


title: emptyvec 30min rep1 [RNA-seq]

description: processed data file: T30Results.csv

value: pBAD24 empty

value: 30 minutes


title: PBMC_CTRL_PANO_1

source_name: PBMC


title: PBMC_CTRL_PANO_2


title: adjacent tissue, 5B

value: adjacent tissue


title: STM430

status: Public on Oct 15 2021

city: Boston

first: Sonu

last: Subudhi

address: 100 Blossom St, Cox 7

department: Radiation Oncology

institute: Massachusetts General Hospital

data_processing: Nanostring raw data was normalized to housekeeping genes (CLTC, GUSB, PGK1, SDHA and TUBB).

source_name: Human liver

extract_protocol: RNA extraction was performed on 5-20 μg of liver tissue using the miRNeasy Mini Kit (Qiagen) for flash-frozen samples or the RNA-later liver or High Pure FFPET RNA Isolation Kit (Roche Life Science) for Formalin-Fixed Paraffin-Embedded tissue (FFPET) samples, according to manufacturer’s instructions. RNA quantity and quality were assessed using an Agilent 2100 bioanalyzer (Santa Clara, CA). RIN numbers, ranging from 1.5 to 9 are appropriate for use with the nCounter Technology

value: Human liver

tag: race

value: Black or African American

tag: bmi

tag: Sex

value: Female

tag: diabetes

value: No

tag: alt

tag: ast

tag: nafld stage

value: Steatosis


title: STM492

tag: tissue

value: White

value: Male

value: Yes


title: PBMC_CTRL_DMSO_1

tag: treatment

tag: polarization

value: anti-H3K27ac (Abcam Cat# ab4729, RRID:AB_2118291)


title: symE 0min rep1 [RNA-seq]

tag: strain

value: MG1655 PCP18-araE

value: pBAD24 symE

value: RNA with rRNA subtracted


title: STM165


title: hepatocellular carcinoma, 6A

value: hepatocellular carcinoma


title: emptyvec 0min rep2 [RNA-seq]

value: 0 minutes


title: ChIP_DMSO_IFNLPS_1

tag: cell line

value: DMSO

value: IFNLPS

tag: chip antibody


title: WCA107


title: emptyvec 0min rep1 [RNA-seq]

tag: plasmid

value: pBAD24 empty

tag: induction


title: STM183

value: Human liver

tag: age


title: D

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

description: A small leaf-mining moth, Stomphastis sp. (Lepidoptera: Gracillariidae) was imported from Peru to Australia in 2014.

data_processing:
The CLC Genomics Workbench version 21.0.5 was used for bioinformatics analyses. Both libraries were trimmed from any vector or adapter sequences remaining.  Low quality reads (quality score below 0.05) and reads with more than two ambiguous nucleotides were discarded. In the absence of a reference genome, we used a de novo assembly approach (word size 25, bubble size 50 and minimum contig length 300 bp) to process this data.
The contigs were corrected by mapping all reads against the assembled sequences (min. length fraction, maximum mismatch, insertion, and deletion cost of 0.8, 2, 3 and 3 respectively). The Read Per Kilobase of transcript per Million mapped reads (RPKMs) value was calculated for each assembled contigs.
Genome_build: Fasta, De novo Assembly
Supplementary_files_format_and_content: gene expression profile of assembled contigs and the BLAST results as processed data.

organism: unclassified Stomphastis

source_name: Affected Larvae

growth_protocol: The leaf-mining moth (Stomphastis sp.) was imported from Peru to Australia in 2014. The insect colony has been maintained in the Department of Agriculture and Fisheries quarantine facility in Brisbane as a potential biological control agent of a weed, Bellyache bush (Jatropha gossypiifolia).

extract_protocol:
Twenty larvae with and without oblivious sign of disease were preserved in an RNA stabilization reagent (RNAprotect®, QIAGEN Cat No.:76104) for further RNA extraction and sequencing. The whole larvae were transferred to Qiazol lysis reagent for RNA extraction according to the manufacturer’s instructions (QIAGEN; Cat No.: 79306). The RNA samples were treated with DNase I for 1 h at 37°C and then their concentrations were measured using a spectrophotometer and integrity was ensured through analysis of RNA on a 1% (w/v) agarose gel.
After checking the RNA quality, total RNA from two samples (infected and uninfected) were submitted to the Genewiz sequencing facility (Jiangsu, China) for library preparation (after eukaryote ribosomal RNA depletion) and strand specific total RNA sequencing on NovaSeq platform.

value: Whole Larvae

tag: culture method

value: Lab Colony


title: STM339

tag: race

value: Black or African American

value: Female

value: No


title: WCA211

value: White

tag: bmi

value: Normal


title: WCA322

value: Other

tag: Sex


title: WCA099

tag: diabetes

value: Yes


title: WCA036

tag: alt

value: Steatosis


title: H

source_name: Unaffected larvae


title: WCA184

tag: ast


title: STM405

value: Male

tag: nafld stage


title: WCA151

tag: tissue


title: KCN490


title: WCA143


title: WCA039


title: WCA090


title: WCA019


title: WCA220


title: WCA006


title: WCA312


title: WCA276


title: WCA246


title: WCA261


title: WCA133


title: WCA125


title: WCA197


title: WCA254


title: WCA043


title: WCA177


title: WCA236


title: WCA152


title: WCA172


title: WCA207


title: STM244


title: STM291


title: WCA251


title: WCA175


title: WCA164


title: WCA188


title: WCA153


title: WCA087


title: STM271


title: STM247


title: STM322


title: STM253


title: STM313


title: STM263


title: WCA182


title: STM261


title: STM270


title: STM310


title: STM198

value: Unknown


title: STM248


title: STM254


title: STM284


title: STM301


title: STM416


title: STM324


title: STM249


title: STM274


title: STM420


title: STM268


title: STM327


title: STM427


title: STM308


title: STM251


title: STM285


title: STM250


title: STM318


title: STM319


title: STM303


title: STM193


title: STM216


title: WCA057


title: STM418


title: STM431


title: STM443


title: STM459


title: STM410


title: STM414


title: STM194


title: STM164


title: STM480


title: STM223


title: STM203


title: STM163


title: STM222


title: STM463


title: STM460


title: STM374


title: STM396


title: STM498


title: STM229


title: STM380


title: STM218


title: STM168


title: STM160


title: STM429


title: STM446


title: STM445


title: STM489


title: STM235


title: STM496


title: STM149


title: STM187


title: STM453


title: STM152


title: STM146


title: STM161


title: STM397


title: STM238


title: STM158


title: STM475


title: STM175


title: STM059


title: STM192


title: STM151


title: STM232


title: STM240


title: STM368


title: mir-4423 overexpression, 48 h post-transfection, replicate 4

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: Transcriptome data for HeLa cell culture after transfection of mir-4423 plasmid

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, gene-level probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.

label: Biotin

source_name: HeLa cells + mir-4423 plasmid

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 210 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: The HeLa cells were cultured in DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 50 U/ml penicillin-streptomycin (Thermo Fisher Scientific) in T25 flasks (Greiner Bio-One).

extract_protocol: Total RNA was isolated 24 h and 48 h after transfection with the miRNeasy Mini Kit (Qiagen).

treatment_protocol: The cells were transiently transfected with the mir-199a-1 expression plasmid (HmiR0296-MR04, GeneCopoeia), the mir-4423 expression plasmid (HmiR1083-MR04, GeneCopoeia) or the negative control plasmid (CmiR0001-MR04, GeneCopoeia) using the FuGENE HD transfection reagent (Promega).

value: HeLa

value: mir-4423 expression plasmid

tag: time point


title: STM436


title: STM150


title: STM191


title: STM180


title: mir-4423 overexpression, 24 h post-transfection, replicate 1


title: STM356


title: STM071


title: STM236


title: STM028


title: STM199


title: STM138


title: STM154


title: STM451


title: STM423


title: STM494


title: STM055


title: STM018


title: STM186


title: mir-199a-1 overexpression, 24 h post-transfection, replicate 2

description: Transcriptome data for HeLa cell culture after transfection of mir-199a-1 plasmid

source_name: HeLa cells + mir-199a-1 plasmid

value: mir-199a-1 expression plasmid


title: mir-199a-1 overexpression, 48 h post-transfection, replicate 3


title: negative control, 48 h post-transfection, replicate 3

description: Transcriptome data for HeLa cell culture after transfection of control plasmid

source_name: HeLa cells + control plasmid

value: negative control plasmid


title: STM234

value: Human liver


title: STM212


title: STM220


title: mir-4423 overexpression, 48 h post-transfection, replicate 1


title: STM210


title: STM110


title: mir-4423 overexpression, 48 h post-transfection, replicate 2


title: mir-4423 overexpression, 48 h post-transfection, replicate 3


title: mir-199a-1 overexpression, 48 h post-transfection, replicate 4


title: STM419


title: negative control, 24 h post-transfection, replicate 2


title: 12W-4

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Remove the 3' linker sequence in the reads, and remove the reads without inserts due to the connector self-ligation. Remove the reads with low-quality sequence and reads containing the unknown base N, too short(<18nt) or too long(> 32 nt).
Useing fastx_tool 0.04 to ffilter the low quality data , and using bowtie version 1.1.1 for genome mapping.
The expression level of each transcript was calculated according to the (TPM) method. miRDeep2 was used to quantify gene abundances
Differential miRNA expression analysis was done using R package DEGseq
Genome_build: ARS1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Capra hircus

source_name: Goat kid

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeqTM stranded total RNA Kit(San Diego, CA)  was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 12 weeks of age

value: liver


title: STM147


title: mir-4423 overexpression, 24 h post-transfection, replicate 2


title: STM143

value: Black or African American


title: STM119

value: Female


title: STM060


title: 8W-5

value: 8 weeks of age


title: STM104

value: White


title: mir-199a-1 overexpression, 48 h post-transfection, replicate 1


title: STM226


title: STM157

value: No

value: Normal


title: 8W-2


title: 8W-1


title: STM100

value: Yes


title: STM122


title: STM051


title: 12W-5


title: 4W-3

value: 4 weeks of age


title: negative control, 48 h post-transfection, replicate 1


title: STM215


title: mir-199a-1 overexpression, 48 h post-transfection, replicate 2


title: 4W-5


title: mir-199a-1 overexpression, 24 h post-transfection, replicate 1


title: 12W-1


title: negative control, 48 h post-transfection, replicate 2


title: 12W-2


title: 4W-1


title: STM162


title: 12W-3


title: negative control, 48 h post-transfection, replicate 4


title: 2W-3

value: 2 weeks of age


title: STM086


title: STM019


title: 8W-4


title: 2W-1


title: 4W-4


title: STM041

value: Male


title: STM217


title: STM072


title: STM098


title: 8W-3


title: STM005


title: STM182


title: STM116


title: STM049


title: negative control, 24 h post-transfection, replicate 1

value: HeLa


title: STM053


title: STM013


title: 2W-2


title: STM010


title: 2W-5


title: STM025


title: STM052


title: STM139


title: STM121


title: Patient ID 46

first: Glenn

middle: J

last: Hanna

address: 450 Brookline Avenue, Dana 2-140

department: Medical Oncology

institute: Dana-Farber Cancer Institute, Harvard Medical School

data_processing: A version of the Tumor Inflammation Signature (TIS) [18], an 18-gene signature that measures a pre-existing but suppressed adaptive immune response within various cancers was utilized. Significantly differentially expressed genes and additional signatures were computed using Nanostring nSolver Advanced Analysis Module after normalization to default housekeeping genes with at least 100 counts.

source_name: Oral leukoplakia

label_protocol: The nCounter Analysis System is based on a novel digital color-coded barcode technology and PCI provides a highly multiplexed gene expression panel designed to quantitate 770 genes that fall into four functional categories (infiltrating immune cell types, immunological function, tumor-specific antigens, and housekeeping genes).

extract_protocol: Isolated RNA was run on Bioanalyzer to obtain DV200 values (Fragment above 200bp) using Agilent RNA 6000 Pico kit (Agilent Technologies, Santa Clara, CA). A minimum of 100 nanograms of isolated RNA with greater than DV200 per sample was loaded and run on the HuV1_CancerImmu_v1_1 Nanostring platform for analysis of the NanoString PanCancer Immune Profiling Panel (PCI), as previously described [17].

treatment_protocol: RNA from each OL specimen was isolated from cores punched from areas of epithelial dysplasia (High Pure FFPET RNA Isolation Kit, Roche Diagnostics, Indianapolis, Indiana) marked on FFPE tissue slides and quantified (NanoDrop Products; Thermo Scientific, Wilmington, DE).

tag: histology

value: PL

tag: smoking status

value: N

tag: gender

value: M


title: Ctrl SMC_HA-2

city: Pittsburgh

first: Delphine

last: Gomez

state: PA

address: 200 Lothrop Street

department: Medicine, division of Cardiology

institute: University of Pittsburgh

data_processing:
Library strategy: CUT&Tag
Paired-end raw reads were aligned to Rn6 using Bowtie2. Tracks were generated by deepTools2 Bamcoverage with normalized counts as bins per million (BPM) and visualized with IGV. Peaks were called using MACS2 callpeak with cut off FDR (q-value) at 0.05. Peaks were annotated by ChIPseeker with rn6.ncbiRefSeq as the annotation source.
Genome_build: Rn6
Supplementary_files_format_and_content: bigwig file of each CUT&Tag seq sample
Supplementary_files_format_and_content: Annotated peak files for CUT&Tag seq sample

source_name: Aortic SMC

growth_protocol: Cell lines were cultured in growth medium (DMEM/F12, Gibco) supplemented with FBS (10%, Corning), L-glutamine (1.6 mM, Gibco) and penicillin-streptomcyin (100 U/ml, Gibco).

extract_protocol:
Genomic DNA after immunoprecipitation was extracted  by CUT&Tag-IT Assay Kit (Active motif) following manufacturer's protocol. 500,000 cells were used for CUT&Tag assay. After binding with Concanavalin A beads, cells were incubated with primary antibody targeting HA-tag (Abcam ab9110) overnight at 4℃. Samples were then incubated with Guinea Pig anti-Rabbit antibody, CUT&Tag-IT Assembled pA-Tn5 Transposomes. After tagmentation, released DNA was extracted by DNA purification column for library preparation and SPRI Beads clean-up.
DNA library was perpared by illumina Nextera primers provided  with CUT&Tag-IT Assay Kit.

treatment_protocol: Cells were treated with Adv-HA-TET2 for 24 hours in growing medium before harvesting for CUT&Tag Seq

tag: cell line

value: WT

tag: cell type

value: Aortic SMC

tag: treatment

tag: cut&tag antibody

value: HA-Tag, Abcam, ab9110


title: STM095

value: Human liver

value: Unknown

tag: age


title: Myocd-LSD1_HA-1


title: Patient ID 44

description: A minimum of 100 nanograms of isolated RNA with greater than DV200 per sample was loaded and run on the HuV1_CancerImmu_v1_1 Nanostring platform for analysis of the NanoString PanCancer Immune Profiling Panel (PCI), as previously described

value: F


title: 1D-4

value: 1 day of age

value: liver


title: 2W-4


title: 1D-5


title: STM031

tag: race

value: White

value: Female

value: No


title: Myocd-LSD1_FLAG_4

data_processing:
Library strategy: CUT&Tag
CUT&Tag Seq: Paired-end raw reads were aligned to Rn6 using Bowtie2. Tracks were generated by deepTools2 Bamcoverage with normalized counts as bins per million (BPM) and visualized with IGV. Peaks were called using MACS2 callpeak with cut off FDR (q-value) at 0.05. Peaks were annotated by ChIPseeker with rn6.ncbiRefSeq as the annotation source. Differential binding analysis of H3K4m2 enrichment was performed by DiffBind with significant threshold at FDR<0.05.
Genome_build: Rn6
Supplementary_files_format_and_content: bigwig file of each sample
Supplementary_files_format_and_content: Annotated peak files for CUT&Tag seq sample
Supplementary_files_format_and_content: Differential binding peak file comparing Myocd-LSD1 and Myocd-LSD1NF H3K4me2

extract_protocol:
Genomic DNA after immunoprecipitation was extracted  by CUT&Tag-IT Assay Kit (Active motif) following manufacturer's protocol. 500,000 cells were used for CUT&Tag assay. After binding with Concanavalin A beads, cells were incubated with primary antibody targeting H3K4me2 (Activemotif 39141) or FLAG (Sigma F7425) overnight at 4℃. Samples were then incubated with Guinea Pig anti-Rabbit antibody, CUT&Tag-IT Assembled pA-Tn5 Transposomes. After tagmentation, released DNA was extracted by DNA purification column for library preparation and SPRI Beads clean-up.
DNA library was perpared by illumina Nextera primers provided  with CUT&Tag-IT Assay Kit.

value: Myocd-LSD1 (FLAG-tagged)

value: FLAG, Sigma, F7425


title: STM118

value: Black or African American

tag: bmi

value: Normal


title: Patient ID 49

value: PL

value: N


title: STM006

tag: Sex


title: 4W-2

value: 4 weeks of age


title: STM054

tag: diabetes


title: Myocd-LSD1_FLAG_3

value: Aortic SMC


title: STM023

tag: alt


title: Patient ID 47

value: M


title: Patient ID 43


title: STM231

value: Human liver

tag: ast


title: STM035

tag: nafld stage


title: 1D-2

tag: tissue


title: 1D-1


title: Patient ID 41


title: Patient ID 48


title: STM117


title: STM077

value: Yes


title: STM125


title: Ctrl SMC_H3K4me2-3

value: WT

value: Activemotif, H3K4me2, 39141


title: STM272


title: STM259


title: STM038


title: STM211


title: Ctrl SMC_HA-1

value: HA-Tag, Abcam, ab9110


title: STM132


title: Patient ID 45


title: STM001

value: White


title: STM069

value: Female


title: STM030

value: No


title: Patient ID 37

value: F


title: Patient ID 42


title: STM169

value: Male


title: STM135


title: STM015


title: Myocd-LSD1_FLAG_2

value: Myocd-LSD1 (FLAG-tagged)

value: FLAG, Sigma, F7425


title: Ctrl SMC_H3K4me2-1


title: Ctrl SMC_H3K4me2-2


title: STM068


title: Myocd-LSD1_FLAG_1


title: STM185


title: STM042


title: Patient ID 40

value: PL


title: Patient ID 39


title: STM057

value: Normal


title: STM209

value: Steatosis


title: Patient ID 36

value: N


title: Patient ID 38


title: STM159


title: STM197


title: 1D-3

value: 1 day of age

value: liver


title: Patient ID 35

value: M


title: Patient ID 33

value: PEL


title: Myocd-LSD1NF_H3K4me2-3

description:
chipseeker_Myocd-LSD1NF_H3K4me2.xlsx
Diffbind_Myocd-LSD1_Myocd-LSD1NF.xlsx

value: Aortic SMC

value: Activemotif, H3K4me2, 39141


title: Patient ID 32


title: Myocd-LSD1NF_H3K4me2-2


title: STM188

value: Human liver

value: Black or African American


title: Myocd-LSD1_H3K4me2-2

description:
Chipseeker_Myocd-LSD1_H3K4me2.xlsx
Diffbind_Myocd-LSD1_Myocd-LSD1NF.xlsx


title: STM213

value: White

value: No


title: STM134

value: Female


title: Patient ID 34

value: F


title: STM376

value: Male


title: STM179


title: TOC-08-ACC

type: genomic

city: São Paulo

first: Caroline

middle: Perez

last: Camilo

state: São Paulo

address: Rua Doutor Ovídio Pires de Campos, 785

department: Institute of Psychiatry

country: Brazil

institute: University of São Paulo

hyb_protocol: DNA was bisulfite-converted using the EZ DNA methylation kit (Zymo Research, Irvine, California, USA), according to the manufacturer's instructions and hybridized in the Illumina Infinium HumanMethylation450 BeadChip (Illumina Inc., San Diego, California, USA), using standard Illumina protocol.

scan_protocol: Arrays were scanned with the iScan SQ scanner (Illumina).

data_processing:
Data processing were performed using GenomeStudio software (v.2011.1), with the methylation module v.1.9.0 (Illumina).
Average beta values.

label: Cy3, Cy5

source_name: OCD patient, ID 08, DNA_anterior cingulate gyrus

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted using QIAsymphony DNA Kit (Qiagen, Hilden, Mettmann, Germany) on QIAsymphony platform, according to the manufacturer’s instructions.

value: Brain_anterior cingulate gyrus

tag: sample group

value: OCD

tag: education (years)

tag: alcohol

value: Never

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph

tag: hemisphere

value: Left


title: Myocd-LSD1_H3K4me2-3

tag: cell line

tag: cell type

tag: cut&tag antibody


title: TOC-08-OFC

source_name: OCD patient, ID 08, DNA_orbitofrontal cortex

value: Brain_orbitofrontal cortex

tag: gender

tag: age


title: STM174

tag: race

tag: bmi

tag: Sex

tag: diabetes

tag: alt

value: Normal


title: STM329

tag: tissue

value: Yes

tag: ast

tag: nafld stage


title: Patient ID 31

tag: histology

value: PEL

tag: smoking status

value: N


title: STM345


title: STM398

value: Steatosis


title: Myocd-LSD1NF_H3K4me2-1

value: Aortic SMC

value: Activemotif, H3K4me2, 39141


title: STM366

value: Human liver

value: White


title: STM189

value: Female

value: No


title: STM219

value: Black or African American


title: STM355

value: Male


title: STM101


title: Myocd-LSD1_H3K4me2-1


title: STM462


title: TOC-08-PT

source_name: OCD patient, ID 08, DNA_putamen

tag: sample group

value: OCD

tag: education (years)

tag: alcohol

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph


title: Patient ID 29

tag: gender

value: M


title: TOC-07-OFC

source_name: OCD patient, ID 07, DNA_orbitofrontal cortex

tag: age

value: Stopped

tag: hemisphere

value: Right


title: STM434

tag: race

tag: bmi

tag: Sex

tag: diabetes


title: TOC-08-CN

source_name: OCD patient, ID 08, DNA_caudate nucleus

tag: tissue

value: Brain_caudate nucleus

value: Never

value: Left


title: Patient ID 28

tag: histology

value: PEL

value: F


title: Patient ID 30

tag: smoking status


title: TOC-07-CN

source_name: OCD patient, ID 07, DNA_caudate nucleus

tag: sample group

value: Yes


title: TOC-08-NAC

source_name: OCD patient, ID 08, DNA_nucleus accumbens

value: Brain_nucleus accumbens

tag: education (years)


title: STM357

value: Human liver

tag: alt

tag: ast

tag: nafld stage

value: Steatosis


title: Patient ID 26

value: LL


title: Patient ID 24

value: C


title: Patient ID 25

value: N


title: STM389

value: White

value: Female

value: No


title: Patient ID 22


title: STM367

value: Black or African American


title: TOC-07-NAC

source_name: OCD patient, ID 07, DNA_nucleus accumbens

value: OCD

value: Male

tag: alcohol

value: Stopped

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

value: Right


title: STM358

source_name: Human liver

tag: age


title: STM432

tag: race


title: STM020

tag: bmi

value: Normal


title: STM365

tag: Sex


title: Patient ID 23

value: F

tag: gender


title: STM105

tag: tissue

tag: diabetes


title: Patient ID 21

tag: histology

tag: smoking status


title: TOC-07-PT

source_name: OCD patient, ID 07, DNA_putamen

tag: sample group

tag: education (years)

value: Yes

tag: ph

tag: hemisphere


title: STM382

tag: alt

tag: ast

tag: nafld stage


title: STM332


title: STM325


title: Patient ID 27

value: M


title: STM372

value: Human liver


title: TOC-07-ACC

source_name: OCD patient, ID 07, DNA_anterior cingulate gyrus

value: Brain_anterior cingulate gyrus

tag: alcohol

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)


title: TOC-06-PT

source_name: OCD patient, ID 06, DNA_putamen

tag: age

value: Never

value: Left


title: STM465

tag: race

tag: bmi

tag: Sex

value: Steatosis


title: STM388

tag: tissue

value: White

tag: diabetes


title: Patient ID 20

tag: histology

value: LL

tag: smoking status

tag: gender


title: Patient ID 18

value: N


title: TOC-06-ACC

source_name: OCD patient, ID 06, DNA_anterior cingulate gyrus

tag: sample group

tag: education (years)

tag: ph

tag: hemisphere


title: STM482

value: Black or African American

value: Female

value: No

tag: alt

tag: ast

tag: nafld stage


title: STM468


title: STM464

value: Male


title: TOC-05-PT

source_name: OCD patient, ID 05, DNA_putamen

value: OCD

tag: alcohol

tag: tobacco

value: Stopped

tag: brain volume (ml)

tag: brain weight (g)


title: Patient ID 16

value: F


title: Patient ID 19


title: STM456

tag: race

tag: bmi

tag: age

tag: Sex


title: TOC-06-CN

source_name: OCD patient, ID 06, DNA_caudate nucleus

tag: tissue

value: Brain_caudate nucleus

value: Yes


title: Patient ID 17

source_name: Oral leukoplakia

tag: histology

tag: smoking status

tag: gender

value: M


title: TOC-05-CN

source_name: OCD patient, ID 05, DNA_caudate nucleus

tag: sample group

tag: education (years)

tag: ph


title: STM470

value: Human liver

tag: diabetes

tag: alt

tag: ast


title: STM045

tag: nafld stage


title: STM046


title: STM407


title: STM381


title: STM111

value: Normal


title: TOC-05-ACC

source_name: OCD patient, ID 05, DNA_anterior cingulate gyrus

value: Brain_anterior cingulate gyrus

tag: alcohol

value: Never

tag: tobacco

tag: brain volume (ml)

tag: hemisphere

value: Left


title: Patient ID 14

value: LL


title: TOC-04-PT

source_name: OCD patient, ID 04, DNA_putamen

tag: age

tag: brain weight (g)

value: Right


title: TOC-04-NAC

source_name: OCD patient, ID 04, DNA_nucleus accumbens

tag: tissue

value: Brain_nucleus accumbens


title: Patient ID 13

tag: histology


title: STM348

tag: race

value: White

tag: bmi

tag: Sex

value: Female


title: STM083

value: Black or African American

value: No


title: TOC-04-ACC

source_name: OCD patient, ID 04, DNA_anterior cingulate gyrus

tag: sample group

value: OCD

tag: gender

value: Male

tag: education (years)


title: STM363

tag: diabetes

tag: alt

value: Steatosis


title: Patient ID 15

tag: smoking status

value: F


title: Patient ID 12


title: Patient ID 11

value: M


title: Patient ID 10

value: N


title: STM082

value: Human liver

tag: ast

tag: nafld stage

value: Normal


title: STM409


title: STM373

value: Yes


title: STM490


title: TOC-02-OFC

source_name: OCD patient, ID 02, DNA_orbitofrontal cortex

value: Brain_orbitofrontal cortex

tag: alcohol

value: Never

tag: tobacco

tag: brain volume (ml)

tag: ph

value: Left


title: TOC-03-ACC

source_name: OCD patient, ID 03, DNA_anterior cingulate gyrus

tag: tissue

value: Brain_anterior cingulate gyrus

tag: age

tag: brain weight (g)

tag: hemisphere


title: STM377

tag: race

tag: bmi

tag: Sex


title: STM473

value: White


title: TOC-03-OFC

source_name: OCD patient, ID 03, DNA_orbitofrontal cortex

tag: sample group

tag: gender

value: Female

tag: education (years)


title: STM335

value: Black or African American

tag: diabetes

tag: alt


title: Patient ID 9

tag: histology

value: LL

tag: smoking status


title: TOC-04-OFC

source_name: OCD patient, ID 04, DNA_orbitofrontal cortex

value: OCD

tag: alcohol

tag: tobacco

value: Right


title: STM461

source_name: Human liver

value: No

tag: ast

tag: nafld stage

value: Steatosis


title: TOC-02-CN

source_name: OCD patient, ID 02, DNA_caudate nucleus

tag: tissue

value: Brain_caudate nucleus

value: Male

tag: age

tag: brain volume (ml)

tag: ph


title: STM472

value: Human liver

tag: race

tag: bmi


title: STM444

tag: Sex


title: STM458


title: STM349


title: WCA035


title: STM262


title: STM455

value: Normal


title: WCA334

value: Refused


title: Patient ID 6

value: F

tag: gender


title: Patient ID 8

value: N


title: TOC-02-NAC

source_name: OCD patient, ID 02, DNA_nucleus accumbens

value: Brain_nucleus accumbens

tag: sample group

tag: education (years)

value: Never

tag: brain weight (g)

tag: hemisphere

value: Left


title: TOC-04-CN

source_name: OCD patient, ID 04, DNA_caudate nucleus


title: TOC-02-ACC

source_name: OCD patient, ID 02, DNA_anterior cingulate gyrus

value: Brain_anterior cingulate gyrus


title: STM474

value: White

tag: diabetes

value: Yes

tag: alt


title: Patient ID 7

tag: histology

value: LL

tag: smoking status

value: M


title: WCA135

value: Female

value: No

tag: ast

tag: nafld stage


title: Patient ID 5

value: C


title: WCA186

tag: tissue

value: Black or African American

tag: age

value: Steatosis


title: WCA147

value: Human liver

value: Male


title: WCA198


title: Patient ID 4

value: F


title: TOC-01-ACC

source_name: OCD patient, ID 01, DNA_anterior cingulate gyrus

value: OCD

tag: alcohol

value: Stopped

tag: tobacco

tag: brain volume (ml)

tag: ph

value: Right


title: STM417

tag: race

tag: bmi

tag: Sex


title: Patient ID 2

value: EL

value: N

tag: gender


title: Patient ID 3


title: WCA132

value: White

value: Normal


title: STM266


title: STM273


title: Patient ID 1


title: CON-3b-ACC

source_name: Control, ID 3b, DNA_anterior cingulate gyrus

value: Brain_anterior cingulate gyrus

tag: sample group

value: Control

tag: education (years)

value: Never

value: Yes

tag: brain weight (g)

tag: hemisphere

value: Left


title: CON-3b-CN

source_name: Control, ID 3b, DNA_caudate nucleus

value: Brain_caudate nucleus

value: Female


title: STM276

value: Human liver

tag: diabetes

value: No

tag: alt


title: CON-3b-NAC

source_name: Control, ID 3b, DNA_nucleus accumbens

value: Brain_nucleus accumbens


title: TOC-02-PT

source_name: OCD patient, ID 02, DNA_putamen

value: OCD

value: Male


title: STM437

tag: ast

tag: nafld stage


title: STM438

tag: tissue

value: Black or African American

tag: age


title: MSCV control rep1

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to ENSEMBL mm10 genome build using subread. Read counts were quantified at the gene and exon level using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file include raw exon counts for every exon and every sample

growth_protocol: Ba/F3 cells expressing empty vector control (MSCV) were routinely cultured in the presence of 0.5ng/ml of murine IL-3. Ba/F3 cells transformed by BCR-ABL1 or SFPQ-ABL1 were cultured in the absence of IL-3.

extract_protocol:
Exponentially growing Ba/F3 cells were washed, pelleted and snap frozen prior to RNA extraction. RNA was extracted from Ba/F3 cell pellets using the PureLink RNA Mini Kit (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: pro-B cells

value: blood

tag: genotype

value: MSCV

tag: cell line

tag: treatment

value: untreated


title: STM296

tag: race

value: White

tag: bmi


title: WCA078

tag: Sex


title: SFPQ rep1


title: CON-3b-PT

source_name: Control, ID 3b, DNA_putamen

tag: sample group

value: Control

tag: gender

tag: alcohol

tag: tobacco

tag: brain volume (ml)

tag: ph


title: TOC-01-OFC

source_name: OCD patient, ID 01, DNA_orbitofrontal cortex

value: Brain_orbitofrontal cortex

tag: education (years)

value: Stopped

tag: brain weight (g)

tag: hemisphere

value: Right


title: MSCV control rep2

tag: tissue


title: WCA145

tag: age

tag: diabetes

value: Yes

tag: alt

tag: ast

tag: nafld stage

value: Steatosis


title: CON-3b-OFC

source_name: Control, ID 3b, DNA_orbitofrontal cortex

value: Female

value: Never

value: Left


title: BCR rep1

tag: cell type

tag: genotype

tag: cell line

tag: treatment


title: CON-08-CN

source_name: Control, ID 08, DNA_caudate nucleus

value: Brain_caudate nucleus

tag: sample group

tag: gender

tag: alcohol


title: BCR rep2


title: WCA168

value: Human liver

tag: race

tag: bmi

tag: Sex

value: No

value: Normal


title: WCA127


title: WCA042


title: SFPQ rep2

value: pro-B cells

value: blood


title: STM422

value: Black or African American


title: CON-08-PT

source_name: Control, ID 08, DNA_putamen

tag: education (years)

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph

tag: hemisphere


title: CornealEndothelium_FECD_pool2_rep2

city: Adelaide

first: Mark

middle: A

last: Corbett

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

institute: University of Adelaide

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.8.0). It was vst transformed and quantile normalized.

source_name: Corneal Endothelium

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: H

tag: tissue

value: corneal epithelium

tag: disease state

value: FECD


title: CornealEndothelium_Unaffected_4_rep2

value: L

value: normal


title: WCA013

tag: age

tag: diabetes

tag: alt

tag: ast

tag: nafld stage


title: CON-08-OFC

source_name: Control, ID 08, DNA_orbitofrontal cortex

value: Brain_orbitofrontal cortex

tag: sample group

value: Control

tag: gender

tag: alcohol

value: Yes


title: CornealEndothelium_Unaffected_2_rep2

value: J


title: BCR rep3

tag: cell type

tag: genotype

tag: cell line

tag: treatment

value: untreated


title: CON-08-NAC

source_name: Control, ID 08, DNA_nucleus accumbens

value: Brain_nucleus accumbens

value: Female

tag: education (years)

value: Never

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

value: Left


title: MSCV control rep3

value: pro-B cells

tag: tissue

value: MSCV


title: CON-08-ACC

source_name: Control, ID 08, DNA_anterior cingulate gyrus

value: Brain_anterior cingulate gyrus

tag: age

tag: ph

tag: hemisphere


title: WCA063

source_name: Human liver

value: Human liver

tag: race

value: White

tag: bmi

tag: Sex

tag: diabetes

value: No

tag: alt

tag: ast

value: Steatosis


title: CornealEndothelium_Unaffected_3_rep2

value: K

value: corneal epithelium

tag: disease state

value: normal


title: WCA093

value: Yes

tag: nafld stage


title: CornealEndothelium_FECD_pool3_rep2

value: I

value: FECD


title: WCA053


title: CON-07-ACC

source_name: Control, ID 07, DNA_anterior cingulate gyrus

tag: sample group

value: Control

tag: gender

value: Male

tag: alcohol

value: Right


title: CornealEndothelium_Unaffected_4_rep1

value: F


title: SFPQ rep3

tag: cell type

value: pro-B cells

value: blood

tag: genotype

tag: cell line

tag: treatment

value: untreated


title: CornealEndothelium_FECD_pool1_rep2

value: G

tag: tissue


title: CON-07-NAC

source_name: Control, ID 07, DNA_nucleus accumbens

value: Brain_nucleus accumbens

tag: age

tag: education (years)

value: Never

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph

tag: hemisphere


title: WCA018

value: Human liver

tag: race

value: White

tag: bmi

tag: Sex

tag: diabetes

tag: alt

tag: ast

value: Steatosis


title: KCN294/WCA080

value: No

tag: nafld stage


title: BCR rep4

tag: cell type

tag: genotype

tag: cell line


title: CON-06-NAC

source_name: Control, ID 06, DNA_nucleus accumbens

tag: tissue

tag: sample group

tag: gender

tag: age

tag: alcohol

value: Yes

value: Stopped

value: Left


title: CornealEndothelium_Unaffected_2_rep1

value: D

value: corneal epithelium

tag: disease state

value: normal


title: WCA171

value: Female


title: CON-07-PT

source_name: Control, ID 07, DNA_putamen

value: Control

value: Male

tag: education (years)

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph

tag: hemisphere

value: Right


title: CornealEndothelium_FECD_pool3_rep1

value: C

value: FECD


title: CornealEndothelium_Unaffected_3_rep1

value: E


title: CornealEndothelium_FECD_pool2_rep1

value: B


title: CornealEndothelium_FECD_pool1_rep1

value: A


title: CON-07-CN

source_name: Control, ID 07, DNA_caudate nucleus

value: Brain_caudate nucleus

value: Never


title: CON-06-PT

source_name: Control, ID 06, DNA_putamen

value: Yes


title: CON-07-OFC

source_name: Control, ID 07, DNA_orbitofrontal cortex

value: Brain_orbitofrontal cortex


title: MSCV control rep4

value: pro-B cells

value: blood

value: MSCV

tag: treatment

value: untreated


title: WCA089

value: Human liver

tag: race

value: White

tag: bmi

tag: Sex

value: Female

tag: diabetes

tag: alt

tag: ast

tag: nafld stage


title: 12mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 1

city: Irvine

first: Kim

last: Green

state: CA

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Illumina HiSeq4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM)  were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: Excel Workbook file includes RPKM values for all Samples.

source_name: Hippocampus

extract_protocol:
Brains were removed, microdissected into cortex, hippocampus, and thalamus/striatum, and flash frozen on dry ice.  RNA was extracted using Rneasy Mini Kit (Qiagen). cDNA synthesis, amplification, library construction and sequencing were performed by Novogene Inc. using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: C57BL/6, Apoe(fl/fl), 5xFAD, Csf1r-cre

tag: brain region

value: Hippocampus


title: 12mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 4


title: CON-06-CN

source_name: Control, ID 06, DNA_caudate nucleus

tag: tissue

tag: sample group

value: Control

tag: gender

value: Male

tag: age

tag: alcohol

value: Stopped

value: Left


title: 12mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 5


title: 12mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 2


title: SFPQ rep4

tag: cell type

tag: genotype

tag: cell line


title: WCA094

tag: race

value: No

value: Normal


title: WCA183

tag: bmi

value: Yes


title: WCA202

tag: Sex


title: CON-05-PT

source_name: Control, ID 05, DNA_putamen

tag: education (years)

value: Never

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph

tag: hemisphere

value: Right


title: CON-05-CN

source_name: Control, ID 05, DNA_caudate nucleus

tag: tissue

value: Brain_caudate nucleus


title: WCA204

tag: diabetes

tag: alt

tag: ast

tag: nafld stage


title: CON-06-ACC

source_name: Control, ID 06, DNA_anterior cingulate gyrus

value: Brain_anterior cingulate gyrus

tag: sample group

tag: gender

tag: age

tag: alcohol


title: 12mo Apoe(fl/fl) 5xFAD Hippocampus 7

tag: strain

tag: brain region


title: 12mo Apoe(fl/fl) 5xFAD Hippocampus 2


title: 12mo Apoe(fl/fl) 5xFAD Hippocampus 1


title: WCA384

tag: race

tag: bmi

tag: Sex


title: 12mo Apoe(fl/fl) Csf1r-cre Hippocampus 7

value: C57BL/6, Apoe(fl/fl), Csf1r-cre


title: WCA391

value: Human liver


title: 12mo Apoe(fl/fl) Csf1r-cre Hippocampus 6


title: WCA134

value: White


title: 12mo Apoe(fl/fl) Csf1r-cre Hippocampus 5


title: 12mo Apoe(fl/fl) 5xFAD Hippocampus 4


title: CON-05-ACC

source_name: Control, ID 05, DNA_anterior cingulate gyrus

value: Female

tag: education (years)

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)


title: 12mo Apoe(fl/fl) Csf1r-cre Hippocampus 4


title: CON-02a-ACC

source_name: Control, ID 02a, DNA_anterior cingulate gyrus

tag: tissue

tag: ph

tag: hemisphere


title: WCA126

tag: diabetes

tag: alt

tag: ast

tag: nafld stage


title: 12mo Apoe(fl/fl) 5xFAD Hippocampus 6

value: C57BL/6, Apoe(fl/fl), 5xFAD, Csf1r-cre


title: CON-02a-CN

source_name: Control, ID 02a, DNA_caudate nucleus

tag: sample group

tag: gender

tag: age

tag: alcohol


title: WCA179

tag: race

tag: bmi


title: CON-02a-NAC

source_name: Control, ID 02a, DNA_nucleus accumbens

value: Brain_nucleus accumbens

tag: education (years)


title: 12mo Apoe(fl/fl) Csf1r-cre Hippocampus 3

tag: strain

tag: brain region

value: Hippocampus


title: 12mo Apoe(fl/fl) Csf1r-cre Hippocampus 2


title: WCA092

source_name: Human liver

value: Black or African American

tag: Sex

value: Male


title: WCA185

tag: tissue


title: CON-02a-OFC

source_name: Control, ID 02a, DNA_orbitofrontal cortex

value: Brain_orbitofrontal cortex

value: Control

tag: tobacco

tag: brain volume (ml)

tag: brain weight (g)

tag: ph

value: Left


title: WCA009

tag: diabetes

value: Yes

tag: alt

tag: ast


title: WCA380

value: No

tag: nafld stage


title: CON-02a-PT

source_name: Control, ID 02a, DNA_putamen

tag: sample group

tag: gender

tag: age

value: Never

tag: hemisphere


title: CON-05-NAC

source_name: Control, ID 05, DNA_nucleus accumbens

tag: education (years)

tag: alcohol

value: Stopped

value: Right


title: CON-04-CN

source_name: Control, ID 04, DNA_caudate nucleus

value: Brain_caudate nucleus


title: 12mo Apoe(fl/fl) 5xFAD Hippocampus 3

tag: strain

tag: brain region


title: 12mo Apoe(fl/fl) 5xFAD Csf1r-cre Hippocampus 3


title: 12mo Apoe(fl/fl) 5xFAD Hippocampus 5


title: CON-04-ACC

source_name: Control, ID 04, DNA_anterior cingulate gyrus

tag: tissue

value: Brain_anterior cingulate gyrus


title: CON-04-NAC

source_name: Control, ID 04, DNA_nucleus accumbens

tag: tobacco


title: WCA392

value: Human liver

tag: race

value: White

tag: bmi

tag: Sex


title: CON-04-PT

source_name: Control, ID 04, DNA_putamen

tag: brain volume (ml)

tag: brain weight (g)

tag: ph


title: 12mo Apoe(fl/fl) Hippocampus 3

source_name: Hippocampus

value: C57BL/6, Apoe(fl/fl)


title: 12mo Apoe(fl/fl) Hippocampus 2


title: WCA315

value: Refused

value: Female

tag: diabetes

tag: alt

tag: ast

tag: nafld stage

value: Normal


title: CON-01a-CN

source_name: Control, ID 01a, DNA_caudate nucleus

tag: sample group

tag: gender

value: Male

tag: age

tag: hemisphere


title: CON-01a-OFC

source_name: Control, ID 01a, DNA_orbitofrontal cortex

value: Brain_orbitofrontal cortex

tag: education (years)

tag: alcohol