title: TREM-24


title: 21m-1

status: Public on Nov 11 2020

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

library_source: genomic

data_processing:
Reduced alignment index generated using BSSeeker2 v2.1.8 with the following parameters; --aligner=bowtie2 -r -l 40 -u 500 -c C-CGG
Trimmed fastq files aligned using BSSeeker2 v2.1.8 using the following parameters; --aligner=bowtie2 --bt2--end-to-end --bt2-p 16 -r --low=40 --up=500 -f bam
Methylation values were called for methylat from alignments using BSSeeker2 v2.1.8 using the default parameters;
Genome_build: rn6
Supplementary_files_format_and_content: CGmap methylation call files; tab separated text file;  (1) chromosome (2) nucleotide on Watson (+) strand (3) position (4) context (CG/CHG/CHH) (5) dinucleotide-context (CA/CC/CG/CT) (6) methylation-level = #_of_C / (#_of_C + #_of_T) (7) #_of_C (8) = #_of_C + #_of_T (

molecule: genomic DNA

organism: Rattus norvegicus

source_name: whole blood

extract_protocol:
500ul of whole blood was collected via retro-orbital bleedings into heparinized tubes, spun, and the plasma removed. Buffy coat and red blood cells were frozen at -80 degrees C until DNA extraction. Following proteinase K and RNAse A treatments, DNA was isolated from rat blood cells using QIAmp DNA Mini Kit following manufacturer’s instructions using a QIAcube automated device. DNA was eluted from columns in 200 µL of AE buffer, concentrated in 20 µL 10 mM Tris-HCl, pH 8.5, 0.1 mM EDTA using Genomic DNA Clean & Concentrator-10, and quantified using a Qubit 2.0.
100ng of DNA isolated from whole blood was digested with MspI restriction enzyme (NEB, Ipswich, MA, USA), carried out end-repair/adenylation (NEB) and ligation with TruSeq barcoded adapters (Illumina, San Diego, CA, USA). DNA fragments of size range 200-300bp were selected with SPRI magnetic beads (ABM, Richmond, BC, CA), followed by bisulfite treatment (Millipore, Billerica, MA, USA), and PCR amplification (Bioline, Taunton, MA, USA). Libraries were sequenced by multiplexing 8 libraries per lane on the Illumina HiSeq2500 sequencer, with 100bp single end reads.

tag: strain

tag: age (months)

tag: Sex

value: male


title: 10m-2


title: MCI-NC_007

type: RNA

city: Obu

first: Daichi

last: Shigemizu

state: Aichi

address: 7-430 Morioka-cho

country: Japan

institute: National Center for Geriatrics and Gerontology

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.)

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.

molecule: total RNA

organism: Homo sapiens

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: diagnosis

value: MCI-NC

tag: age

tag: day


title: 13m-2


title: TREM-21

city: jacksonville

last: Zhao

address: 4500 San Pablo Rd S

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-Seq analytic pipeline: MAP-RSeq Version 3.0 (Kalari et al., 2014).
Reads were mapped to the mouse reference genome mm10 using STAR v.2.5.2b using default settings (Dobin et al., 2013). The gene counts were generated using FeatureCounts v.1.5.1 (Liao et al., 2014) with the gene definitions files from Ensembl v78. Quality checks after alignment was done using RSeqQC v.3.0.0 (Wang et al., 2012).
Conditional Quantile Normalization (CQN) was performed on the raw gene counts to correct for gene length differences, GC bias, global technical variations, and to obtain similar quantile-by-quantile distributions of gene expression levels across samples (Hansen et al., 2012). Based on the bi-modal distribution of the CQN normalized and log2-transformed reads per kb per million (RPKM) gene expression values, genes with average log2 RPKM >= 1 in at least one group were considered expressed. Using this selection threshold, 18,100 genes were included in the downstream analysis.
Sample TREM-17 was revealed as outlier by Principal Component Analysis (PCA), and was subsequently removed from downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: .txt file of raw gene counts

organism: Mus musculus

source_name: cortex

extract_protocol:
Total RNA was extracted from the cortex using Trizol reagent and cleaned using RNeasy spin columns with DNase treatment to remove contaminating genomic DNA.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions, employing poly-A mRNA enrichment using oligo-dT magnetic beads

treatment_protocol: Mice were treated with tamoxifen to induce TREM2 expression in microglia. The control mice were given vehicle (corn oil).

tag: background strain

tag: genotype

value: TREM2-WT+/+; Cx3cr1CreER/+

tag: treatment

value: Control


title: 5m-1


title: 3m-3


title: 18m-4


title: TREM-16


title: 9m-5


title: 11m-3


title: 15m-2


title: 20m-3


title: TREM-8

value: TREM2-R47H+/+; Cx3cr1CreER/+


title: MCI-NC_004

value: female


title: TREM-11


title: 18m-2


title: 24m-5


title: MCI-NC_006


title: MCI-NC_003


title: 2m-5


title: 1m-1


title: MCI-NC_002


title: 1m-4


title: 12m-1


title: MCI-NC_001


title: MCI-C_083

value: MCI-C


title: TREM-4


title: MCI-NC_005


title: 5m-6


title: TREM-18


title: 14m-1


title: 27m-2


title: 16m-2


title: 6m-5


title: TREM-10


title: 16m-4


title: MCI-C_082


title: MCI-C_081


title: 22m-3


title: TREM-1


title: MCI-C_080


title: 14m-4


title: 6m-2


title: 2m-6


title: 9m-3


title: TREM-7


title: 4m-6


title: MCI-C_079


title: 8m-2


title: KO_chow_diet_rep_3

city: Cambridge

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

country: United Kingdom

institute: WT-MRC Institute of Metabolic Science

data_processing:
Raw fastq files were trimmed using Cutadapt 2.10 and aligned to the reference features using STAR v. 2.7
The amount of reads per feature was quantified using Feature Counts 1.6.2 of the Subread package
Supplementary_files_format_and_content: Processed data file contains the reads counts for each feature as tab separated values

source_name: Mouse Inguinal Adipose Tissue

growth_protocol: Inguinal adipose tissue from mice fed 24 weeks chow diet

extract_protocol:
RNA was extracted using RNeasy Mini isolation kit
TruSeq
Single End, 50

treatment_protocol: Chow diet

value: Adig-/-

value: Chow Diet

tag: tissue

value: Inguinal Adipose Tissue


title: KO_chow_diet_rep_5


title: KO_chow_diet_rep_4


title: 25m-1


title: KO_chow_diet_rep_2


title: MCI-C_078


title: 13m-4


title: 23m-4


title: MCI-C_076


title: MCI-C_077


title: 23m-3


title: 11m-5


title: Wild_type_chow diet_rep_5

value: Wild Type


title: Wild_type_chow diet_rep_4


title: MCI-C_075


title: 18m-1


title: 22m-2


title: MCI-C_072


title: MCI-C_073


title: 3m-4


title: 16m-5


title: 10m-5


title: 16m-3


title: Wild_type_chow diet_rep_2


title: Wild_type_chow diet_rep_3


title: 13m-5


title: Wild_type_chow diet_rep_1


title: MCI-C_071


title: 20m-4


title: KO_chow_diet_rep_1


title: Scramble treated_sample3

city: Paris

first: Hafid

last: Ait-Oufella

address: 56, Rue Leblanc

country: France

institute: Inserm

description:
Control
SAMPLE 3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: GUSB, HPRT , HSP90AB1, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control (i.e., Scramble/LR12) ratios.

label: SYBR Green

source_name: Aorta

label_protocol: :Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: Total Aorta

value: apoE KO

tag: activation agent

value: control

tag: time

value: 7 days


title: KRAS knockout metastasis derived cell line B2

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

data_processing:
Sequencing data was pre-processed with Novogene RNAseq pipeline.
Mapping: STAR version 2.6.1, mismatch=2
Quantification: HTSeq versio 0.6.1, -m union
Genome_build: mm10
Supplementary_files_format_and_content: processed data includes BAM file for each sample and merged FPKM comma-separated values file

source_name: PDAC

growth_protocol: Cells were grown in DMEM medium supplemented with 5% fetal calf serum

extract_protocol:
Total cellular RNA was prepared from cultured cells using standard techniques. Quantification and input quality control were performed at Novogene.
RNA-seq libraries were prepared at Novogene.

tag: passage

tag: cell type

value: PDAC

value: KRAS KO


title: MCI-C_069

value: male


title: LR-12 treated_sample4

description:
Treated
SAMPLE 4

value: treated


title: KRAS/SMAD4 double knockout cell line B3

value: KRAS/SMAD4 KO


title: 21m-4


title: MCI-C_074


title: KRAS knockout metastasis derived cell line B1


title: 10m-4


title: 25m-4


title: KRAS knockout cell line B4_5


title: Scramble treated_sample1

description:
Control
SAMPLE 1


title: LR-12 treated_sample2

description:
Treated
SAMPLE 2

value: Treated


title: 1m-5


title: MCI-C_067


title: 4m-4


title: MCI-C_066


title: 9m-1


title: KRAS intact metastasis derived cell line A3

value: KRAS +


title: KRAS intact metastasis derived cell line A2


title: MCI-C_070

value: female


title: KRAS intact metastasis derived cell line A1


title: 21m-5


title: MCI-C_068

value: MCI-C


title: MCI-C_065


title: KRAS intact tumor-derived cell line B6


title: 5m-3


title: MCI-C_062


title: mSpleen_Ctcf_3

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

data_processing:
The RNA-seq data passed the quality control conducted using FastQC and MulitQC
Sequencing reads were mapped to the mouse reference genome GRCm38/mm10 using STAR software
Differentially gene expression analysis was performed using the Bioconductor package DESeq2; genes with low read counts (<5) were removed from the analysis
Differential alternative splicing was anlayzed using rMATS
Differential intron retention was analyzed using IRFinder
Genome_build: mm10

source_name: Spleen

extract_protocol:
Total RNA from WT and Ctcf+/- tissues (<30 mg weight) were homogenized with TRIzol (Invitrogen) and cleaned up by TURBO DNA-free kit (Invitrogen). The RNA integrity was evaluated using a Bioanalyzer showing an RNA integrity number (RIN) over 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: adult

value: Ctcf haploinsufficiency

value: Spleen


title: MCI-C_061


title: mSpleen_Ctcf_1


title: mSpleen_WT_3


title: MCI-C_063


title: 8m-5


title: MCI-C_060


title: MCI-C_059


title: 12m-4


title: 15m-4


title: 3m-5


title: MCI-C_064


title: 13m-6


title: MCI-C_058


title: MCI-C_057


title: Mutant RvDaosR treated with CHP replicate 2

city: Delhi

first: Vinay

middle: K.

last: Nadnicoori

state: DELHI

address: National Institute of Immunology, Near JNU EAST GATE, ARUNA ASAF ALI MARG, NEW DELHI-110067

country: India

institute: National Institute of Immunology

description: RvDaosR + CHP_2

data_processing:
Read quality using FastQC
Alignment with Bowtie 2
Read counts using htseq-count
Differential expression analysis using DEseq2
Genome_build:  ASM19595v2
Supplementary_files_format_and_content: Processed data are read counts for each sample with the first column indicating gene identifier and the second colum indicating the number of reads mapped.

organism: Mycobacterium tuberculosis

source_name: Mycobacterial Cells

growth_protocol: Mycobacterial cells were grown in 7H9-ADS media at 0.05 OD

extract_protocol:
Total RNA was extracted using trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 0.2 OD cells were treated with 50 micromolar of CHP for 24 hours

value: Treated with CHP

value: mutant of Rv1332/ AosR


title: Mutant RvDaosR replicate 3

value: untreated


title: Mutant RvDaosR treated with CHP replicate 1

description: RvDaosR + CHP_1


title: mSpleen_WT_2

value: control


title: Mutant RvDaosR replicate 1


title: Mutant RvDaosR treated with CHP replicate 3

description: RvDaosR + CHP_3


title: 1m-3


title: mSpleen_Ctcf_2


title: MCI-C_056


title: mMuscle_Ctcf_3

source_name: Muscle (quadriceps femoris)

value: Muscle (quadriceps femoris)


title: HCT116 TRA2B4 #1

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

description: Gene expression in pEB multi-TRA2B4 full-length overexpressing cells

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4858A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: The total RNA was extracted using RNAiso Plus reagent (Thermo Fisher Scientific).

treatment_protocol: HCT116 cells were then transfected with either empty, TRA2B4, or an exon 2-expression pEB-multi vector (Wako, Osaka, Japan) using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer’s protocol. The stably transfected cells were selected using medium containing 5 µg/ml of Blasticidin S . (InvivoGen, San Diego, CA) for ~7 days.

tag: cell line

value: HCT116  cells

value: colon cancer


title: Wild type H37Rv treated with CHP replicate 3

description: Rv + CHP_3

value: wild type


title: 2m-3

value: male


title: 3m-1


title: Mutant RvDaosR replicate 2


title: mMuscle_Ctcf_2


title: HCT116 TRA2B4 #2


title: MCI-C_055


title: HCT116 exon 2 #1

description: Gene expression in pEB multi-TRA2B4 exon 2 overexpressing cells


title: mSpleen_WT_1


title: mMuscle_Ctcf_1


title: Wild type H37Rv replicate 3


title: Wild type H37Rv treated with CHP replicate 1

description: Rv + CHP_1


title: Wild type H37Rv replicate 2


title: HCT116 exon 2 #2


title: 27m-6


title: HCT116 mock

description: Gene expression in pEB multi-overexpressing cells


title: MCI-C_054


title: mMuscle_WT_3


title: mMuscle_WT_2


title: mMuscle_WT_1


title: 27m-5


title: 6m-6


title: mKidney_Ctcf_3

source_name: Kidney

value: Kidney


title: 9m-6


title: mKidney_Ctcf_2


title: Dam::Pcl_SD_4days 3

city: Ann Arbor

first: Monica

last: Dus

state: Michigan

address: 1105 N University, 4224

institute: University of Michigan

data_processing:
Library strategy: DNA-seq
Reads were aligned using Bowtie2
Reads are extended to 300bp or closest GATC
Bam output is used to generate the ratio file between Dam::Pcl and Dam in bedgraph format
Peaks were identified from log2(Dam::Pcl/Dam) ratio files using find_peaks (FDR<0.01)
Genome_build: BDGP6
Supplementary_files_format_and_content: Bigwig and Bedgraph files showing nomrmalized coverage

organism: Drosophila melanogaster

source_name: Gr5a sensory neurons

growth_protocol: Male and feamle age-matched flies were collected 2 days after eclosure and housed in vials of 35. Flies were placed on their specific dietary condition at day 5 until day 6 at 20C tehn moved to 29C for an additional day to induce Dam. Samples were collected and DNA isolated.

extract_protocol:
Three biological replicates were used for each condition, and each replicate consisted of 300 heads. For tissue collections, briefly heads were collected using pre-chilled sieves in liquid nitrogen on dry ice. Frozen heads were then lysed. DNA was extracted from frozen heads following kit instructions. For identification of methylated regions briefly, purified DNA was digested by DpnI followed by PCR purification of digested sequences. TaDa adaptors were ligated by T4 DNA ligase . Adapter ligated DNA was PCR amplified according to protocol, and subsequently purified. Purified DNA was digested with DpnII followed by sonication to yield fragments averaging 200-300bp. TaDa adaptors were removed from sonicated DNA by digestion.
Libraries were generated using the Takara ThruPlex kit (cat #022818) using 3ng input and 10 cycles of PCR. All libraries were sequenced on the Illumina NextSeq platform (High-output kit v2 75 cycles).

treatment_protocol: Flies were placed either on a control diet (5% sucrose) or sugar diet (30% sucrose)

value: Gr5a sensory neurons

tag: condition

value: sugar diet


title: Dam::Pcl_SD_4days 2


title: 11m-6

tag: strain


title: MCI-C_053

value: female


title: 15m-6

tag: age (months)


title: MCI-C_049

value: MCI-C

tag: Sex


title: Dam::Pcl_SD_4days 1


title: MCI-C_052

tag: diagnosis


title: 7m-1


title: mKidney_WT_2

value: adult


title: MCI-C_048

tag: age


title: MCI-C_051

tag: day


title: MCI-C_050


title: MCI-C_047


title: Wild type H37Rv treated with CHP replicate 2

description: Rv + CHP_2


title: Wild type H37Rv replicate 1


title: mKidney_WT_1


title: 19m-6


title: Dam::Pcl_CD_4days 3

value: control diet


title: Dam::Pcl_CD_4days 2


title: mKidney_WT_3


title: Dam::Pcl_CD_4days 1


title: MCI-C_046


title: 17m-4


title: Col1a1GFP+ cells EAE

city: La Jolla

first: Cayce

last: Dorrier

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Sequencing files were run through the 10X CellRanger 2.1.1 pipeline to generate gene counts data
Further analysis was completed using Seurat v3 and the sctransform pipeline
Resolution parameter of clustering was set to 0.2. Wilcox method was used for differential expression analysis, with min.pct = 0.25 and logfc.threshold = 0.25
singleR was used to annotate single-cells using the Immgen reference
Genome_build: mm10

source_name: spinal cord

extract_protocol:
Spinal cords were dissociated using both chemical and mechanical dissociation methods and single, GFP+ cells were sorted using FACS sorting
RNA libraries were prepared for sequencing using the 10x Genomics v2 standard protocols

value: spinal cord

value: Col1a1GFP; C57/BL6 background

tag: disease state

value: EAE


title: MCI-C_045


title: MCI-C_044


title: 14m-6


title: 7m-6


title: Whole SC EAE

data_processing:
Sequencing files were run through the 10X CellRanger 2.1.1 pipeline to generate gene counts data
Further analysis was completed using Seurat v3 and the sctransform pipeline
Resolution parameter of clustering was set to 0.2. Wilcox method was used for differential expression analysis, with min.pct = 0.25 and logfc.threshold = 0.25
singleR was used to annotate single-cells using the Immgen reference
Genome_build: mm10
Supplementary_files_format_and_content: txt, count matrix for sample

extract_protocol:
Spinal cords were dissociated using both chemical and mechanical dissociation methods and single cells were sorted using FACS sorting
RNA libraries were prepared for sequencing using the 10x Genomics v2 standard protocols


title: 3m-6


title: 25m-3


title: WSC Control M3

data_processing:
Sequenced reads were mapped to Ensembl mm9 v67 whole genome using tophat v2.0.11 and bowtie2 v2.2.1 with parameters --no-coverage-search -m 2 -a 5 -p 7
Alignment files were sorted using SAMtools v.0.1.19
Count tables were generated using HTSeq-0.6.1
Differential expression was analyzed using DESeq2
Genome_build: Ensembl mm9 v67
Supplementary_files_format_and_content: .xls file with the raw counts and counts per million (CPM) for each sample.

extract_protocol:
Spinal cords were dissociated using both chemical and mechanical dissociation methods and GFP+ cells were enriched using FACS sorting
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were sequenced using the HiSeq4000 using paired-end 100 base pair reads

tag: eae stage

value: health


title: mKidney_Ctcf_1

tag: genotype

value: Ctcf haploinsufficiency


title: Dam_SD_4days 3


title: MCI-C_043


title: Dam_SD_4days 2


title: Col1a1GFP+ cells health 2

tag: tissue

value: healthy


title: 22m-6


title: Col1a1GFP+ cells health 1


title: Dam_SD_4days 1


title: MCI-C_042


title: MCI-C_041


title: MCI-C_040


title: MCI-C_039


title: MCI-C_038


title: 23m-5


title: Dam_CD_4days 3


title: EAE D10 2

value: C57BL/6 Col1a1GFP

value: EAE D10 Post Symptom Onset


title: EAE D10 1


title: Dam_CD_4days 1


title: Pcl_SD_7 days 3

data_processing:
Reads were aligned using STAR  (version: 020201). --quantMode GeneCounts
Convert .sam files to .bam files using samtools (version 1.4).
Determine differential RNA abundance using DeSeq2 (version 1.18.0). dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition)
Genome_build: BDGP6
Supplementary_files_format_and_content: HTSeq counts, text format, gene ID, union, intersection_strict, intersection_nonempty

growth_protocol: Male flies were collected 2 days after eclosure and housed in vials of 35. Flies were placed on their specific dietary condition a day 5 until day 12 which samples were collected.

extract_protocol:
Three biological replicates were used for each condition, and each replicate consisted of 300 heads. For tissue collections, briefly heads were collected using pre-chilled sieves in liquid nitrogen on dry ice. Frozen heads were then lysed. From the lysate total RNA was extracted by TRIzol LS Reagent and used as input. The remainder of the lysate was incubated with Dynabeads protein G  to preclear samples for 2 hours and subsequently incubated with Dynabeads protein G coated with an anti-Flag antibody. The lysate-beads mixture was incubated at 4°C with rotation for 2 hours, then washed in buffer. RNA was extracted from ribosomes bound to the beads by TRIzol Reagent.
Samples were ribo-depleted, DNase treated, and libraries were prepared using the Nugen Ovation SoLo RNA-Seq System for Drosophila (0502) by the University of Michigan sequencing core facility. Library concentrations were determined by qPCR.


title: Dam_CD_4days 2


title: EAE D10 3


title: MCI-C_037


title: EAE D5 3

value: EAE D5 Post Symptom Onset


title: Pcl_CD_7 days 3


title: Pcl_SD_7 days 2


title: MCI-C_034


title: WSC Control M1


title: Pcl_SD_7 days 1


title: MCI-C_035

value: male


title: Pcl_CD_7 days 2


title: MCI-C_036


title: EAE D5 2


title: EAE D5 1


title: Pcl_CD_7 days 1


title: Control 4


title: MCI-C_032


title: MCI-C_031


title: Control 3


title: Gr5a_CD>CD_14days 3

growth_protocol: Male flies were collected 2 days after eclosure and housed in vials of 35. Flies were placed on their specific dietary condition at day 5 until day 12 which samples were collected. For CD>CD and SD>CD experiments flies were placed on their specific dietary condition at day 5 until day 12 which which the diet was then switched for a subsequent 7 days until day 19.

extract_protocol:
2-3 biological replicates were used for each condition, and each replicate consisted of 300 heads. For tissue collections, briefly heads were collected using pre-chilled sieves in liquid nitrogen on dry ice. Frozen heads were then lysed. From the lysate total RNA was extracted by TRIzol LS Reagent and used as input. The remainder of the lysate was incubated with Dynabeads protein G  to preclear samples for 2 hours and subsequently incubated with Dynabeads protein G coated with an anti-Flag antibody. The lysate-beads mixture was incubated at 4°C with rotation for 2 hours, then washed in buffer. RNA was extracted from ribosomes bound to the beads by TRIzol Reagent.
Samples were ribo-depleted, DNase treated, and libraries were prepared using the Nugen Ovation SoLo RNA-Seq System for Drosophila (0502) by the University of Michigan sequencing core facility. Library concentrations were determined by qPCR.

value: sugar>control


title: Gr5a_CD>CD_14days 4

value: Gr5a sensory neurons


title: MCI-C_033


title: Control 1


title: Gr5a_CD>CD_14days 2


title: MCI-C_029


title: round spermatids_m6A IP_rep2

city: Shanghai

first: Zhen

last: Lin

state: Shanghai

address: 320 Yue Yang Road

department: Shanghai  Institute of Biochemistry and Cell Biology

country: China

institute: University of Chinese Academy of Sciences

description: round spermatids

data_processing:
sequencing reads were aligned to the reference genome (mm10) using TopHat (v2.0.14)
To call m6A peaks, the longest isoform of each human gene was scanned using a 100 nt sliding window with 10 nt steps. To reduce bias from potentially inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with read counts < 1/20 of the top window in both m6A IP and input sample were excluded. For each gene, the read count in each window was normalized by the median count of all windows of that gene.
The window was called positive if FDR < 1% and log2 (enrichment score) ≥ 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): (a) read count of the IP sample in the current peak/window, (b) median read count of the IP sample in all 100 nt windows on the current mRNA, (c) read count of the input sample in the current peak/window, and (d) median read count of the input sample in all 100 nt windows on the current mRNA. The enrichment score of each window was calculated as (a × d)/(b × c).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with enrichment scores for every gene from different stages

source_name: round spermatids

extract_protocol:
total RNA was harvested using Trizol reagent. PolyA mRNA was enriched using GenElute mRNA Miniprep Kit. mRNA was sonicated to ~100 nt, mixed with 2.5 mg affinity-purified anti-m6A polyclonal antibody (Synaptic Systems) in IP buffer (150 mM NaCl, 0.1% NP-40, and 10 mM Tris-HCl, pH 7.4), and incubated for 2 h at 4 °C. The an- tibody-RNA complex was isolated by incubation with protein A beads (Invitrogen) at 4 °C for 2 h. The beads were washed three times and eluted competitively with an m6A monophosphate solution. RNA in the eluate was isolated using RNA Clean and Concentrator (Zymo Research) and used for library preparation with TruSeq stranded mRNA sample preparation kit (Illumina).
RNA in the eluate was isolated using RNA Clean and Concentrator (Zymo Research) and used for library preparation with TruSeq stranded mRNA sample preparation kit (Illumina).

tag: antibody

value: anti-m6A antibody (Synaptic System, 202003)

value: round spermatids


title: MCI-C_028

value: MCI-C

value: female


title: round spermatids_m6A IP_rep1

description: round spermatids


title: Border Zone(BZ)-1

city: harbin

first: yang

last: zhang

address: baojian road #157

institute: harbin medical university

hyb_protocol: Affymetrix Mouse Transcriptome Array 1.0 (Affymetrix Inc.) was hybridized with labled sample at 45ºC for 16h in GeneChip Hybridization Oven 640 (Affymetrix Inc.) .The washing and staining steps were performed using GeneChip2 Hybridization, Wash, and Stain Kit (Affymetrix Inc.) in GeneChip2 Fluidics Station 450 (Affymetrix Inc.).

scan_protocol: GeneChips were scanned by GeneChip2 Scanner 3000 7G (Affymetrix Inc.) and quantified with image and signal intensities.

data_processing: The data was analyzed by the RMA algorithm in Affymetrix Expression Console Software v1.0 for normalization. Affymetrix Transcriptome Analysis Console V3.0 was used for further comparative analysis.

label: biotin

source_name: heart

label_protocol: 100ng of total RNA was generated to fragmented biotinylated cDNA using GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix Inc.) according to the manufacturer’s instructions

growth_protocol: Male C57BL/6J mice at age of  8 weeks old were used.

extract_protocol: Total RNA was extracted from heart tissues by using Trizol reagent (QIAGEN lnc.).

treatment_protocol: Three C57BL/6J mice (8 weeks old) were subjected to the 45 mins ligation of left anterior descending coronary artery followed 24h reperfusion to induce myocardial ischemia reperfusion injury. The left anterior descending coronary artery was constricted with a 9-0 silk suture paralleled with a 1 mm diameter blunt needle, which was removed after 45 mins constriction. The heart were removed 24 hours later and the left ventricle tissue were separated into normal zone, ischemia zone and ischemia border zone.

value: 8 weeks

tag: brain

value: Border Zone(BZ)


title: Gr5a_CD>CD_14days 1

value: control diet


title: round spermatids_m6A input_rep2

description: round spermatids


title: MCI-C_027


title: Non-ischemia zone(NIZ)-2

value: Non-ischemia zone(NIZ)


title: round spermatids_m6A input_rep1

description: round spermatids


title: Border Zone(BZ)-2


title: Border Zone(BZ)-3


title: Non-ischemia zone(NIZ)-1


title: Ischemic zone(IZ)-3

value: Ischemic zone(IZ)


title: Non-ischemia zone(NIZ)-3


title: Ischemic zone(IZ)-2


title: Gr5a_SD_3days 1

value: sugar diet


title: Ischemic zone(IZ)-1


title: MCI-C_026


title: Gr5a_SD_7days 2


title: pachytene/diplotene spermatocytes_m6A IP_rep1

description: pachytene/diplotene spermatocytes

source_name: pachytene/diplotene spermatocytes

value: pachytene/diplotene spermatocytes


title: Gr5a_SD_7days 1


title: K562_NonTargeting_2

city: Århus N

first: Trine Line

middle: Hauge

last: Okholm

address: Palle Juul-Jensens Boulevard 99

department: Department of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

data_processing:
Reads were trimmed with Trim Galore v0.4.1 and cutadapt v1.15
Mapping to hg19 was performed with bwa v0.7.17 and samtools v1.9
We used the CIRI2 pipeline v2.0.6 to detect circRNAs. The CIRI2 pipeline was run with a gene transfer format (GTF) file (hg19) to annotate the overlapping gene of the circRNAs
Expression values of circRNAs were normalized to total reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include counts per million (CPM) values for each circRNA in each sample

extract_protocol: Total RNA sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase for Illumina Platforms (KAPA Biosystems)

tag: tissue source

value: Chronic myelogenous leukemia

tag: sirna

value: NonTargeting

tag: replicate


title: pachytene/diplotene spermatocytes_m6A input_rep2

description: pachytene/diplotene spermatocytes

tag: cell type


title: MCI-C_025

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).


title: pachytene/diplotene spermatocytes_m6A IP_rep2

description: pachytene/diplotene spermatocytes


title: K562_KHSRP_2

tag: cell line

value: KHSRP


title: K562_KHSRP_1


title: Gr5a_CD_7days 2

tag: condition


title: Gr5a_CD_7days 3


title: MCI-C_024


title: K562_NonTargeting_1


title: Gr5a_SD_3days 2


title: MCI-C_030


title: MCI-C_021


title: MCI-C_022


title: pachytene/diplotene spermatocytes_m6A input_rep1

description: pachytene/diplotene spermatocytes

tag: strain


title: preleptotene spermatocytes_m6A IP_rep2

description: preleptotene spermatocytes

source_name: preleptotene spermatocytes

value: preleptotene spermatocytes


title: Input_SD_7days 2

source_name: Heads

value: Heads


title: HepG2_NonTargeting_2

value: Hepatocellular carcinoma


title: MCI-C_020

source_name: serum

tag: Sex


title: MCI-C_023

tag: diagnosis


title: preleptotene spermatocytes_m6A IP_rep1

description: preleptotene spermatocytes

value: anti-m6A antibody (Synaptic System, 202003)


title: HepG2_NonTargeting_1


title: Gr5a_CD_7days 1

value: Gr5a sensory neurons


title: type A1 spermatogonia_m6A IP_rep2

description: type A1 spermatogonia

source_name: type A1 spermatogonia

value: type A1 spermatogonia


title: MCI-C_019

value: MCI-C

tag: age

value: female


title: preleptotene spermatocytes_m6A input_rep2

description: preleptotene spermatocytes


title: Input_CD_7days 2


title: MCI-C_017

value: male

tag: day


title: type A1 spermatogonia_m6A input_rep2

description: type A1 spermatogonia


title: Input_CD_7days 1

value: control diet


title: HepG2_KHSRP_2


title: HepG2_KHSRP_1


title: Input_CD_7days 3


title: MCI-C_018


title: MCI-C_016


title: preleptotene spermatocytes_m6A input_rep1

description: preleptotene spermatocytes


title: 16Soy6

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

description:
43L-Soy16_S44_L006
Soy diet #6

data_processing:
Sequenced reads were performed quality assessment using FastQC.
Sequenced reads were then aligend to Rattus norvegicus Rnor_6.0 reference genome using ArrayStar
Raw read counts then obtained from ArrayStar were then analyzed using DESeq2
N/A
N/A
Genome_build: Rattus norvegicus Rnor_6.0
Supplementary_files_format_and_content: normalized counts for each sample and expression data.

extract_protocol:
Total RNA from liver tissues was isolated using the Trizol reagent (ThermoFisher, Waltham, MA) and then the quality of isolated RNA was first assessed using the conventional A260/280 ratio and A260/230 ratio measurement (SpectraMax i3x; Molecular Devices, Sunnyvale, CA, USA) which were all satisfactory. In addition, RNA Integrity Number (also known as RIN) was assessed using the RNA R6K assay for the Agilent 2200 TapeStation (Agilent Technology, Santa Clara, CA, USA) in which RINs ranged between 8.5 and 9.5 hence satisfactory.
Illumina TruSeq RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Zucker rat

tag: diet

value: Liver


title: 16Soy8

description:
49L-Soy16_S12_L008
Soy diet #8


title: 16Soy5

description:
42L-Soy16_S36_L005
Soy diet #5


title: type A1 spermatogonia_m6A input_rep1

description: type A1 spermatogonia


title: Input_SD_7days 1

value: sugar diet


title: Metformin+FK506-2

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: spleen

growth_protocol: CD4+T cell isolated from normal C57BL/6 mice were stimulated with anti-CD3 (0.5ug/ml)  for 3days in complete culture medium (RPMI 1640 supplemented with 10% [v/v] heat-inactivated fetal calf serum).

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

treatment_protocol: CD4+T cell isolated from normal C57BL/6 mice were stimulated with anti-CD3 (0.5ug/ml) in the presence of Metformin or FK506 alone or combined Metformin and FK506 for 3days.

tag: treatment

value: CD4+ T cells

value: spleen

value: wild type


title: 16Soy4

description:
39L-Soy16_S28_L004
Soy diet #4


title: MCI-C_015

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.


title: MCI-C_014


title: type A1 spermatogonia_m6A IP_rep1

description: type A1 spermatogonia


title: 16Soy7

description:
47L-Soy16_S52_L007
Soy diet #7


title: 16Soy3

description:
38L-Soy16_S20_L003
Soy diet #3


title: undifferentiated spermatogonia_m6A IP_rep1

description: undifferentiated spermatogonia

source_name: undifferentiated spermatogonia

value: undifferentiated spermatogonia


title: undifferentiated spermatogonia_m6A input_rep2

description: undifferentiated spermatogonia


title: Metformin+FK506-3

tag: genotype


title: Metformin+FK506-1

tag: tissue


title: Metformin-2

value: Metformin


title: 16Soy2

description:
36L-Soy16_S4_L007
Soy diet #2


title: undifferentiated spermatogonia_m6A input_rep1

description: undifferentiated spermatogonia

tag: antibody


title: 16Soy1

description:
34L-Soy16_S4_L001
Soy diet #1


title: 16Con8

description:
16L-Con16_S11_L008
Control diet #8

value: Control _casein


title: Metformin-1


title: DMS, extra set (SARS-CoV-2), replicate #2

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description:
In vitro re-folded SARS-CoV-2 RNA, DMS treated
DMS_invitro.wig

data_processing:
Library strategy: DMS-MaPseq
Analysis of SHAPE-MaP data has been conducted using RNA Framework v2.6.9 (https://github.com/dincarnato/RNAFramework). Reads pre-processing and mapping was performed using the rf-map module (parameters: -ctn -cmn 0 -cqo -cq5 20 -b2 -mp "--very-sensitive-local"). Reads were trimmed of terminal Ns and low-quality bases (Phred < 20). Reads with internal Ns were discarded. Mapping was performed using the “very-sensitive-local” preset of Bowtie2. The mutational signal was then derived using the rf-count module (parameters: -m -rd), enabling the right re-alignment of deletions. When processing SARS-CoV-2 data, a mask file containing the sequences of primer pairing regions was passed along (through the -mf parameter). Generated RC files from both the even and odd sets, containing per base mutation counts and coverage, were then combined in a single RC file using the rf-rctools module (mode: merge). Data normalization was performed using the rf-norm module (parameters: -sm 3 -nm 3 -n 1000 -mm 1), by setting the minimum base coverage to 1,000X and the maximum mutation frequency to 1, and by using the Siegfried et al., 2014 scoring scheme and box-plot normalization of SHAPE reactivities.
Supplementary_files_format_and_content: Additional data files (RC/XML files for analysis with RNA Framework [http://www.rnaframework.com]) are available at: http://www.incarnatolab.com/datasets/SARS_Manfredonia_2020.php

organism: Severe acute respiratory syndrome coronavirus 2

extract_protocol:
Cells pellets were lysed by direct addition of 1 mL ice-cold QIAzol, followed by a brief incubation at 56°C for 5 min to completely dissolve cell aggregates. 200 µl of chloroform were added, followed by vigorous vortexing for 15 sec. Samples were then incubated at room temperature for 2 min, after which they were centrifuged at 12,500 x g for 15 min (4°C). After centrifugation, the upper aqueous phase was transferred to a clean 2 mL tube, and mixed with 2 volumes of 100% ethanol by vigorous vortexing. The entire volume was then transferred to an RNA Clean & Concentrator™-5 column and RNA was purified as per manufacturer instructions. RNA integrity was ensured by gel electrophoresis on a denaturing 2% agarose gel. Before proceeding to library preparation, traces of genomic DNA were removed by treatment with 2 U TURBO™ DNase at 37°C for 20 min.
For multiplex DMS-MaPseq, 70 oligonucleotide pairs, tiling the entire length of the SARS-CoV-2 genome (29,903 nt), were automatically designed using Primer3 and the following parameters: amplicon size between 480 and 520 bp, maximum poly(N) length between 2 and 3, minimum/optimal/maximum oligonucleotide size of 20/25/30, minimum/optimal/maximum Tm of 56/60/62 degrees, minimum/optimal/maximum GC content of 30/50/65 %. Also, pairs were designed in such a way that the target amplicon would include the target region of the reverse primer from the previous set and of the forward primer of the following set. Primers were then searched against the GENCODE v33 human transcriptome, keeping only those with less than 60% predicted base-pairing, or more than 60% predicted base-pairing and more than 2 mismatched bases at the 3’ end. For reverse transcription, all reverse primers were equimolarly pooled to yield a 100 μM RT primer mix. An additional anchored oligo-dT primer (TTTTTTTTTTTTTTTTTTTTVN) was added to the mix. For each sample, two 20 μl reverse transcription reactions were carried out. 3 μg of total RNA were mixed with 0.5 μl RT primer mix and 2 μl dNTPs (10 mM each), incubated at 70°C for 5 min and then transferred immediately to ice for 1 min. Reactions were then supplemented with 4 μl 5× RT Buffer [250 mM Tris–HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, and 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50). Reactions were incubated at 42°C for 5 min, then at 57°C for 2 h. To break the RT-RNA–cDNA complex, 1 μl 5 M NaOH was added, and samples were boiled at 95°C for 3 min. cDNA from every two reactions was purified on a single RNA Clean & Concentrator-5 column and eluted in 36 μl NF H2O. For targeted amplification, primer pairs were split into 2 non-overlapping sets, odd and even. For each of these sets, pairs were pooled in smaller sets of 3-4 pairs, as follows: 1-19-37-55, 2-20-38-56, 3-21-39-57, 4-22-40-58, 5-23-41-59, 6-24-42-60, 7-25-43-61, 8-26-44-62, 9-27-45-63, 10-28-46-64, 11-29-47-65, 12-30-48-66, 13-31-49-67, 14-32-50-68, 15-33-51-69, 16-34-52-70, 17-35-53, 18-36-54. The complete primer list can be found in Table S1. PCR reactions were carried out in 50 μl, using 2 μl of eluted cDNA, 0.3 mM final each dNTP, 0.1 μM final each primer in the set and 2.5 U TaKaRa Taq™ DNA Polymerase (TaKaRa, cat. R001A). Cycling was performed using a touch-down approach. Briefly, for the first 10 cycles the annealing temperature was lowered by 0.5°C per cycle, starting at 58°C. Then, 20 additional cycles were performed at the lowest temperature. PCR products were purified using 1 volume of NucleoMag NGS Clean-up and Size Select beads (Macherey Nagel, cat. 744970), checked on a 2% agarose gel. Each primer set gave a single specific band of the expected size. PCR products were equimolarly pooled to yield the final odd and even sets. 500 ng of each set were fragmented in a final volume of 20 μl, using 2 μl of NEBNext dsDNA Fragmentase (New England Biolabs, cat. M0348), supplemented with 1 μl 200 mM MgCl2, by incubating at 37°C for 25 min. This yielded fragments in the range of ~50-200 bp. Reactions were purified using 1 volume of NucleoMag NGS Clean-up and Size Select beads. 5 ng of fragmented DNA were then used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, cat. E7645L), as per manufacturer instructions.

treatment_protocol: Approximately 5x10^6 infected cells were resuspended in 1 mL of QIAzol Lysis Reagent (Qiagen, cat. 79306) and 200 μl of chloroform were added. Sample was vigorously vortexed for 15 sec and then incubated for 2 min at room temperature, after which it was centrifuged for 15 min at 12,500 x g (4°C). The upper aqueous phase was collected in a clean 2 mL tube, supplemented with 1 mL (~2 volumes) of 100% ethanol and then loaded on an RNA Clean & Concentrator-25 column (Zymo Research, cat. R1017). For in vitro folding, ~2 μg of total RNA in a volume of 39 μl were denatured at 95°C for 2 min, then transferred immediately to ice and incubated for 1 min. 10 μl of ice-cold 5X RNA Folding Buffer [500 mM HEPES pH 7.9; 500 mM NaCl] supplemented with 20 U of SUPERase•In™ RNase Inhibitor (ThermoFisher Scientific, cat. AM2696) were added. RNA was then incubated for 10 min at 37 °C to allow secondary structure formation. Subsequently, 1 μl of 500 mM MgCl2 (pre-warmed at 37°C) was added and RNA was further incubated for 20 min at 37°C to allow tertiary structure formation. For probing of RNA, DMS (from a 1:6 dilution in ethanol) was added to a final concentration of 150 mM and samples were incubated at 37°C for 2 min. Reaction was then quenched by addition of 1 volume DTT 1 M.

tag: sample type

value: In vitro re-folded SARS-CoV-2 RNA

value: DMS


title: MCI-C_011


title: FK506-3


title: MCI-C_012


title: undifferentiated spermatogonia_m6A IP_rep2

description: undifferentiated spermatogonia

value: anti-m6A antibody (Synaptic System, 202003)


title: 16Con7

description:
14L-Con16_S51_L007
Control diet #7


title: DMS, even set (SARS-CoV-2), replicate #2


title: FK506-2


title: MCI-C_009


title: FK506-1


title: 16Con6

description:
11L-Con16_S43_L006
Control diet #6


title: MCI-C_010


title: Metformin-3


title: DMS, odd set (SARS-CoV-2), replicate #2

source_name: DMS, odd set (SARS-CoV-2), replicate #2


title: MCI-C_013


title: Control-3

description: Th0 3

value: Control


title: 16Con5

description:
9L-Con16_S35_L005
Control diet #5


title: 16Con4

description:
7L-Con16_S27_L004
Control diet #4


title: MCI-C_008

value: MCI-C


title: DMS, even set (SARS-CoV-2), replicate #1


title: DMS, extra set (SARS-CoV-2), replicate #1


title: Control-2

description: Th0 2


title: 16Con3

description:
6L-Con16_S19_L003
Control diet #3


title: MCI-C_006

value: female


title: Control-1

description: Th0 1


title: DMS, odd set (SARS-CoV-2), replicate #1

source_name: DMS, odd set (SARS-CoV-2), replicate #1


title: 16Con2

description:
4L-Con16_S3_L007
Control diet #2


title: H3K4me3_rep3

status: Public on Nov 10 2020

city: Kyoto

first: Shuntaro

last: Ikeda

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

institute: Kyoto University

data_processing:
Sequencing reads were aligned to the bovine genome (Bos_taurus_UMD_3.1.1/bosTau8, Jun. 2014) using Bowtie (version 1.2.3). The mapping duplicates were removed by Picard (http://broadinstitute.github.io/picard/). Peak calling was performed by using the Model-based Analysis of ChIP-Seq (MACS, version 1.4.2) with corresponding input samples as control to generate bed files.
Genome_build: bosTau8
Supplementary_files_format_and_content: Bed files containing information about called peaks: the name of the chromosome, the starting and ending positions of the feature in the chromosomes, the name of the BED lines, and scores.

organism: Bos taurus

source_name: bovine blastocysts

growth_protocol: Bovine blastocysts were in vitro produced by in vitro fertilization (IVF) and further cultured in mSOF up to day 8 (IVF = day 0).

extract_protocol:
Blastocyst-stage embryos at 192 h post IVF were collected as approximately 11 embryos per biological replicate for ChIP. ChIP for small cell numbers was performed with a Low Cell ChIP-Seq Kit (Active Motif) according to the manufacturer’s manual (version A3) with some modifications. The blastocysts were freed from the zona pellucida by using pronase before crosslinking with formaldehyde. After crosslink-quenching, the sample was sonicated to shear chromatin using a Bioruptor UCD-250 (Cosmo Bio) for 30 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 2 min at 18,000 x g and the supernatant (200 μL) was transferred to a new tube. The 200-µL sample of sheared chromatin was divided into a 10-µL aliquot as “input” and the rest (190 µl). The latter aliquot was processed for ChIP using 3 µg anti-H3K4me3 antibody (pAb-003-050, Diagenode) as indicated in the user manual. The input and ChIPed DNA was decrosslinked, purified, and resuspended in 40 µL low-EDTA TE buffer.
Sequencing libraries of the ChIPed DNA were constructed by using Next Gen DNA Library Kit and Next Gen Indexing Kit (Active Motif) following the manufacturer’s instruction.

treatment_protocol: The culture was chemically semi-defined (bovine serum albumin was added) and performed under low oxygen tension (5%).

tag: source

value: in vitro produced

tag: day after ivf

value: day 8

tag: chip antibody

value: anti-H3K4me3 (Diagenode pAb-003-050)


title: 16Con1

description:
2L-Con16_S3_L001
Control diet #1

value: Zucker rat

value: Liver


title: Col1a1GFP+ cells health 3

data_processing:
Sequencing files were run through the 10X CellRanger 2.1.1 pipeline to generate gene counts data
Further analysis was completed using Seurat v3 and the sctransform pipeline
Resolution parameter of clustering was set to 0.5. Wilcox method was used for differential expression analysis, with min.pct = 0.25 and logfc.threshold = 0.25
singleR was used to annotate single-cells using the Immgen reference
Genome_build: mm10

extract_protocol:
Spinal cords were dissociated using both chemical and mechanical dissociation methods and single, GFP+ cells were sorted using FACS sorting
RNA libraries were prepared for sequencing using the 10x Genomics v2 standard protocols
Libraries were sequenced using the HiSeq4000 (1-3) or NovaSeq 6000 (4,5)

tag: strain background

tag: disease state

value: healthy

value: spinal cord


title: MCI-C_002

city: Obu

last: Shigemizu

address: 7-430 Morioka-cho

institute: National Center for Geriatrics and Gerontology


title: MCI-C_003

value: male


title: Biopsy 1, PCM1- nuclei

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

country: Sweden

institute: Lund University

description: Nuclear RNA

data_processing:
Raw base calls were read into the Cellranger software v2.1.1. for demultiplexing, mapping and quality control
Reads were aligned to the human reference genome build GRCh38 based on a custom gene annotation file includin pre-mRNAs. Barcodes with no reads were filtered out. The resulting gene count matrices were reviewed and nuclei with >300 and <2000 features were retained for further analysis
Gene count matrices were read into Seurat v3.0 for analysis, creating objects based upon nuclei containing at least one feature and features present in at least one nuclei.
In Seurat, molecular counts were normalized for differences in sequencing depth across nuclei with variance stabilization using regularized negative binomial regression as implemented in the sctransform algorithm.
Dimensionality reduction was then conducted through principal component analysis. Based on the first 50 principal components, two-dimensional projections were created using the Uniform Manifold Approximation and Projection (UMAP) technique.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv
Supplementary_files_format_and_content: mtx

source_name: Nuclei from human cardiac tissue

extract_protocol:
After tissue homogenization, nuclei were isolated by sucrose gradient centrifugation and stained with a PCM1 antibody. PCM1+ and PCM1- nuclei were sorted using FACS.
Nuclear suspensions were loaded into the 10x Genomics Chromium Controller for library preparation. Libraries were prepared for approximately 4000 nuclei per sample.
Sequencing of libraries was conducted on a NovaSeq 6000 instrument targeting >50,000 reads per nuclei.

value: Left ventricle

value: Dilated cardiomyopathy

tag: pcm1 staining

value: Negative


title: Biopsy 1, PCM1+ nuclei

description: Nuclear RNA

value: Positive


title: Biopsy 2, PCM1- nuclei

description: Nuclear RNA


title: MCI-C_007

first: Daichi


title: Col1a1GFP+ cells EAE 2

value: EAE


title: Input_rep3


title: Input_rep2


title: H3K4me3_rep2


title: MCI-C_001


title: Input_rep1

tag: cell type

value: blastocyst


title: H3K4me3_rep1


title: MCI-C_005

tag: Sex


title: HeLa 1000 cells rep 2

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
Library strategy: tagHi-C
Sequence adapters were remove by cutadapt (version 2.6).
HiC-Pro (version 2.7.9) was used to process Hi-C and tagHi-C data.
The contact matrix was normalized by ICE method.
hicpro2juicbox was used to transform valid contacts to “.hic” files, and these files were imported to juicebox for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: hic

source_name: cervical cancer cells

growth_protocol: HeLa cells and GM12878 cells were grown in RPMI-1640 medium containing 10% fetal bovine serum at 37°C and 5% CO2. Cells were cultured to ∼80% confluence and then collected with PBS.

extract_protocol:
After crosslinking reversal, DNA was extracted with Phenol:Chloroform, pH 6.7/8.0 and quantified with Qubit.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HeLa

value: cervical cancer cells


title: HeLa 500 cells rep 2


title: MCI-C_004

tag: diagnosis

value: MCI-C

tag: age


title: HeLa 500 cells rep 1


title: HeLa 1 million cells


title: GM12878 200 cells rep

source_name: lymphoblastoid cell line

value: lymphoblastoid cell line


title: HeLa 500 cells rep 3


title: GM12878 500 cells rep 2


title: HeLa 1000 cells rep 1


title: GM12878 500 cells rep 1


title: Heart neonatal replicate 1

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna

data_processing:
The reads were mapped with STAR 2.5.3a to the mouse genome (mm10).
The counts for each gene were obtained by using –quantMode GeneCounts commands in STAR, and the other parameters during alignment were set to default.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole heart

extract_protocol:
Animals post-natal day 1, 4 weeks, 14 weeks, 1 year and 1.5 years old were used for determination of gene expression analysis. PDGFR⍺ cardiac fibroblasts were isolated by flow cytometry from hearts of animals at the above respective ages to determine changes in gene expression in cardiac fibroblasts.
RNA was isolated from the heart tissue or cardiac fibroblasts using RNeasy Mini kit (Qiagen) and used to generate RNA-Seq libraries followed by sequencing using Illumina 4000 platform.

value: Whole heart

value: cardiac cells

tag: strain

value: neonate


title: Heart neonatal replicate 2


title: Heart 1 year replicate 2

value: 1-year old


title: Heart 4 week replicate 2

value: 4-week old


title: Heart neonatal replicate 3


title: Heart 4 week replicate 1


title: Heart 18 month replicate 2

value: 18-month old


title: Heart 1 year replicate 3


title: Heart 18 month replicate 3


title: Heart 4 week replicate 3


title: LPS+IFN-g stimulated BMDMs 10x single-cell RNAseq dataset

city: New Haven

first: Miller-Jensen

last: Lab

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

data_processing:
CellRanger software package (v2.1.1) was used for alignment, filtering, barcode reading and demultiplexing, prior to analysis in python.
Genome_build: mm10
Supplementary_files_format_and_content: 10X Genomics Filtered Gene BC Barcodes
Supplementary_files_format_and_content: 10X Genomics Filtered Gene BC Genes
Supplementary_files_format_and_content: 10X Genomics Filtered Gene BC Matrix

source_name: Bone marrow-derived macrophages

growth_protocol: BMDMs were plated and stimulated in BMDM media + 10 ng/ml M-CSF. Cells were plated in non-TC treated 6- or 12-well plates (Falcon) at a density of 100,000 cells per cm2 and allowed to adhere overnight. Cells were then stimulated at the indicated doses and times using LPS (Invivogen), IFN-γ (Peprotech) and/or IL-4 (Peprotech).

extract_protocol:
Stimulated BMDMs were lifted in ice-cold PBS+ 5 mM EDTA with gentle scraping, washed, counted, and immediately processed at low density for scRNA-seq using the 10X platform (10X Genomics). Library construction and sequencing was performed by the Yale Center for Genomic Analysis according to the manufacturer’s recommendations.
Library construction was performed by the Yale Center for Genomic Analysis according to the manufacturer’s recommendations (10X Genomics).

treatment_protocol: BMDMs were stimulated with 10 ng/ml LPS+10 ng/ml IFN-γ and/or 100 ng/ml IL-4.

value: Bone marrow-derived macrophages

tag: treatment

value: LPS+IFNg for 6 hours


title: LPS+IFN-g+IL-4 stimulated BMDMs 10x single-cell RNAseq dataset

value: LPS+IFNg + IL-4 for 6 hours


title: Control BMDMs 10x single-cell RNAseq dataset

value: Unstimulated


title: IL-4 stimulated BMDMs 10x single-cell RNAseq dataset

value: IL-4 for 6 hours


title: Heart 14 week replicate 3

value: 14-week old


title: Heart 18 month replicate 1


title: Heart 14 week replicate 2


title: GM12878 1000 cells rep 2


title: Heart 14 week replicate 1


title: Fibroblast 4 week replicate 3

source_name: PDGFR⍺ cardiac fibroblasts

value: PDGFR⍺ cardiac fibroblasts

value: PDGFRalpha cardiac fibroblasts


title: Fibroblast neonatal replicate 2


title: Fibroblast neonatal replicate 3


title: GM12878 1000 cells rep 1


title: Fibroblast 4 week replicate 2


title: Fibroblast 1 year replicate 5


title: Fibroblast neonatal replicate 1


title: Fibroblast 4 week replicate 1


title: Fibroblast 1 year replicate 4


title: GM12878 1 million cells


title: Heart 1 year replicate 1


title: Fibroblast 18 month replicate 5


title: Fibroblast 18 month replicate 4


title: Fibroblast 14 week replicate 4


title: Fibroblast 14 week replicate 6


title: Gastruloids_Day6_batch2

city: Lausanne

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

description:
GAS_Day6_batch2_S3
Gastruloids 6 days after onset of 3D culture.

data_processing:
alignment with cellranger v3.1
filtering with Seurat v3.1 (>2000 genes, 1.5 to 15% mitochondrial RNA)
Genome_build: mm10
Supplementary_files_format_and_content: compressed (gz) sparse count matrix in mtx format, barcodes (cells, column names) in tsv format, and features (genes, row names) in tsv format, all equivalent to the cellranger export formats; as well as the cell metadata in tsv format, with standard Seurat v3 structuring.

growth_protocol: mESCs were cultured in DMEM supplemented with 10% FBS/LIF/2i. For gastruloids, 300 mESCs were aggregated in N2B27, and exposed to 3μM Chi between 48 and 72h. Between 96-144h, gastruloids were cultured in N2B27 containing 30ng ml-1 bFGF , 5ng ml-1 VEGF 165 and 0.5mM L-ascorbic acid phosphate. From 96h, half medium was changed daily. At 144h, N2B27 was used for medium change.

extract_protocol:
Cells were dissociated with TrypLE for 2x4 min, blocked with 10% serum, and washed with N2B27 medium.
10x Genomics Chromium 3’ chemistry v3.1

tag: cell type source

value: mouse embryonic stem cells (mESCs)

tag: tissue/cell type

value: Gastruloids

tag: day

tag: batch


title: Gastruloids_Day6_batch3

description:
GAS_Day6_batch3_S7
Gastruloids 6 days after onset of 3D culture.


title: Gastruloids_Day7_batch2

description:
GAS_Day7_batch2_S8
Gastruloids 7 days after onset of 3D culture.


title: Gastruloids_Day4_batch4

description:
GAS_Day4_batch4_S1
Gastruloids 4 days after onset of 3D culture.


title: Gastruloids_Day5_batch3

description:
GAS_Day5_batch3_S2
Gastruloids 5 days after onset of 3D culture.


title: ATAC_R61_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: ATAC-seq experiment

data_processing:
Sequence reads of the samples were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/ATAC-seq)

source_name: Mice hippocampus

extract_protocol:
ATAC-seq: ATAC-seq experiments were performed as previously described (PubmedID: 24097267), with slight modifications, in 3 independent biological replicates using hippocampal tissue from 25-week-old wild-type and R6/1 mice. Briefly, a frozen mouse hippocampi for each biological replicate was pulverized using a grinder and pestle settle on dry ice, and tissue powder was lysed in LB1 buffer for nuclear isolation. Approximately 50.000 nuclei were used for the transposition reaction followed by 13 cycles of PCR amplification. “Nucleosome free” and “mono-nucleosome fragments” were obtained by size-selection of DNA fragments between 170 and 400 bp using SPRIselect beads before single-end sequencing to generate 50 bp reads on the Hi-Seq 4000 platform.
Libraries were prepared according to Illumina instructions.

treatment_protocol: Frozen hippocampal tissue from WT and R6/1 mice

tag: genotype/variation

tag: tissue

value: hippocampal tissue

value: 30-week-old mice


title: ATAC_R61_R1

description: ATAC-seq experiment

tag: chip antibody


title: Dot1L-BKO 2 ATAC-seq

city: Berkeley

first: Danielle

last: Yi

state: CA

address: 220 Morgan Hall

institute: UC Berkeley

description: Partek_ATAC-Dot1L-2_W1_S3_W2_S3_vs_Dot1t1_S2_Dot1t2_S2_summits

data_processing:
Base-calling was performed by CASAVA bcl2fastq2 v2.2.
Adapters were trimmed using cutadapt-1.2.1.
Reads were aligned to mm10 genome assembly using BWA - 0.7.17, peak-calling was performed by MACS2-2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated by MACS2 and contain summits.

source_name: brown adipose tissue

growth_protocol: Mice were maintained on chow diet until 12 weeks of age.

extract_protocol:
BAT was removed, flash frozen on dry ice, and nuclei were processed using Nextera DNA library kit for ATAC analyses, and the total RNA from BAT was prepared using RNEasy kit (Qiagen)
For ATAC-seq, library construction was performed using Nextera DNA library kit. For RNA-seq, strand-specific libraries were generated from 500 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina)
Manufacturers instructions were followed for preparation of DNA libraries.

treatment_protocol: Mice were sacrified after 4 hours of cold exposrue at 4C at 12 weeks of age


title: Dot1L-BKO 1 ATAC-seq


title: WT 1 RNA-seq

value: WT


title: WT 2 RNA-seq


title: WT 2 ATAC-seq


title: WT 1 ATAC-seq


title: Dot1L-BKO 1 RNA-seq


title: Dot1L-BKO 2 RNA-seq


title: Gastruloids_Day4_batch5

description:
GAS_Day4_batch5_S5
Gastruloids 4 days after onset of 3D culture.


title: ATAC_WT_R1

description: ATAC-seq experiment


title: RNA_R61_R8

description: RNA-seq experiment

data_processing:
Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Analysis of differential expression performed by DESeq2 (PubMed ID 25516281)
Genome_build: mm9
Supplementary_files_format_and_content: Files .txt (RNAseq expression values)

extract_protocol:
RNA-seq: RNA was isolated from 9 independent biological replicates for each genotype using the Qiagen RNeasy Plus Kit according to the manufacturer’s instructions. Quality assessment was performed using Bioanalyser eukaryiotic total RNA nano series II chip and all samples achieved a RNA integration number (RIN) between 9-10. Libraries were prepared from 9 biological replicates of each condition using the Truseq Stranded mRNA Library Prep Kit following manufacturer’s instructions and sequenced using the HiSeq-2500 sequencing platform.
Libraries were prepared according to Illumina instructions.


title: RNA_R61_R7

description: RNA-seq experiment


title: ATAC_WT_R2

description: ATAC-seq experiment


title: RNA_R61_R6

description: RNA-seq experiment


title: ATAC_WT_R3

description: ATAC-seq experiment


title: ATAC_R61_R3

description: ATAC-seq experiment


title: Gastruloids_Day7_batch1

description:
GAS_Day7_batch1_S4
Gastruloids 7 days after onset of 3D culture.


title: Gastruloids_Day5_batch4

description:
GAS_Day5_batch4_S6
Gastruloids 5 days after onset of 3D culture.


title: RNA_R61_R4

description: RNA-seq experiment


title: RNA_R61_R5

description: RNA-seq experiment


title: RNA_R61_R3

description: RNA-seq experiment


title: RNA_R61_R2

description: RNA-seq experiment


title: RNA_R61_R1

description: RNA-seq experiment


title: RNA_WT_R9

description: RNA-seq experiment


title: RNA_WT_R8

description: RNA-seq experiment


title: RNA_WT_R7

description: RNA-seq experiment


title: RNA_R61_R9

description: RNA-seq experiment


title: RNA_WT_R6

description: RNA-seq experiment


title: RNA_WT_R4

description: RNA-seq experiment


title: RNA_WT_R3

description: RNA-seq experiment


title: RNA_WT_R5

description: RNA-seq experiment


title: RNA_WT_R1

description: RNA-seq experiment


title: ChIP_INPUT_R61_R3_3

description: ChIP-seq experiment

data_processing:
Sequence reads of the samples were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1. All the replicates of the same condition were pooled in a single file.
Genome-wide profiles in BedGraph format are the subtraction of Input samples from the LB1 pool of experiments
Domain detection of the LB1 pool against the INPUT pool at WT and R6/1 conditions were performed with EDD (PubMed ID 24782521). Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/ATAC-seq)
Files *.bed (BED, ChIP-seq signal enriched regions)

extract_protocol:
ChIP-seq: Frozen hippocampus from 5 mice were pooled together, homogenized in PBS supplemented with proteinase inhibitors  and posteriorly cross-linked with formaldehyde 1% for 15 minutes at r. t. Cross-linking reaction was stopped by a 5 minutes incubation with 2 M glycine and the cross-linked material was washed 3 times with ice-cold PBS. Cells were lysed and nuclei were extracted using nuclei extraction buffer. Purified nuclear fraction was subjected to sonication using Bioruptor Pico (Diagenode) to obtain DNA fragments of 200-500 bp. Sonicated chromatin was incubated with anti-rabbit magnetic bead pre-complexed with 10 µg of α-lamin B1 antibody O/N at 4 ºC. After 6 washes with RIPA buffer, chromatin was eluted and de-crosslinked by O/N incubation at 65 ºC, followed by a 30 minutes RNAse and 2 hours Proteinase K treatments. DNA purification was carried out with MinElute PCR Purification KIT and libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit from Illumina according to the manufacturer’s instructions. DNA size selection was performed after PCR amplification using E-Gel Precast Agarose Electrophoresis System. Samples were sequenced single-end using 50 bp reads on the Hi-Seq 4000 platforms. For each biological replicate (R1, R2 and R3), three samples corresponding to their respective sequencing lane are provided.
Libraries were prepared according to Illumina instructions.


title: ChIP_INPUT_R61_R3_1

description: ChIP-seq experiment


title: RNA_WT_R2

description: RNA-seq experiment


title: ChIP_INPUT_R61_R1_3

description: ChIP-seq experiment


title: ChIP_INPUT_R61_R2_2

description: ChIP-seq experiment


title: ChIP_INPUT_R61_R3_2

description: ChIP-seq experiment


title: ChIP_INPUT_R61_R2_3

description: ChIP-seq experiment


title: ChIP_INPUT_R61_R1_2

description: ChIP-seq experiment


title: ChIP_LB1_R61_R3_3

description: ChIP-seq experiment

value: Rabbit anti-Lamin B1 polyclonal antibody, Abcam, Cat# ab16048


title: ChIP_INPUT_R61_R1_1

description: ChIP-seq experiment


title: ChIP_LB1_R61_R3_2

description: ChIP-seq experiment


title: ChIP_LB1_R61_R2_3

description: ChIP-seq experiment


title: ChIP_LB1_R61_R3_1

description: ChIP-seq experiment


title: ChIP_LB1_R61_R2_2

description: ChIP-seq experiment


title: ChIP_LB1_R61_R1_3

description: ChIP-seq experiment


title: ChIP_LB1_R61_R2_1

description: ChIP-seq experiment


title: ChIP_LB1_R61_R1_1

description: ChIP-seq experiment


title: ChIP_LB1_R61_R1_2

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R3_3

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R3_2

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R3_1

description: ChIP-seq experiment


title: ChIP_INPUT_R61_R2_1

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R2_3

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R2_2

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R2_1

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R1_3

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R1_2

description: ChIP-seq experiment


title: ChIP_LB1_WT_R3_1

description: ChIP-seq experiment


title: ChIP_INPUT_WT_R1_1

description: ChIP-seq experiment


title: ChIP_LB1_WT_R3_2

description: ChIP-seq experiment


title: ChIP_LB1_WT_R2_3

description: ChIP-seq experiment


title: ChIP_LB1_WT_R3_3

description: ChIP-seq experiment


title: ChIP_LB1_WT_R1_2

description: ChIP-seq experiment


title: ChIP_LB1_WT_R1_1

description: ChIP-seq experiment


title: ChIP_LB1_WT_R2_1

description: ChIP-seq experiment


title: ChIP_LB1_WT_R2_2

description: ChIP-seq experiment


title: ChIP_LB1_WT_R1_3

description: ChIP-seq experiment


title: kidney_No_ABMRh_167

city: Leuven

first: Jasper

last: Callemeyn

address: Herestraat 49

department: Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven University

description: Gene expression data from kidney allograft biopsy

hyb_protocol: Fragmented cRNA was hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix). The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Arrays were scanned on the GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Resulting image files (.dat files) were generated using the GeneChip® Command Console® Software (AGCC), and intensity values for each probe cell (.cel file) were calculated.

label: Biotin

source_name: Kidney allograft biopsy

label_protocol: Extracted RNA was amplified and biotinylated to complementary RNA (cRNA) using the GeneChip® 3' IVT PLUS Reagent Kit (Affymetrix Inc., High Wycombe HP10 0HH, UK)

extract_protocol: Total RNA was isolated from the kidney allograft biopsy specimens -using the Allprep DNA/RNA/miRNA Universal Kit® (Qiagen Benelux BV) on a QIAcube instrument (Qiagen Benelux BV).

tag: phenotype

value: No ABMRh


title: kidney_DSAnegABMRh_21

value: DSAnegABMRh


title: kidney_DSAnegABMRh_26


title: kidney_No_ABMRh_168


title: kidney_DSAposABMRh_30

value: DSAposABMRh


title: kidney_DSAnegABMRh_24


title: kidney_DSAnegABMRh_23


title: kidney_DSAnegABMRh_17


title: kidney_DSAnegABMRh_20


title: kidney_DSAnegABMRh_22


title: kidney_DSAnegABMRh_18


title: kidney_DSAnegABMRh_25


title: kidney_DSAnegABMRh_19


title: kidney_DSAposABMRh_28


title: kidney_No_ABMRh_163


title: kidney_No_ABMRh_165


title: kidney_No_ABMRh_166


title: kidney_DSAposABMRh_27


title: kidney_No_ABMRh_162


title: kidney_DSAposABMRh_26


title: kidney_No_ABMRh_159


title: kidney_DSAposABMRh_24


title: kidney_DSAposABMRh_29


title: kidney_DSAposABMRh_25


title: kidney_No_ABMRh_161


title: kidney_No_ABMRh_164


title: kidney_No_ABMRh_158


title: kidney_No_ABMRh_160


title: kidney_No_ABMRh_157


title: kidney_No_ABMRh_152


title: kidney_No_ABMRh_155


title: kidney_No_ABMRh_153


title: kidney_DSAposABMRh_22


title: kidney_No_ABMRh_149


title: kidney_No_ABMRh_151


title: kidney_No_ABMRh_150


title: kidney_No_ABMRh_154


title: kidney_No_ABMRh_146


title: kidney_No_ABMRh_145


title: kidney_DSAposABMRh_21


title: kidney_No_ABMRh_156


title: kidney_DSAnegABMRh_15


title: kidney_No_ABMRh_143


title: kidney_No_ABMRh_142


title: kidney_No_ABMRh_148


title: kidney_No_ABMRh_140


title: kidney_No_ABMRh_144


title: kidney_No_ABMRh_138


title: kidney_No_ABMRh_139


title: kidney_DSAposABMRh_18


title: kidney_DSAposABMRh_19


title: kidney_No_ABMRh_137


title: kidney_No_ABMRh_147


title: kidney_No_ABMRh_135


title: kidney_No_ABMRh_141


title: kidney_No_ABMRh_133


title: kidney_No_ABMRh_123


title: kidney_DSAnegABMRh_14


title: kidney_No_ABMRh_125


title: kidney_No_ABMRh_131


title: kidney_No_ABMRh_136


title: kidney_No_ABMRh_122


title: kidney_No_ABMRh_134


title: kidney_No_ABMRh_129


title: kidney_DSAnegABMRh_16


title: kidney_No_ABMRh_128


title: kidney_DSAposABMRh_17


title: kidney_No_ABMRh_127


title: kidney_No_ABMRh_132


title: kidney_DSAnegABMRh_13


title: kidney_DSAposABMRh_15


title: kidney_No_ABMRh_130


title: kidney_No_ABMRh_119


title: kidney_No_ABMRh_121


title: kidney_DSAposABMRh_16


title: kidney_No_ABMRh_126


title: kidney_DSAnegABMRh_12


title: kidney_No_ABMRh_120


title: kidney_No_ABMRh_124


title: kidney_No_ABMRh_117


title: kidney_No_ABMRh_118


title: kidney_No_ABMRh_116


title: kidney_No_ABMRh_114


title: kidney_No_ABMRh_115


title: kidney_No_ABMRh_113


title: kidney_DSAnegABMRh_11


title: kidney_No_ABMRh_110


title: kidney_No_ABMRh_111


title: kidney_No_ABMRh_104


title: kidney_No_ABMRh_102


title: kidney_No_ABMRh_101


title: kidney_No_ABMRh_107


title: kidney_No_ABMRh_97


title: kidney_No_ABMRh_103


title: kidney_No_ABMRh_105


title: kidney_No_ABMRh_112


title: kidney_No_ABMRh_108


title: kidney_No_ABMRh_98


title: kidney_No_ABMRh_106


title: kidney_DSAposABMRh_12


title: kidney_DSAposABMRh_14


title: kidney_No_ABMRh_109


title: kidney_No_ABMRh_100


title: kidney_No_ABMRh_99


title: ATAC-seq for CD127low monocytes D95

city: Beijing

first: Bin

address: Zheng Yutong Building room D311

institute: Tsinghua University

data_processing:
ATAC-seq paired-end reads were collected. Adapter sequences were trimmed from the ends of reads by Cutadapt (v1.14), and the reads that failed to pass the quality control (Q > 10) were discarded.
Tophat (v2.1.0) was used for RNA-seq single-end reads alignment with the following parameters: --min-segment-intron 50 --no-novel-indels --no-coverage-search.  Bowtie2 (v2.2.5) was used for ATAC-seq paired-end reads alignment with maximum 1000 bp fragment length and no more than one mismatch for each alignment seed with 15 bp in length.
Differentially expressed genes between CD127high and CD127low monocytes were identified by using DESeq2 (v1.27.9).
After alignment, the ATAC-seq peaks were called for CD127hgih and CD127low monocytes from three donors as significantly opened chromatin regions by using MACS2 (v2.1.1) (FDR < 0.05).
Differentially opened chromatin regions (OCR) between CD127high and CD127low monocytes were identified by using edgeR (v3.28.1).
Genome_build: hg38
Supplementary_files_format_and_content: Expression_summary.txt is the table containing the gene expression (FPKM) and statistical analysis result (p-value) by edgeR. Six .bed files are the ATAC-seq peaks called by MACS2 for each sample.

source_name: Buffy coat

extract_protocol: Buffy coat from healthy blood donor was diluted by PBS, and PBMC were isolated by Ficol gradient. CD14+ monocytes were isolated from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec). CD14+ monocytes were treated with LPS for 6 h, and CD127high and CD127low monocytes were sorted by FACS. For ATAC-seq, cells were washed by PBS and 50000 cell were re-suspended in 50 μL of lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) and nuclei were digested with Tn5 enzyme. DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina protocols. Instrument Hiseq X ten.  For RNA-seq, RNA was extracted using TRIzol, and total RNA was polyA enriched. RNA libraries were prepared for sequencing using TruSeq mRNA-seq Sample Preparation Kit(Illunima). Instrument BGISEQ-500RS.

value: Human CD14+ monocytes

tag: disease state

value: Healthy

tag: subtype

value: LPS


title: ATAC-seq for CD127high monocytes D95

tag: cell type


title: ATAC-seq for CD127low monocytes D94


title: kidney_No_ABMRh_95


title: kidney_No_ABMRh_94


title: kidney_No_ABMRh_93


title: ATAC-seq for CD127high monocytes D94


title: ATAC-seq for CD127high monocytes D92


title: kidney_No_ABMRh_96


title: ATAC-seq for CD127low monocytes D92


title: kidney_No_ABMRh_92


title: kidney_No_ABMRh_91


title: M5_TCR_day10_LCMV_armstrong

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Day 10 LCMV armstrong

data_processing:
Reads were aligned to mouse reference genome mm10
Single cell TCR data were filtered to select the best TCR alpha and beta chain at the clonal level, based on full length, productive CDR3 regions and expression level
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

extract_protocol:
Chromium single cell 5' kit V2 from 10x genomics
Chromium single cell 5' kit V2 from 10x genomics for single cell gene expression (GEX) and single cell TCR library

treatment_protocol: Activated antigen specific CD4 T cells (CD4+CD44+GP66+) were sorted from five C57BL/6J mice at day 10 post acute LCMV armstrong infection and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5’ v2 and v3 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)

value: C57BL/6 mice

tag: infection

value: LCMV armstrong

value: spleen


title: M3_TCR_day10_LCMV_armstrong

description: Day 10 LCMV armstrong


title: M4_TCR_day10_LCMV_armstrong

description: Day 10 LCMV armstrong


title: kidney_DSAposABMRh_20


title: kidney_No_ABMRh_89


title: kidney_No_ABMRh_85


title: kidney_No_ABMRh_87


title: M4_GEX_day10_LCMV_armstrong

description: Day 10 LCMV armstrong


title: kidney_No_ABMRh_84


title: kidney_No_ABMRh_90


title: kidney_No_ABMRh_86


title: kidney_No_ABMRh_82


title: M3_GEX_day10_LCMV_armstrong

description: Day 10 LCMV armstrong


title: kidney_DSAposABMRh_23


title: kidney_No_ABMRh_88


title: kidney_No_ABMRh_81


title: kidney_No_ABMRh_80


title: M5_GEX_day10_LCMV_armstrong

description: Day 10 LCMV armstrong


title: M2_GEX_day10_LCMV_armstrong

description: Day 10 LCMV armstrong


title: Cardiomyocyte (day 25-30)_Rep4

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

description: in vitro

data_processing:
read filtering and cropping of reads to same length using trimmomatic
mapping of reads to Gencode GRCh38 v.32 reference transcript annotation using STAR in 2-pass mode (v2.7.3a)
counts are generated from Stringtie
Genome_build: GRCh38 v .32
Supplementary_files_format_and_content: counts

source_name: PGP1 iPSC derived cardiomyocyte

extract_protocol:
Total RNA was isolated from iPSCs at day-2 (mesoderm) or days 25-30 (cardiomyocytes) of differentiation using Trizol. For each sample, RNA from biological replicates (n=4) was collected and TruSeq Stranded mRNA libraries were sequenced on an Illumina NextSeq 500/550 v2.5 platform (Illumina) as single-end reads.
TruSeq Stranded mRNA library preparation kit (Illumina)

treatment_protocol: Human iPSC PGP1 cells were differentiated into into mesoderm (day-2) or cardiomyocytes (days 25-30). Briefly, on day 0 of differentiation 12 μM CHIR99021 in RPMI 1640 supplemented with B27 minus insulin and GlutaMAX  were added for 24 hours. On day 3, cells were treated with 5 μM IWP-4 for 48 hours. On Day 9, cells were maintained in RPMI with B27 supplement. On Day 13, cardiomyocytes were enriched by metabolic selection by previously described methods (Tohyama et al., 2013). Following selection, cardiomyocytes were re-plated onto fibronectin-coated tissue culture plates. Cardiomyocytes were replenished with RPMI-B27 every other day.

tag: source cell line

tag: cell differentiation status

value: iPSC derived cardiomyocyte


title: M1_GEX_day10_LCMV_armstrong

description: Day 10 LCMV armstrong


title: Cardiomyocyte (day 25-30)_Rep3

description: in vitro


title: Mesoderm (day 2)_Rep4

description: in vitro

source_name: PGP1 iPSC derived mesoderm

value: iPSC derived mesoderm


title: Mesoderm (day 2)_Rep3

description: in vitro


title: S24 Spontaneous labor Female 2

city: St. Louis

first: Arvind

last: Palanisamy

state: MO

address: 660 S Euclid Ave

department: Anesthesiology

institute: Washington University School of Medicine

description: Spontaneous labor

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl Rnor_5.0.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Female 2

extract_protocol:
Total RNA was extracted from the right cerebral cortex using RNAeasy kit (Qiagen). Only RNA with RIN > 9.5 were used for RNA-seq.
oligo-dT

value: Sprague Dawley

tag: sample type

value: spontaneous labor

tag: gender

value: female

value: Cerebral cortex

tag: age

value: Postnatal day 0


title: kidney_No_ABMRh_79


title: S16 Spontaneous labor Female 2

description: Spontaneous labor

tag: strain


title: S17 Spontaneous labor Male 1

description: Spontaneous labor

source_name: Male 1

value: male


title: S20 Spontaneous labor Female 2

description: Spontaneous labor


title: S19 Spontaneous labor Female 1

description: Spontaneous labor

source_name: Female 1


title: S22 Spontaneous labor Male 2

description: Spontaneous labor

source_name: Male 2


title: S23 Spontaneous labor Female 1

description: Spontaneous labor


title: S21 Spontaneous labor Male 1

description: Spontaneous labor


title: S15 Spontaneous labor Female 1

description: Spontaneous labor


title: kidney_DSAposABMRh_11


title: kidney_No_ABMRh_78

value: No ABMRh


title: kidney_No_ABMRh_77


title: kidney_No_ABMRh_76


title: kidney_No_ABMRh_75


title: kidney_DSAnegABMRh_10

value: DSAnegABMRh


title: kidney_No_ABMRh_74


title: Cardiomyocyte (day 25-30)_Rep2

description: in vitro


title: kidney_No_ABMRh_73


title: Mesoderm (day 2)_Rep2

description: in vitro


title: S14 Spontaneous labor Male 2

description: Spontaneous labor


title: Cardiomyocyte (day 25-30)_Rep1

description: in vitro


title: S13 Spontaneous labor Male 1

description: Spontaneous labor


title: kidney_No_ABMRh_72


title: S18 Spontaneous labor Male 2

description: Spontaneous labor


title: Mesoderm (day 2)_Rep1

description: in vitro


title: S12 Saline pump Female 2

description: Saline pump

value: saline pump


title: S11 Saline pump Female 1

description: Saline pump


title: kidney_No_ABMRh_71


title: S10 Saline pump Male 2

description: Saline pump


title: iPSC_Rep3

description: in vitro

source_name: PGP1 iPSC

value: iPSC


title: iPSC_Rep2

description: in vitro


title: S9 Saline pump Male 1

description: Saline pump


title: S7 Saline pump Female 1

description: Saline pump


title: S6 Saline pump Male 2

description: Saline pump


title: S3 Saline pump Female 1

description: Saline pump


title: S2 Saline pump Male 2

description: Saline pump


title: LVshARID1A_Input_for_H3K4me3&H3K27me3

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: Input library from lentiviral shARID1A infected 12Z cells

data_processing:
Technical replicates were combined from both flow cells.
Raw reads for IPs and inputs were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Library molecular complexity was then estimated from duplicate rates by ATACseqQC and preseqR, and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call H3K4me3 narrow peaks and H3K27me3 broad peaks (FDR < 0.05) for each ChIP replicate against the input control with flags `--nomodel --extsize 146` to bypass model building.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Differential ChIP analysis was computed with csaw. Briefly, a consensus peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peaks called in each condition. The replicate intersection criteria used here are less stringent than the naïve overlap; any partial intersect between ChIP replicates was accepted as a query region tested for differential binding. ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average logCPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a non-linear loess-based normalization to the peak count matrix, as is implemented in csaw, to assume a symmetrical MA distribution. A design matrix was then constructed from one “condition” variable, without an intercept. The count matrix and loess offsets were then supplied to edgeR for estimating dispersions and fitting the quasi-likelihood generalized linear model for hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kilobases, and the most significant probability was used to represent the merged region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate narrow and broad peak sets (FDR < 0.05 MACS2 output) and naïve replicate-overlapping peaks. Non-thresholded differential ChIP results from csaw are also reported as a tab-separated values (TSV) file.

source_name: 12Z cell line

growth_protocol: 12Z cells were cultured in DMEM/F12 media supplemented with 10% FBS, 1% L-glutamine, and 1% Penicllin-Streptomycin.

extract_protocol:
72 hours following lentiviral transduction, cells were treated with 1% formaldehyde in cell culture media for 15 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 4x10^6 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions. IPs were performed using the SimpleChIP Enzymatic Chromatin IP Kit per the manufacturers’ instructions. 10 uL H3K4me3 (Cell Signaling, 9751) or 10 uL H3K27me3 (Cell Signaling, 9733) antibody was used per IP sample (effectively 1:50). DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input material and IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 75 bp, single-end sequencing was performed on an Illumina NextSeq 500 sequencer using 75 cycle HO sequencing kits (v2) (Illumina Inc., San Diego, CA, USA), with all libraries run across 2 flowcells to return a minimum read depth of 80M reads per input library and 40M read per IP library. Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: Cells were transduced with lentiviral particles which expressed shRNA targeting ARID1A (shARID1A) or non-targeting control (shNONtg) at 100 units per cell multiplicity of infection. Growth media was replaced 24 hours after trandsuction.

tag: cell line


title: S5 Saline pump Male 1

description: Saline pump


title: kidney_DSAposABMRh_10

value: DSAposABMRh


title: S8 Saline pump Female 2

description: Saline pump


title: kidney_No_ABMRh_70


title: S4 Saline pump Female 2

description: Saline pump


title: iPSC_Rep4

description: in vitro


title: S1 Saline pump Male 1

description: Saline pump


title: LVshARID1A_H3K27me3_rep2

description: H3K27me3 ChIP (replicate 2) library from lentiviral shARID1A infected 12Z cells


title: iPSC_Rep1

description: in vitro


title: kidney_DSAnegABMRh_9


title: kidney_No_ABMRh_69


title: kidney_No_ABMRh_68


title: kidney_No_ABMRh_67


title: kidney_No_ABMRh_66


title: LVshARID1A_H3K4me3_rep2

description: H3K4me3 ChIP (replicate 2) library from lentiviral shARID1A infected 12Z cells


title: kidney_DSAposABMRh_13


title: LVshARID1A_H3K27me3_rep1

description: H3K27me3 ChIP (replicate 1) library from lentiviral shARID1A infected 12Z cells


title: LVshARID1A_H3K4me3_rep1

description: H3K4me3 ChIP (replicate 1) library from lentiviral shARID1A infected 12Z cells


title: LVshNONtg_Input_for_H3K4me3&H3K27me3

description: Input library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells

value: shNONtg (control)


title: LVshNONtg_H3K27me3_rep1

description: H3K27me3 ChIP (replicate 1) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: kidney_DSAnegABMRh_8


title: LBW female liver, biological rep2

city: London

first: Ousseynou

last: Sarr

state: United States

address: 1811 Creekside Street

department: Physiology & Pharmacology

country: Canada

institute: Western universitry

description:
53_TRT023B01B01_01
Gene expression data from young adult offspring fed a control diet

hyb_protocol: After fragmentation and labeling, 2.1 µg cDNA was hybridized onto Guinea Pig Gene 1.1 ST Array Plate (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using the GeneTitan® Instrument (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) (version 4.0, Life Technologies) using Affymetrix default analysis settings and Summarization Method as normalization method.

organism: Cavia porcellus

source_name: guinea pig liver at postnatal day 150

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss-cDNA with the GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific).

growth_protocol: Uterine artery ablation-induced low birth weight (LBW) and normal birth weight (NBW) male and female guinea pig offspring were fed a control diet from weaning until postnatal day 150.

extract_protocol: Trizol extraction of total RNA in livers was performed using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At postnatal day 150, offspring of each sex were fasted overnight, euthanized via CO2 inhalation in the morning (~ 10 am) of the following day and tissue collection conducted. The whole liver was removed and weighed immediately and the right lobe liver was frozen in liquid nitrogen and stored at −80 °C.

value: Dunkin Hartley

value: Female

tag: treatment

value: postnatal day 150

value: Liver


title: kidney_No_ABMRh_65


title: LBW female liver, biological rep3

description:
55_TRT040F02F02_01
Gene expression data from young adult offspring fed a control diet

value: Uterine artery ablation-induced low birth weight (LBW)


title: LBW female liver, biological rep1

description:
52_TRT022A06A06_01
Gene expression data from young adult offspring fed a control diet


title: LVshNONtg_H3K4me3_rep2

description: H3K4me3 ChIP (replicate 2) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: LBW female liver, biological rep4

description:
56_TRT050A01A01_01
Gene expression data from young adult offspring fed a control diet


title: NBW female liver, biological rep3

description:
47_TRT019B06B06_01
Gene expression data from young adult offspring fed a control diet

value: normal birth weight (NBW)


title: NBW female liver, biological rep5

description:
49_TRT021A03A03_01
Gene expression data from young adult offspring fed a control diet


title: NBW female liver, biological rep1

description:
43_TRT026C06C06_01
Gene expression data from young adult offspring fed a control diet


title: LBW male liver, biological rep5

description:
25_TRT012E02E02_01
Gene expression data from young adult offspring fed a control diet

value: Male


title: kidney_No_ABMRh_64

description: Gene expression data from kidney allograft biopsy


title: LBW male liver, biological rep4

description:
24_TRT006D01D01_01
Gene expression data from young adult offspring fed a control diet


title: LBW female liver, biological rep5

description:
58_TRT029C02C02_01
Gene expression data from young adult offspring fed a control diet


title: kidney_No_ABMRh_63


title: NBW female liver, biological rep4

description:
48_TRT020D06D06_01
Gene expression data from young adult offspring fed a control diet


title: LBW male liver, biological rep1

description:
20_TRT003B05B05_01
Gene expression data from young adult offspring fed a control diet


title: LVshNONtg_H3K4me3_rep1

description: H3K4me3 ChIP (replicate 1) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: LVshNONtg_H3K27me3_rep2

description: H3K27me3 ChIP (replicate 2) library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells


title: kidney_No_ABMRh_61


title: LBW male liver, biological rep3

description:
23_TRT005A04A04_01
Gene expression data from young adult offspring fed a control diet


title: NBW male liver, biological rep5

description:
15_TRT002E03E03_01
Gene expression data from young adult offspring fed a control diet


title: NBW female liver, biological rep2

description:
46_TRT027F01F01_01
Gene expression data from young adult offspring fed a control diet


title: kidney_DSAnegABMRh_7


title: RNA-seq for CD127low monocytes D42

description:
Expression_summary.txt
42N

value: Human CD14+ monocytes

value: Healthy

value: LPS